HEADER OXIDOREDUCTASE 18-DEC-12 4IHI TITLE CRYSTAL STRUCTURE OF THE DELTA-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE TITLE 2 FROM MYCOBACTERIUM TUBERCULOSIS BOUND WITH NAD COMPND MOL_ID: 1; COMPND 2 MOLECULE: DELTA-1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROBABLE PYRROLINE-5-CARBOXYLATE DEHYDROGENASE ROCA; COMPND 5 EC: 1.5.1.12; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: MT1224, PRUA, ROCA, RV1187; SOURCE 6 EXPRESSION_SYSTEM: MYCOBACTERIUM SMEGMATIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 1772; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: MC2 4517 KEYWDS ROSSMANN FOLD, PYRROLINE-5-CARBOXYLATE DEHTDROGENASE, PYRROLINE-5- KEYWDS 2 CARBOXYLIC ACID, DEHYDROGENATION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.LAGAUTRIERE,G.BASHIRI,E.N.BAKER REVDAT 3 12-NOV-14 4IHI 1 KEYWDS REVDAT 2 16-APR-14 4IHI 1 JRNL REVDAT 1 18-DEC-13 4IHI 0 JRNL AUTH T.LAGAUTRIERE,G.BASHIRI,N.G.PATERSON,M.BERNEY,G.M.COOK, JRNL AUTH 2 E.N.BAKER JRNL TITL CHARACTERIZATION OF THE PROLINE-UTILIZATION PATHWAY IN JRNL TITL 2 MYCOBACTERIUM TUBERCULOSIS THROUGH STRUCTURAL AND FUNCTIONAL JRNL TITL 3 STUDIES. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 968 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 24699642 JRNL DOI 10.1107/S1399004713034391 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 68453 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.277 REMARK 3 R VALUE (WORKING SET) : 0.275 REMARK 3 FREE R VALUE : 0.307 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3641 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4188 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.4100 REMARK 3 BIN FREE R VALUE SET COUNT : 214 REMARK 3 BIN FREE R VALUE : 0.4390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4098 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.29000 REMARK 3 B22 (A**2) : -0.29000 REMARK 3 B33 (A**2) : 0.43000 REMARK 3 B12 (A**2) : -0.14000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.192 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.184 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.120 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.619 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.832 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.796 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4273 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2827 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5835 ; 1.928 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6837 ; 1.069 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 536 ; 6.778 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 193 ;35.954 ;22.953 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 627 ;14.344 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;21.872 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 649 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4839 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 930 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. STRUCTURE CONSISTS IN AN ARRANGEMENT OF ORDERED AND REMARK 3 DISORDERED LAYERS RESULTING IN GAPS BETWEEN ORDERED MOLECULES. REMARK 3 ALTHOUGH NO MOLECULES ARE MODELLED WITHIN THIS EMPTY LAYER, MAD REMARK 3 DATA FROM SEMET-PRUA CRYSTALS INDICATES THAT PROTEIN ELECTRON REMARK 3 DENSITY EXISTS WITHING THESE GAPS AND SUGGESTS A MOTION OF THE REMARK 3 ENTIRE LAYER. REMARK 4 REMARK 4 4IHI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JAN-13. REMARK 100 THE RCSB ID CODE IS RCSB076758. