HEADER TRANSFERASE 19-NOV-10 3PNL TITLE CRYSTAL STRUCTURE OF E.COLI DHA KINASE DHAK-DHAL COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PTS-DEPENDENT DIHYDROXYACETONE KINASE, DIHYDROXYACETONE- COMPND 3 BINDING SUBUNIT DHAK; COMPND 4 CHAIN: A; COMPND 5 EC: 2.7.-.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PTS-DEPENDENT DIHYDROXYACETONE KINASE, ADP-BINDING SUBUNIT COMPND 9 DHAL; COMPND 10 CHAIN: B; COMPND 11 EC: 2.7.-.-; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: B1200, DHAK, JW5187, YCGT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 13 ORGANISM_TAXID: 83333; SOURCE 14 STRAIN: K-12; SOURCE 15 GENE: B1199, DHAL, JW5186, YCGS; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS STRUCTURAL GENOMICS, MONTREAL-KINGSTON BACTERIAL STRUCTURAL GENOMICS KEYWDS 2 INITIATIVE, BSGI, DHA KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.SHI,L.MCDONALD,A.MATTE,M.CYGLER,I.EKIEL,MONTREAL-KINGSTON BACTERIAL AUTHOR 2 STRUCTURAL GENOMICS INITIATIVE (BSGI) REVDAT 5 08-NOV-17 3PNL 1 REMARK REVDAT 4 13-JUL-11 3PNL 1 VERSN REVDAT 3 16-FEB-11 3PNL 1 JRNL REVDAT 2 19-JAN-11 3PNL 1 JRNL REVDAT 1 12-JAN-11 3PNL 0 JRNL AUTH R.SHI,L.MCDONALD,Q.CUI,A.MATTE,M.CYGLER,I.EKIEL JRNL TITL STRUCTURAL AND MECHANISTIC INSIGHT INTO COVALENT SUBSTRATE JRNL TITL 2 BINDING BY ESCHERICHIA COLI DIHYDROXYACETONE KINASE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 1302 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 21209328 JRNL DOI 10.1073/PNAS.1012596108 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 38041 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1912 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2005 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.2990 REMARK 3 BIN FREE R VALUE SET COUNT : 109 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4255 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 196 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.86000 REMARK 3 B22 (A**2) : 0.86000 REMARK 3 B33 (A**2) : -1.72000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.180 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.142 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.148 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4366 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5924 ; 1.619 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 567 ; 6.268 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 185 ;35.392 ;24.811 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 723 ;18.885 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;18.619 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 678 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3281 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2799 ; 0.740 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4476 ; 1.380 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1567 ; 2.396 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1447 ; 3.872 ; 4.500 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 356 REMARK 3 ORIGIN FOR THE GROUP (A): 16.1766 1.9836 -12.8110 REMARK 3 T TENSOR REMARK 3 T11: -0.0664 T22: -0.0216 REMARK 3 T33: -0.0743 T12: -0.0827 REMARK 3 T13: 0.0775 T23: -0.0974 REMARK 3 L TENSOR REMARK 3 L11: 0.2091 L22: 0.8258 REMARK 3 L33: 1.6694 L12: -0.4140 REMARK 3 L13: -0.0848 L23: 0.0703 REMARK 3 S TENSOR REMARK 3 S11: 0.1154 S12: -0.0845 S13: 0.0139 REMARK 3 S21: -0.1063 S22: 0.1311 S23: -0.0261 REMARK 3 S31: -0.1409 S32: 0.2505 S33: -0.2465 