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