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.953688 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73091 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 REMARK 200 RESOLUTION RANGE LOW (A) : 29.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 80.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 6.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BICINE/TRIS PH 8.1, 12% REMARK 280 POLYETHYLENE GLYCOL (PEG) 1000, 12% PEG 3350, 12% 2-METHYL-2,4- REMARK 280 PENTANDIOL (MPD), 0.03 M SODIUM NITRATE, 0.03 M DISODIUM HYDROGEN REMARK 280 PHOSPHATE AND 0.03 M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z REMARK 290 6555 X-Y,X,Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.500000 -0.866025 0.000000 81.96850 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 141.97361 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 388.05000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 46630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 98000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -136.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 163.93700 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 81.96850 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 141.97361 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 81.96850 REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 141.97361 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 388.05000 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 163.93700 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 388.05000 REMARK 350 BIOMT1 6 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 6 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 388.05000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 42790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 388.05000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 THR A 418 REMARK 465 ASP A 419 REMARK 465 GLU A 420 REMARK 465 SER A 421 REMARK 465 PHE A 422 REMARK 465 VAL A 423 REMARK 465 ILE A 424 REMARK 465 ASP A 543 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 1080 O HOH A 1123 2.03 REMARK 500 O HOH A 822 O HOH A 982 2.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 1135 O HOH A 1135 12557 1.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 272 CG HIS A 272 CD2 0.062 REMARK 500 HIS A 434 CG HIS A 434 CD2 0.061 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 69 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 69 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 103 NE - CZ - NH1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 103 NE - CZ - NH2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG A 157 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 289 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 289 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP A 309 CB - CG - OD1 ANGL. DEV. = 10.2 DEGREES REMARK 500 ASP A 309 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP A 534 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 21 -1.43 69.37 REMARK 500 ARG A 65 68.11 -165.07 REMARK 500 ASP A 140 -71.15 -96.53 REMARK 500 VAL A 142 -73.64 -98.07 REMARK 500 LYS A 326 -164.00 -76.30 REMARK 500 ASP A 400 112.38 -162.24 REMARK 500 ALA A 462 135.25 -170.30 REMARK 500 ALA A 479 146.01 -174.17 REMARK 500 PHE A 498 -148.30 58.