10 20 30 40 50 60 70 80 3DR3 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXIDOREDUCTASE 10-JUL-08 3DR3
TITLE STRUCTURE OF IDP00107, A POTENTIAL N-ACETYL-GAMMA- TITLE 2 GLUTAMYLPHOSPHATE REDUCTASE FROM SHIGELLA FLEXNERI
COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ACETYL-GAMMA-GLUTAMYL-PHOSPHATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AGPR, N-ACETYL-GLUTAMATE SEMIALDEHYDE COMPND 5 DEHYDROGENASE, NAGSA DEHYDROGENASE; COMPND 6 EC: 1.2.1.38; COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHIGELLA FLEXNERI; SOURCE 3 ORGANISM_TAXID: 623; SOURCE 4 STRAIN: 2A STR. 2457T; SOURCE 5 GENE: ARGC, SF4035, S3711; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-GOLD(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMCSG7
KEYWDS CSGID TARGET, ARGC, SHIGELLA FLEXNERI, ESSENTIAL GENE, KEYWDS 2 AMINO-ACID BIOSYNTHESIS, ARGININE BIOSYNTHESIS, CYTOPLASM, KEYWDS 3 NADP, OXIDOREDUCTASE. FUNDED BY THE NATIONAL INSTITUTE OF KEYWDS 4 ALLERGY AND INFECTIOUS DISEASES OF NIH CONTRACT NUMBER KEYWDS 5 HHSN272200700058C, STRUCTURAL GENOMICS, CENTER FOR KEYWDS 6 STRUCTURAL GENOMICS OF INFECTIOUS DISEASES
EXPDTA X-RAY DIFFRACTION
AUTHOR A.U.SINGER,T.SKARINA,O.ONOPRIYENKO,A.M.EDWARDS,W.F.ANDERSON, AUTHOR 2 A.SAVCHENKO,CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS AUTHOR 3 DISEASES (CSGID)
REVDAT 2 24-FEB-09 3DR3 1 VERSN REVDAT 1 05-AUG-08 3DR3 0
JRNL AUTH A.U.SINGER,T.SKARINA,O.ONOPRIYENKO,A.M.EDWARDS, JRNL AUTH 2 W.F.ANDERSON,A.SAVCHENKO JRNL TITL STRUCTURE OF IDP00107, A POTENTIAL JRNL TITL 2 N-ACETYL-GAMMA-GLUTAMYLPHOSPHATE REDUCTASE FROM JRNL TITL 3 SHIGELLA FLEXNERI JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 TITL FUNDED BY THE NATIONAL INSTITUTE OF ALLERGY AND REMARK 1 TITL 2 INFECTIOUS DISEASES OF NIH (CONTRACT NUMBER REMARK 1 TITL 3 HHSN272200700058C). REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN
REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 30510 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1631 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2178 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.53 REMARK 3 BIN R VALUE (WORKING SET) : 0.2020 REMARK 3 BIN FREE R VALUE SET COUNT : 137 REMARK 3 BIN FREE R VALUE : 0.2450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2551 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 392 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 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): 0.134 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.137 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.088 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.143 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2618 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3573 ; 1.549 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 336 ; 6.803 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 110 ;34.685 ;24.909 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 399 ;13.144 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;17.862 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 411 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2006 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1248 ; 0.212 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1793 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 291 ; 0.169 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.107 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 81 ; 0.193 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 36 ; 0.232 ; 0.200 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): 1670 ; 0.865 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2680 ; 1.517 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 970 ; 2.344 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 892 ; 3.618 ; 4.500 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 REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 3DR3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUL-08. REMARK 100 THE RCSB ID CODE IS RCSB048383.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32186 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 16.800 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 31.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 16.00 REMARK 200 R MERGE FOR SHELL (I) : 0.45400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 10.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PROTEIN ATOMS FROM 2G17 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2 M D,L-MALIC ACID AND 0.1 M BIS- REMARK 280 TRIS PROPANE. CRYOPROTECTED WITH N-PARATONE OIL, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 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 76.98133 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 38.49067 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 76.98133 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 38.49067 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 76.98133 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 38.49067 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 76.98133 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 38.49067 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 300 REMARK: AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -158.0 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 -1.000000 0.000000 0.000000 58.64950 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 101.58391 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 -38.49067 REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 58.64950 REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 101.58391 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 -38.49067 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 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 -1.000000 0.000000 0.000000 58.64950 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 101.58391 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 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 -38.49067
REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 340 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 362 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 635 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 702 LIES ON A SPECIAL POSITION.
