HEADER TRANSFERASE 14-MAY-18 5ZW9 TITLE CRYSTAL STRUCTURE OF PYRIDOXAL KINASE (PDXK) FROM SALMONELLA TITLE 2 TYPHIMURIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRIDOXALKINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PL KINASE; COMPND 5 EC: 2.7.1.35; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA CHOLERAESUIS; SOURCE 3 ORGANISM_TAXID: 28901; SOURCE 4 STRAIN: LT2; SOURCE 5 GENE: PDXK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-22B(+) KEYWDS PYRIDOXAL KINASE, BOUND PHOSPHATE, SALMONELLA TYPHIMURIUM, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.DEKA,J.F.BENAZIR,J.N.KALYANI,H.S.SAVITHRI,M.R.N.MURTHY REVDAT 3 22-NOV-23 5ZW9 1 REMARK REVDAT 2 11-DEC-19 5ZW9 1 JRNL REVDAT 1 29-MAY-19 5ZW9 0 JRNL AUTH G.DEKA,J.N.KALYANI,F.B.JAHANGIR,P.SABHARWAL,H.S.SAVITHRI, JRNL AUTH 2 M.R.N.MURTHY JRNL TITL STRUCTURAL AND FUNCTIONAL STUDIES ON SALMONELLA TYPHIMURIUM JRNL TITL 2 PYRIDOXAL KINASE: THE FIRST STRUCTURAL EVIDENCE FOR THE JRNL TITL 3 FORMATION OF SCHIFF BASE WITH THE SUBSTRATE. JRNL REF FEBS J. V. 286 3684 2019 JRNL REFN ISSN 1742-464X JRNL PMID 31116912 JRNL DOI 10.1111/FEBS.14933 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0069 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 89.9 REMARK 3 NUMBER OF REFLECTIONS : 13922 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) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 730 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1075 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.68 REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE SET COUNT : 63 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3881 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 163 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.26000 REMARK 3 B22 (A**2) : 3.53000 REMARK 3 B33 (A**2) : -3.27000 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): 0.433 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.341 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.747 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.915 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.844 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4067 ; 0.005 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3899 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5552 ; 1.038 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8946 ; 1.017 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 534 ; 5.010 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 148 ;32.574 ;24.459 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 618 ;15.708 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;16.187 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 667 ; 0.051 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4576 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 866 ; 0.006 ; 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): 2110 ; 0.867 ; 3.338 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2109 ; 0.867 ; 3.337 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2631 ; 1.552 ; 4.996 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2632 ; 1.552 ; 4.996 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1957 ; 0.697 ; 3.427 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1957 ; 0.696 ; 3.427 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2915 ; 1.239 ; 5.095 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4653 ; 3.801 ;26.690 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4654 ; 3.800 ;26.695 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 16 A 283 1 REMARK 3 1 B 16 B 283 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT THERMAL 1 A (A**2): 2221 ; 2.55 ; 0.50 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 REMARK 4 REMARK 4 5ZW9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1300006742. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14688 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 72.