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 764 DISTANCE = 5.48 ANGSTROMS REMARK 525 HOH A 788 DISTANCE = 5.21 ANGSTROMS REMARK 525 HOH A 799 DISTANCE = 7.91 ANGSTROMS REMARK 525 HOH A 807 DISTANCE = 8.62 ANGSTROMS REMARK 525 HOH A 866 DISTANCE = 5.80 ANGSTROMS REMARK 525 HOH A 876 DISTANCE = 6.25 ANGSTROMS REMARK 525 HOH A 903 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH A 908 DISTANCE = 7.55 ANGSTROMS REMARK 525 HOH A 910 DISTANCE = 5.11 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4IDM RELATED DB: PDB REMARK 900 NATIVE STRUCTURE (SMALL UNIT CELL) REMARK 900 RELATED ID: 4IDS RELATED DB: PDB REMARK 900 NATIVE STRUCTURE (LARGE UNIT CELL) DBREF 4IHI A 1 543 UNP O50443 O50443_MYCTU 1 543 SEQADV 4IHI MET A -19 UNP O50443 EXPRESSION TAG SEQADV 4IHI GLY A -18 UNP O50443 EXPRESSION TAG SEQADV 4IHI SER A -17 UNP O50443 EXPRESSION TAG SEQADV 4IHI SER A -16 UNP O50443 EXPRESSION TAG SEQADV 4IHI HIS A -15 UNP O50443 EXPRESSION TAG SEQADV 4IHI HIS A -14 UNP O50443 EXPRESSION TAG SEQADV 4IHI HIS A -13 UNP O50443 EXPRESSION TAG SEQADV 4IHI HIS A -12 UNP O50443 EXPRESSION TAG SEQADV 4IHI HIS A -11 UNP O50443 EXPRESSION TAG SEQADV 4IHI HIS A -10 UNP O50443 EXPRESSION TAG SEQADV 4IHI SER A -9 UNP O50443 EXPRESSION TAG SEQADV 4IHI SER A -8 UNP O50443 EXPRESSION TAG SEQADV 4IHI GLY A -7 UNP O50443 EXPRESSION TAG SEQADV 4IHI LEU A -6 UNP O50443 EXPRESSION TAG SEQADV 4IHI VAL A -5 UNP O50443 EXPRESSION TAG SEQADV 4IHI PRO A -4 UNP O50443 EXPRESSION TAG SEQADV 4IHI ARG A -3 UNP O50443 EXPRESSION TAG SEQADV 4IHI GLY A -2 UNP O50443 EXPRESSION TAG SEQADV 4IHI SER A -1 UNP O50443 EXPRESSION TAG SEQADV 4IHI HIS A 0 UNP O50443 EXPRESSION TAG SEQADV 4IHI ASP A 505 UNP O50443 GLY 505 ENGINEERED MUTATION SEQRES 1 A 563 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 563 LEU VAL PRO ARG GLY SER HIS MET ASP ALA ILE THR GLN SEQRES 3 A 563 VAL PRO VAL PRO ALA ASN GLU PRO VAL HIS ASP TYR ALA SEQRES 4 A 563 PRO LYS SER PRO GLU ARG THR ARG LEU ARG THR GLU LEU SEQRES 5 A 563 ALA SER LEU ALA ASP HIS PRO ILE ASP LEU PRO HIS VAL SEQRES 6 A 563 ILE GLY GLY ARG HIS ARG MET GLY ASP GLY GLU ARG ILE SEQRES 7 A 563 ASP VAL VAL GLN PRO HIS ARG HIS ALA ALA ARG LEU GLY SEQRES 8 A 563 THR LEU THR ASN ALA THR HIS ALA ASP ALA ALA ALA ALA SEQRES 9 A 563 VAL GLU ALA ALA MET SER ALA LYS SER ASP TRP ALA ALA SEQRES 10 A 563 LEU PRO PHE ASP GLU ARG ALA ALA VAL PHE LEU ARG ALA SEQRES 11 A 563 ALA ASP LEU LEU ALA GLY PRO TRP ARG GLU LYS ILE ALA SEQRES 12 A 563 ALA ALA THR MET LEU GLY GLN SER LYS SER VAL TYR GLN SEQRES 13 A 563 ALA GLU ILE ASP ALA VAL CYS GLU LEU ILE ASP PHE TRP SEQRES 14 A 563 ARG PHE ASN VAL ALA PHE ALA ARG GLN ILE LEU GLU GLN SEQRES 15 A 563 GLN PRO ILE SER GLY PRO GLY GLU TRP ASN ARG ILE ASP SEQRES 16 A 563 TYR ARG PRO LEU ASP GLY PHE VAL TYR ALA ILE THR PRO SEQRES 17 A 563 PHE ASN PHE THR SER ILE ALA GLY ASN LEU PRO THR ALA SEQRES 18 A 563 PRO ALA LEU MET GLY ASN THR VAL ILE TRP LYS PRO SER SEQRES 19 A 563 ILE THR GLN THR LEU ALA ALA TYR LEU THR MET GLN LEU SEQRES 20 A 563 LEU GLU ALA ALA GLY LEU PRO PRO GLY VAL ILE ASN LEU SEQRES 21 A 563 VAL THR GLY ASP GLY PHE ALA VAL SER ASP VAL ALA LEU SEQRES 22 A 563 ALA ASP PRO ARG LEU ALA GLY ILE HIS PHE THR GLY SER SEQRES 23 A 563 THR ALA THR PHE GLY HIS LEU TRP GLN TRP VAL GLY THR SEQRES 24 A 563 ASN ILE GLY ARG TYR HIS SER TYR PRO ARG LEU VAL GLY SEQRES 25 A 563 GLU THR GLY GLY LYS ASP PHE VAL VAL ALA HIS ALA SER SEQRES 26 A 563 ALA ARG PRO ASP VAL LEU ARG THR ALA LEU ILE ARG GLY SEQRES 27 A 563 ALA PHE ASP TYR GLN GLY GLN LYS CYS SER ALA VAL SER SEQRES 28 A 563 ARG ALA PHE ILE ALA HIS SER VAL TRP GLN ARG MET GLY SEQRES 29 A 563 ASP GLU LEU LEU ALA LYS ALA ALA GLU LEU ARG TYR GLY SEQRES 30 A 563 ASP ILE THR ASP LEU SER ASN TYR GLY GLY ALA LEU ILE SEQRES 31 