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 SER A -2 REMARK 465 ASN A -1
REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 141 CG OD1 ND2
REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 CYS A 139 CA CB SG REMARK 480 GLN A 331 CA CB CG CD OE1 NE2
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 399 O HOH A 513 2.13 REMARK 500 OE1 GLN A 331 O HOH A 435 2.13 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 N ALA A 0 O HOH A 659 2654 1.89 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 CYS A 139 CB CYS A 139 SG -0.157 REMARK 500 CYS A 139 CA CYS A 139 C -0.312 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 CYS A 139 N - CA - C ANGL. DEV. = 17.5 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 144 -18.37 -43.40 REMARK 500 GLU A 145 14.97 -141.39 REMARK 500 LYS A 192 145.40 173.46 REMARK 500 SER A 203 -89.70 -144.53 REMARK 500 PHE A 210 17.13 58.50 REMARK 500 LEU A 310 -91.54 -104.36 REMARK 500 ALA A 313 -92.55 -155.17 REMARK 500 SER A 332 -15.58 83.76 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 657 DISTANCE = 6.39 ANGSTROMS
REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 335 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 21 O REMARK 620 2 ASN A 22 O 81.1 REMARK 620 3 HIS A 24 O 99.0 110.1 REMARK 620 4 MET A 27 O 89.7 160.8 87.8 REMARK 620 5 HOH A 448 O 164.6 84.8 91.6 101.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 336 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 264 O REMARK 620 2 LYS A 267 O 87.3 REMARK 620 3 VAL A 270 O 126.8 86.5 REMARK 620 4 HOH A 426 O 104.1 166.1 80.3 REMARK 620 N 1 2 3
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 335 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 336 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLT A 337
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2G17 RELATED DB: PDB REMARK 900 THE STRUCTURE OF N-ACETYL-GAMMA-GLUTAMYL-PHOSPHATE REMARK 900 REDUCTASE FROM SALMONELLA TYPHIMURIUM
DBREF 3DR3 A 1 334 UNP P59310 ARGC_SHIFL 1 334
SEQADV 3DR3 SER A -2 UNP P59310 EXPRESSION TAG SEQADV 3DR3 ASN A -1 UNP P59310 EXPRESSION TAG SEQADV 3DR3 ALA A 0 UNP P59310 EXPRESSION TAG
SEQRES 1 A 337 SER ASN ALA MET LEU ASN THR LEU ILE VAL GLY ALA SER SEQRES 2 A 337 GLY TYR ALA GLY ALA GLU LEU VAL THR TYR VAL ASN ARG SEQRES 3 A 337 HIS PRO HIS MET ASN ILE THR ALA LEU THR VAL SER ALA SEQRES 4 A 337 GLN SER ASN ASP ALA GLY LYS LEU ILE SER ASP LEU HIS SEQRES 5 A 337 PRO GLN LEU LYS GLY ILE VAL GLU LEU PRO LEU GLN PRO SEQRES 6 A 337 MET SER ASP ILE SER GLU PHE SER PRO GLY VAL ASP VAL SEQRES 7 A 337 VAL PHE LEU ALA THR ALA HIS GLU VAL SER HIS ASP LEU SEQRES 8 A 337 ALA PRO GLN PHE LEU GLU ALA GLY CYS VAL VAL PHE ASP SEQRES 9 A 337 LEU SER GLY ALA PHE ARG VAL ASN ASP ALA THR PHE TYR SEQRES 10 A 337 GLU LYS TYR TYR GLY PHE THR HIS GLN TYR PRO GLU LEU SEQRES 11 A 337 LEU GLU GLN ALA ALA TYR GLY LEU ALA GLU TRP CYS GLY SEQRES 12 A 337 ASN LYS LEU LYS GLU ALA ASN LEU ILE ALA VAL PRO GLY SEQRES 13 A 337 CYS TYR PRO THR ALA ALA GLN LEU ALA LEU LYS PRO LEU SEQRES 14 A 337 ILE ASP ALA ASP LEU LEU ASP LEU ASN GLN TRP PRO VAL SEQRES 15 A 337 ILE