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 0 B 1213 REMARK 3 ORIGIN FOR THE GROUP (A): 0.2283 -9.2837 -37.9329 REMARK 3 T TENSOR REMARK 3 T11: -0.0759 T22: -0.0441 REMARK 3 T33: -0.0915 T12: 0.0057 REMARK 3 T13: -0.0058 T23: -0.0657 REMARK 3 L TENSOR REMARK 3 L11: 0.5742 L22: 1.2840 REMARK 3 L33: 2.4077 L12: 0.0482 REMARK 3 L13: 0.2595 L23: 0.4544 REMARK 3 S TENSOR REMARK 3 S11: 0.0270 S12: 0.0972 S13: 0.0109 REMARK 3 S21: -0.0912 S22: -0.0693 S23: 0.0713 REMARK 3 S31: -0.0361 S32: -0.1670 S33: 0.0423 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 REMARK 4 REMARK 4 3PNL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1000062593. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38172 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 49.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.59700 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.5 M SODIUM FORMATE, 0.1M HEPES PH REMARK 280 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 134.38950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 37.28600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 37.28600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.19475 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 37.28600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 37.28600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 201.58425 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 37.28600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.28600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 67.19475 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 37.28600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.28600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 201.58425 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 134.38950 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: Y, X, -Z 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -91.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 GLY A 0 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 GLU A 175 CG CD OE1 OE2 REMARK 470 LYS A 356 CG CD CE NZ 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 NH1 ARG B 120 O HOH B 241 2.13 REMARK 500 O HOH A 387 O HOH A 439 2.13 REMARK 500 O HOH A 424 O HOH A 447 2.18 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 ASN A 6 -124.02 -99.80 REMARK 500 MET A 68 -131.92 -144.85 REMARK 500 VAL A 150 -137.07 -125.45 REMARK 500 ALA A 198 23.72 -79.46 REMARK 500 SER A 229 -50.45 -121.59 REMARK 500 LEU A 323 -123.02 42.78 REMARK 500 SER B 75 -45.64 -148.31 REMARK 500 THR B 95 -76.33 -76.44 REMARK 500 GLN B 96 -150.64 74.55 REMARK 500 ALA B 97 49.56 -68.14 REMARK 500 LYS B 128 55.42 72.31 REMARK 500 REMARK 500 REMARK: NULL 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 MG B1212 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 37 OD1 REMARK 620 2 ADP B1211 O1A 95.2 REMARK 620 3 ADP B1211 O1B 91.5 85.6 REMARK 620 4 ASP B 35 OD2 82.5 177.5 95.4 REMARK 620 5 ASP B 30 OD2 94.1 87.2 171.3 92.0 REMARK 620 6 HOH B 254 O 172.0 92.7 89.8 89.6 85.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1213 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 35 OD1 REMARK 620 2 PHE A 78 O 87.6 REMARK 620 3 HOH B 231 O 121.1 87.0 REMARK 620 4 ADP B1211 O1B 88.2 175.3 93.3 REMARK 620 5 ASP B 37 OD2 119.3 94.9 119.6 89.