A 563 ASP GLN ARG ALA PHE VAL LYS ASN VAL ASP ALA ILE GLU SEQRES 32 A 563 ARG ALA LYS GLY ALA ALA ALA VAL THR VAL ALA VAL GLY SEQRES 33 A 563 GLY GLU TYR ASP ASP SER GLU GLY TYR PHE VAL ARG PRO SEQRES 34 A 563 THR VAL LEU LEU SER ASP ASP PRO THR ASP GLU SER PHE SEQRES 35 A 563 VAL ILE GLU TYR PHE GLY PRO LEU LEU SER VAL HIS VAL SEQRES 36 A 563 TYR PRO ASP GLU ARG TYR GLU GLN ILE LEU ASP VAL ILE SEQRES 37 A 563 ASP THR GLY SER ARG TYR ALA LEU THR GLY ALA VAL ILE SEQRES 38 A 563 ALA ASP ASP ARG GLN ALA VAL LEU THR ALA LEU ASP ARG SEQRES 39 A 563 LEU ARG PHE ALA ALA GLY ASN PHE TYR VAL ASN ASP LYS SEQRES 40 A 563 PRO THR GLY ALA VAL VAL GLY ARG GLN PRO PHE GLY GLY SEQRES 41 A 563 ALA ARG GLY SER ASP THR ASN ASP LYS ALA GLY SER PRO SEQRES 42 A 563 LEU ASN LEU LEU ARG TRP THR SER ALA ARG SER ILE LYS SEQRES 43 A 563 GLU THR PHE VAL ALA ALA THR ASP HIS ILE TYR PRO HIS SEQRES 44 A 563 MET ALA VAL ASP HET NAD A 601 44 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE FORMUL 2 NAD C21 H27 N7 O14 P2 FORMUL 3 HOH *450(H2 O) HELIX 1 1 SER A 22 HIS A 38 1 17 HELIX 2 2 THR A 77 ALA A 97 1 21 HELIX 3 3 PRO A 99 GLY A 116 1 18 HELIX 4 4 TRP A 118 SER A 131 1 14 HELIX 5 5 SER A 133 ALA A 141 1 9 HELIX 6 6 VAL A 142 GLU A 161 1 20 HELIX 7 7 PHE A 191 MET A 205 1 15 HELIX 8 8 SER A 214 THR A 216 5 3 HELIX 9 9 GLN A 217 ALA A 231 1 15 HELIX 10 10 GLY A 245 LEU A 253 1 9 HELIX 11 11 SER A 266 ASN A 280 1 15 HELIX 12 12 ILE A 281 TYR A 284 5 4 HELIX 13 13 ARG A 307 ASP A 321 1 15 HELIX 14 14 TYR A 322 GLN A 325 5 4 HELIX 15 15 HIS A 337 LEU A 354 1 18 HELIX 16 16 ASP A 371 ALA A 388 1 18 HELIX 17 17 PRO A 437 GLU A 439 5 3 HELIX 18 18 ARG A 440 SER A 452 1 13 HELIX 19 19 ASP A 464 LEU A 475 1 12 HELIX 20 20 SER A 512 ARG A 518 1 7 HELIX 21 21 TYR A 537 ALA A 541 5 5 SHEET 1 A 3 ILE A 40 LEU A 42 0 SHEET 2 A 3 ARG A 65 THR A 74 1 O THR A 72 N LEU A 42 SHEET 3 A 3 ARG A 57 GLN A 62 -1 N VAL A 60 O LEU A 70 SHEET 1 B 2 HIS A 44 ILE A 46 0 SHEET 2 B 2 ARG A 49 ARG A 51 -1 O ARG A 49 N ILE A 46 SHEET 1 C 2 GLU A 170 ARG A 177 0 SHEET 2 C 2 SER A 521 THR A 528 -1 O ARG A 523 N ASP A 175 SHEET 1 D 5 ILE A 238 LEU A 240 0 SHEET 2 D 5 VAL A 209 LYS A 212 1 N TRP A 211 O ASN A 239 SHEET 3 D 5 PHE A 182 ILE A 186 1 N ALA A 185 O LYS A 212 SHEET 4 D 5 LEU A 258 THR A 264 1 O HIS A 262 N TYR A 184 SHEET 5 D 5 ARG A 289 GLU A 293 1 O ARG A 289 N ALA A 259 SHEET 1 E 7 VAL A 391 VAL A 395 0 SHEET 2 E 7 THR A 410 SER A 414 -1 O LEU A 413 N THR A 392 SHEET 3 E 7 LEU A 430 TYR A 436 1 O LEU A 431 N THR A 410 SHEET 4 E 7 VAL A 330 ALA A 336 1 N ALA A 333 O HIS A 434 SHEET 5 E 7 ASP A 298 ALA A 302 1 N ALA A 302 O PHE A 334 SHEET 6 E 7 THR A 457 ILE A 461 1 O ALA A 459 N VAL A 301 SHEET 7 E 7 ASN A 481 VAL A 484 1 O TYR A 483 N GLY A 458 SHEET 1 F 2 TYR A 399 ASP A 400 0 SHEET 2 F 2 PHE A 406 VAL A 407 -1 O PHE A 406 N ASP A 400 SITE 1 AC1 31 TYR A 184 ILE A 186 THR A 187 PRO A 188 SITE 2 AC1 31 PHE A 189 ASN A 190 ILE A 194 LYS A 212 SITE 3 AC1 31 SER A 214 ASP A 244 GLY A 245 SER A 249 SITE 4 AC1 31 THR A 264 GLY A 265 SER A 266 THR A 269 SITE 5 AC1 31 GLU A 293 THR A 294 GLY A 295 CYS A 327 SITE 6 AC1 31 PHE A 427 LEU A 456 HOH A 755 HOH A 920 SITE 7 AC1 31 HOH A 929 HOH A 947 HOH A 949 HOH A 988 SITE 8 AC1 31 HOH A1039 HOH A1070 HOH A1071 CRYST1 163.937 163.937 194.025 90.00 90.00 120.00 P 6 2 2 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.006100 0.003522 0.000000 0.00000 SCALE2 0.000000 0.007044 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005154 0.00000 MASTER 493 0 1 21 21 0 8 6 0 0 0 44 END