ASN ALA THR SER GLY VAL SER GLY ALA GLY ARG LYS SEQRES 16 A 337 ALA ALA ILE SER ASN SER PHE CYS GLU VAL SER LEU GLN SEQRES 17 A 337 PRO TYR GLY VAL PHE THR HIS ARG HIS GLN PRO GLU ILE SEQRES 18 A 337 ALA THR HIS LEU GLY ALA ASP VAL ILE PHE THR PRO HIS SEQRES 19 A 337 LEU GLY ASN PHE PRO ARG GLY ILE LEU GLU THR ILE THR SEQRES 20 A 337 CYS ARG LEU LYS SER GLY VAL THR GLN ALA GLN VAL ALA SEQRES 21 A 337 GLN ALA LEU GLN GLN ALA TYR ALA HIS LYS PRO LEU VAL SEQRES 22 A 337 ARG LEU TYR ASP LYS GLY VAL PRO ALA LEU LYS ASN VAL SEQRES 23 A 337 VAL GLY LEU PRO PHE CYS ASP ILE GLY PHE ALA VAL GLN SEQRES 24 A 337 GLY GLU HIS LEU ILE ILE VAL ALA THR GLU ASP ASN LEU SEQRES 25 A 337 LEU LYS GLY ALA ALA ALA GLN ALA VAL GLN CYS ALA ASN SEQRES 26 A 337 ILE ARG PHE GLY TYR ALA GLU THR GLN SER LEU ILE
HET NA A 335 1 HET NA A 336 1 HET MLT A 337 18
HETNAM NA SODIUM ION HETNAM MLT MALATE ION
FORMUL 2 NA 2(NA 1+) FORMUL 4 MLT C4 H5 O5 1- FORMUL 5 HOH *392(H2 O)
HELIX 1 1 GLY A 11 HIS A 24 1 14 HELIX 2 2 LEU A 44 HIS A 49 1 6 HELIX 3 3 PRO A 50 LYS A 53 5 4 HELIX 4 4 ASP A 65 PHE A 69 5 5 HELIX 5 5 ALA A 81 ALA A 95 1 15 HELIX 6 6 ASP A 110 TYR A 118 1 9 HELIX 7 7 TYR A 124 ALA A 131 1 8 HELIX 8 8 GLY A 140 GLU A 145 1 6 HELIX 9 9 GLY A 153 ALA A 169 1 17 HELIX 10 10 VAL A 186 GLY A 190 5 5 HELIX 11 11 SER A 198 VAL A 202 5 5 HELIX 12 12 ARG A 213 GLY A 223 1 11 HELIX 13 13 THR A 252 ALA A 265 1 14 HELIX 14 14 ALA A 279 VAL A 283 5 5 HELIX 15 15 ALA A 313 GLY A 326 1 14
SHEET 1 A 7 LEU A 60 MET A 63 0 SHEET 2 A 7 MET A 27 SER A 35 1 N LEU A 32 O GLN A 61 SHEET 3 A 7 LEU A 2 VAL A 7 1 N LEU A 2 O ASN A 28 SHEET 4 A 7 VAL A 75 LEU A 78 1 O VAL A 75 N LEU A 5 SHEET 5 A 7 VAL A 98 ASP A 101 1 O PHE A 100 N VAL A 76 SHEET 6 A 7 LEU A 148 ALA A 150 1 O ILE A 149 N ASP A 101 SHEET 7 A 7 ALA A 132 TYR A 133 1 N ALA A 132 O LEU A 148 SHEET 1 B 7 LEU A 204 PRO A 206 0 SHEET 2 B 7 ILE A 227 GLY A 233 -1 O LEU A 232 N GLN A 205 SHEET 3 B 7 VAL A 179 SER A 184 1 N ILE A 180 O ILE A 227 SHEET 4 B 7 ILE A 239 ARG A 246 -1 O THR A 242 N ASN A 181 SHEET 5 B 7 HIS A 299 GLU A 306 -1 O ALA A 304 N GLU A 241 SHEET 6 B 7 CYS A 289 GLN A 296 -1 N GLY A 292 O VAL A 303 SHEET 7 B 7 VAL A 270 LEU A 272 1 N ARG A 271 O CYS A 289
LINK O VAL A 21 NA NA A 335 1555 1555 2.55 LINK O ASN A 22 NA NA A 335 1555 1555 2.47 LINK O HIS A 24 NA NA A 335 1555 1555 2.27 LINK O MET A 27 NA NA A 335 1555 1555 2.24 LINK O TYR A 264 NA NA A 336 1555 1555 2.48 LINK O LYS A 267 NA NA A 336 1555 1555 2.34 LINK O VAL A 270 NA NA A 336 1555 1555 2.38 LINK NA NA A 335 O HOH A 448 1555 1555 2.39 LINK NA NA A 336 O HOH A 426 1555 1555 2.58
SITE 1 AC1 4 ASN A 22 HIS A 24 MET A 27 HOH A 448 SITE 1 AC2 3 TYR A 264 LYS A 267 HOH A 426 SITE 1 AC3 13 TYR A 12 GLN A 51 CYS A 200 PRO A 236 SITE 2 AC3 13 ARG A 237 LYS A 281 ASN A 282 LEU A 309 SITE 3 AC3 13 HOH A 363 HOH A 457 HOH A 489 HOH A 601 SITE 4 AC3 13 HOH A 703
CRYST1 117.299 117.299 115.472 90.00 90.00 120.00 P 62 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 0.008525 0.004922 0.000000 0.00000
SCALE2 0.000000 0.009844 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008660 0.00000