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1228 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 1211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1213 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3PNQ RELATED DB: PDB REMARK 900 RELATED ID: 3PNK RELATED DB: PDB REMARK 900 RELATED ID: 3PNM RELATED DB: PDB REMARK 900 RELATED ID: 3PNO RELATED DB: PDB DBREF 3PNL A 2 356 UNP P76015 DHAK_ECOLI 2 356 DBREF 3PNL B 2 210 UNP P76014 DHAL_ECOLI 2 210 SEQADV 3PNL GLY A 0 UNP P76015 EXPRESSION TAG SEQADV 3PNL SER A 1 UNP P76015 EXPRESSION TAG SEQADV 3PNL GLY B 0 UNP P76014 EXPRESSION TAG SEQADV 3PNL SER B 1 UNP P76014 EXPRESSION TAG SEQRES 1 A 357 GLY SER LYS LYS LEU ILE ASN ASP VAL GLN ASP VAL LEU SEQRES 2 A 357 ASP GLU GLN LEU ALA GLY LEU ALA LYS ALA HIS PRO SER SEQRES 3 A 357 LEU THR LEU HIS GLN ASP PRO VAL TYR VAL THR ARG ALA SEQRES 4 A 357 ASP ALA PRO VAL ALA GLY LYS VAL ALA LEU LEU SER GLY SEQRES 5 A 357 GLY GLY SER GLY HIS GLU PRO MET HIS CYS GLY TYR ILE SEQRES 6 A 357 GLY GLN GLY MET LEU SER GLY ALA CYS PRO GLY GLU ILE SEQRES 7 A 357 PHE THR SER PRO THR PRO ASP LYS ILE PHE GLU CYS ALA SEQRES 8 A 357 MET GLN VAL ASP GLY GLY GLU GLY VAL LEU LEU ILE ILE SEQRES 9 A 357 LYS ASN TYR THR GLY ASP ILE LEU ASN PHE GLU THR ALA SEQRES 10 A 357 THR GLU LEU LEU HIS ASP SER GLY VAL LYS VAL THR THR SEQRES 11 A 357 VAL VAL ILE ASP ASP ASP VAL ALA VAL LYS ASP SER LEU SEQRES 12 A 357 TYR THR ALA GLY ARG ARG GLY VAL ALA ASN THR VAL LEU SEQRES 13 A 357 ILE GLU LYS LEU VAL GLY ALA ALA ALA GLU ARG GLY ASP SEQRES 14 A 357 SER LEU ASP ALA CYS ALA GLU LEU GLY ARG LYS LEU ASN SEQRES 15 A 357 ASN GLN GLY HIS SER ILE GLY ILE ALA LEU GLY ALA CYS SEQRES 16 A 357 THR VAL PRO ALA ALA GLY LYS PRO SER PHE THR LEU ALA SEQRES 17 A 357 ASP ASN GLU MET GLU PHE GLY VAL GLY ILE HIS GLY GLU SEQRES 18 A 357 PRO GLY ILE ASP ARG ARG PRO PHE SER SER LEU ASP GLN SEQRES 19 A 357 THR VAL ASP GLU MET PHE ASP THR LEU LEU VAL ASN GLY SEQRES 20 A 357 SER TYR HIS ARG THR LEU ARG PHE TRP ASP TYR GLN GLN SEQRES 21 A 357 GLY SER TRP GLN GLU GLU GLN GLN THR LYS GLN PRO LEU SEQRES 22 A 357 GLN SER GLY ASP ARG VAL ILE ALA LEU VAL ASN ASN LEU SEQRES 23 A 357 GLY ALA THR PRO LEU SER GLU LEU TYR GLY VAL TYR ASN SEQRES 24 A 357 ARG LEU THR THR ARG CYS GLN GLN ALA GLY LEU THR ILE SEQRES 25 A 357 GLU ARG ASN LEU ILE GLY ALA TYR CYS THR SER LEU ASP SEQRES 26 A 357 MET THR GLY PHE SER ILE THR LEU LEU LYS VAL ASP ASP SEQRES 27 A 357 GLU THR LEU ALA LEU TRP ASP ALA PRO VAL HIS THR PRO SEQRES 28 A 357 ALA LEU ASN TRP GLY LYS SEQRES 1 B 211 GLY SER SER LEU SER ARG THR GLN ILE VAL ASN TRP LEU SEQRES 2 B 211 THR ARG CYS GLY ASP ILE PHE SER THR GLU SER GLU TYR SEQRES 3 B 211 LEU THR GLY LEU ASP ARG GLU ILE GLY ASP ALA ASP HIS SEQRES 4 B 211 GLY LEU ASN MET ASN ARG GLY PHE SER LYS VAL VAL GLU SEQRES 5 B 211 LYS LEU PRO ALA ILE ALA ASP LYS ASP ILE GLY PHE ILE SEQRES 6 B 211 LEU LYS ASN THR GLY MET THR LEU LEU SER SER VAL GLY SEQRES 7 B 211 GLY ALA SER GLY PRO LEU PHE GLY THR PHE PHE ILE ARG SEQRES 8 B 211 ALA ALA GLN ALA THR GLN ALA ARG GLN SER LEU THR LEU SEQRES 9 B 211 GLU GLU LEU TYR GLN MET PHE ARG ASP GLY ALA ASP GLY SEQRES 10 B 211 VAL ILE SER ARG GLY LYS ALA GLU PRO GLY ASP LYS THR SEQRES 11 B 211 MET CYS ASP VAL TRP VAL PRO VAL VAL GLU SER LEU ARG SEQRES 12 B 211 GLN SER SER GLU GLN ASN LEU SER VAL PRO VAL ALA LEU SEQRES 13 B 211 GLU ALA ALA SER SER ILE ALA GLU SER ALA ALA GLN SER SEQRES 14 B 211 THR ILE THR MET GLN ALA ARG LYS GLY ARG ALA SER TYR SEQRES 15 B 211 LEU GLY GLU ARG SER ILE GLY HIS GLN ASP PRO GLY ALA SEQRES 16 B 211 THR SER VAL MET PHE MET MET GLN MET LEU ALA LEU ALA SEQRES 17 B 211 ALA LYS GLU HET GOL A1228 6 HET ADP B1211 27 HET MG B1212 1 HET MG B1213 1 HETNAM GOL GLYCEROL HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL C3 H8 O3 FORMUL 4 ADP C10 H15 N5 O10 P2 FORMUL 5 MG 2(MG 2+) FORMUL 7 HOH *196(H2 O) HELIX 1 1 ASP A 7 GLN A 9 5 3 HELIX 2 2 ASP A 10 HIS A 23 1 14 HELIX 3 3 HIS A 60 ILE A 64 5 5 HELIX 4 4 THR A 82 ASP A 94 1 13 HELIX 5 5 TYR A 106 ASP A 122 1 17 HELIX 6 6 ALA A 151 GLY A 167 1 17 HELIX 7 7 SER A 169 ASN A 182 1 14 HELIX 8 8 SER A 230 ASN A 245 1 16 HELIX 9 9 PRO A 289 ALA A 307 1 19 HELIX 10 10 ASP A 336 ALA A 345 1 10 HELIX 11 11 ARG B 5 GLU B 22 1 18 HELIX 12 12 GLU B 22 ILE B 33 1 12 HELIX 13 13 ASP B 37 LEU B 53 1 17 HELIX 14 14 PRO B 54 ALA B 57 5 4 HELIX 15 15 ASP B 60 SER B 74 1 15 HELIX 16 16 ALA B 79 GLN B 96 1 18 HELIX 17 17 LEU B 103 LYS B 122 1 20 HELIX 18 18 MET B 130 GLN B 147 1 18 HELIX 19 19 SER B 150 THR B 169 1 20 HELIX 20 20 ILE B 170 MET B 172 5 3 HELIX 21 21 GLY B 177 ILE B 187 5 11 HELIX 22 22 ASP B 191 LYS B 209 1 19 SHEET 1 A 6 LEU A 26 HIS A 29 0 SHEET 2 A 6 TYR A 34 ARG A 37 -1 O THR A 36 N THR A 27 SHEET 3 A 6 GLY A 71 ILE A 77 -1 O ALA A 72 N VAL A 35 SHEET 4 A 6 ALA A 47 SER A 54 1 N GLY A 52 O GLY A 75 SHEET 5 A 6 VAL A 99 LYS A 104 1 O LEU A 100 N ALA A 47 SHEET 6 A 6 VAL A 127 ILE A 132 1 O ILE A 132 N ILE A 103 SHEET 1 B 6 ASP A 224 PRO A 227 0 SHEET 2 B 6 GLU A 210 PHE A 213 -1 N PHE A 213 O ASP A 224 SHEET 3 B 6 GLY A 184 GLY A 192 -1 N ALA A 190 O GLU A 212 SHEET 4 B 6 THR A 326 VAL A 335 -1 O THR A 326 N LEU A 191 SHEET 5 B 6 ARG A 277 ASN A 284 -1 N ARG A 277 O VAL A 335 SHEET 6 B 6 THR A 310 GLY A 317 1 O GLU A 312 N VAL A 278 SHEET 1 C 2 TYR A 248 ASP A 256 0 SHEET 2 C 2 SER A 261 LYS A 269 -1 O LYS A 269 N TYR A 248 SHEET 1 D 2 VAL A 347 HIS A 348 0 SHEET 2 D 2 ASN A 353 TRP A 354 -1 O TRP A 354 N VAL A 347 SHEET 1 E 2 SER B 2 SER B 4 0 SHEET 2 E 2 SER B 100 THR B 102 -1 O LEU B 101 N LEU B 3 LINK OD1 ASP B 37 MG MG B1212 1555 1555 1.93 LINK O1A ADP B1211 MG MG B1212 1555 1555 2.04 LINK O1B ADP B1211 MG MG B1212 1555 1555 2.05 LINK OD2 ASP B 35 MG MG B1212 1555 1555 2.06 LINK OD2 ASP B 30 MG MG B1212 1555 1555 2.12 LINK MG MG B1212 O HOH B 254 1555 1555 2.15 LINK OD1 ASP B 35 MG MG B1213 1555 1555 2.24 LINK O PHE A 78 MG MG B1213 1555 1555 2.26 LINK MG MG B1213 O HOH B 231 1555 1555 2.35 LINK O1B ADP B1211 MG MG B1213 1555 1555 2.45 LINK OD2 ASP B 37 MG MG B1213 1555 1555 2.46 LINK NE2 HIS A 218 C2 GOL A1228 1555 1555 1.68 CISPEP 1 ASP A 31 PRO A 32 0 3.45 CISPEP 2 ALA A 40 PRO A 41 0 0.34 CISPEP 3 GLU A 57 PRO A 58 0 9.19 CISPEP 4 MET A 59 HIS A 60 0 7.84 SITE 1 AC1 10 GLY A 52 GLY A 53 HIS A 56 PHE A 78 SITE 2 AC1 10 SER A 80 LYS A 104 ASP A 109 HIS A 218 SITE 3 AC1 10 ARG B 178 HOH B 231 SITE 1 AC2 25 THR A 107 HOH A 359 ASP B 30 ASP B 35 SITE 2 AC2 25 ASP B 37 HIS B 38 ASN B 41 GLY B 78 SITE 3 AC2 25 ALA B 79 SER B 80 LEU B 83 GLY B 121 SITE 4 AC2 25 THR B 129 MET B 130 GLY B 177 ASP B 191 SITE 5 AC2 25 PRO B 192 GLY B 193 HOH B 215 HOH B 216 SITE 6 AC2 25 HOH B 231 HOH B 243 HOH B 254 MG B1212 SITE 7 AC2 25 MG B1213 SITE 1 AC3 6 ASP B 30 ASP B 35 ASP B 37 HOH B 254 SITE 2 AC3 6 ADP B1211 MG B1213 SITE 1 AC4 6 PHE A 78 ASP B 35 ASP B 37 HOH B 231 SITE 2 AC4 6 ADP B1211 MG B1212 CRYST1 74.572 74.572 268.779 90.00 90.00 90.00 P 41 21 2 8 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 0.013410 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013410 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003721 0.00000 MASTER 409 0 4 22 18 0 14 6 0 0 0 45 END