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.13000 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) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 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: 2DDM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 10% 2-PROPANOL, 100 MM REMARK 280 HEPES PH 7.5, BATCH MODE, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 -1.000000 0.000000 0.000000 32.55500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.76000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.44500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.76000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.55500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.44500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: 4270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 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 MET A 1 REMARK 465 GLY A 2 REMARK 465 GLN A 3 REMARK 465 GLU A 4 REMARK 465 SER A 5 REMARK 465 ASP A 6 REMARK 465 ILE A 7 REMARK 465 GLN A 8 REMARK 465 SER A 9 REMARK 465 VAL A 10 REMARK 465 LEU A 11 REMARK 465 PHE A 12 REMARK 465 ASP A 13 REMARK 465 ASP A 14 REMARK 465 ASN A 15 REMARK 465 VAL A 228 REMARK 465 ALA A 229 REMARK 465 ALA A 284 REMARK 465 GLY A 285 REMARK 465 GLU A 286 REMARK 465 ALA A 287 REMARK 465 ARG A 288 REMARK 465 LEU A 289 REMARK 465 GLU A 290 REMARK 465 HIS A 291 REMARK 465 HIS A 292 REMARK 465 HIS A 293 REMARK 465 HIS A 294 REMARK 465 HIS A 295 REMARK 465 HIS A 296 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 GLN B 3 REMARK 465 GLU B 4 REMARK 465 SER B 5 REMARK 465 ASP B 6 REMARK 465 ILE B 7 REMARK 465 GLN B 8 REMARK 465 SER B 9 REMARK 465 VAL B 10 REMARK 465 LEU B 11 REMARK 465 PHE B 12 REMARK 465 ASP B 13 REMARK 465 ASP B 14 REMARK 465 LEU B 207 REMARK 465 GLU B 208 REMARK 465 THR B 209 REMARK 465 PRO B 226 REMARK 465 ARG B 227 REMARK 465 VAL B 228 REMARK 465 ALA B 229 REMARK 465 THR B 230 REMARK 465 GLU B 231 REMARK 465 ALA B 284 REMARK 465 GLY B 285 REMARK 465 GLU B 286 REMARK 465 ALA B 287 REMARK 465 ARG B 288 REMARK 465 LEU B 289 REMARK 465 GLU B 290 REMARK 465 HIS B 291 REMARK 465 HIS B 292 REMARK 465 HIS B 293 REMARK 465 HIS B 294 REMARK 465 HIS B 295 REMARK 465 HIS B 296 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 ARG A 17 NH1 NH2 REMARK 470 LYS A 45 CE NZ REMARK 470 GLU A 76 OE1 OE2 REMARK 470 LYS A 113 CD CE NZ REMARK 470 SER A 206 CB OG REMARK 470 LEU A 207 CG CD1 CD2 REMARK 470 GLU A 208 CG CD OE1 OE2 REMARK 470 ILE A 210 CD1 REMARK 470 VAL A 212 CG1 CG2 REMARK 470 VAL A 215 CB CG1 CG2 REMARK 470 THR A 216 CB OG1 CG2 REMARK 470 ALA A 217 CB REMARK 470 GLN A 218 CG CD OE1 NE2 REMARK 470 ARG A 227 C O CZ NH1 NH2 REMARK 470 GLU A 231 CG CD OE1 OE2 REMARK 470 LYS A 233 CE NZ REMARK 470 LYS A 258 CE NZ REMARK 470 GLN A 272 CG CD NE2 REMARK 470 ILE A 280 CD1 REMARK 470 LYS B 66 NZ REMARK 470 LYS B 113 CD CE NZ REMARK 470 LYS B 174 CE NZ REMARK 470 GLU B 180 CB CG CD OE1 OE2 REMARK 470 LYS B 195 CE NZ REMARK 470 GLU B 205 CG CD OE1 OE2 REMARK 470 SER B 206 OG REMARK 470 ILE B 210 CD1 REMARK 470 VAL B 212 CG1 CG2 REMARK 470 VAL B 215 CB CG1 CG2 REMARK 470 THR B 216 CB OG1 CG2 REMARK 470 ALA B 217 O REMARK 470 HIS B 225 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 233 CG CD CE NZ REMARK 470 LYS B 252 CE REMARK 470 LYS B 258 NZ REMARK 470 LEU B 265 CG CD1 CD2 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 64 CG HIS A 64 CD2 0.060 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 GLN A 27 -167.60 -168.18 REMARK 500 HIS A 122 72.24 -119.34 REMARK 500 GLU A 205 79.08 -119.20 REMARK 500 SER A 206 -117.79 105.45 REMARK 500 LEU A 207 32.85 -84.72 REMARK 500 VAL A 215 45.51 -77.76 REMARK 500 GLN B 27 -166.84 -167.68 REMARK 500 HIS B 122 73.03 -118.41 REMARK 500 GLU B 205 75.10 -115.55 REMARK 500 VAL B 215 45.36 -87.08 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 A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PO4 A 301 O2 REMARK 620 2 HOH A 476 O 142.2 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PE4 B 303 DBREF1 5ZW9 A 1 288 UNP A0A0M0PWM4_SALCE DBREF2 5ZW9 A A0A0M0PWM4 1 288 DBREF1 5ZW9 B 1 288 UNP A0A0M0PWM4_SALCE DBREF2 5ZW9 B A0A0M0PWM4 1 288 SEQADV 5ZW9 LEU A 289 UNP A0A0M0PWM EXPRESSION TAG SEQADV 5ZW9 GLU A 290 UNP A0A0M0PWM EXPRESSION TAG SEQADV 5ZW9 HIS A 291 UNP A0A0M0PWM EXPRESSION TAG SEQADV 5ZW9 HIS A 292 UNP A0A0M0PWM EXPRESSION TAG SEQADV 5ZW9 HIS A 293 UNP A0A0M0PWM EXPRESSION TAG SEQADV 5ZW9 HIS A 294 UNP A0A0M0PWM EXPRESSION TAG SEQADV 5ZW9 HIS A 295 UNP A0A0M0PWM EXPRESSION TAG SEQADV 5ZW9 HIS A 296 UNP A0A0M0PWM EXPRESSION TAG SEQADV 5ZW9 LEU B 289 UNP A0A0M0PWM EXPRESSION TAG SEQADV 5ZW9 GLU B 290 UNP A0A0M0PWM EXPRESSION TAG SEQADV 5ZW9 HIS B 291 UNP A0A0M0PWM EXPRESSION TAG SEQADV 5ZW9 HIS B 292 UNP A0A0M0PWM EXPRESSION TAG SEQADV 5ZW9 HIS B 293 UNP A0A0M0PWM EXPRESSION TAG SEQADV 5ZW9 HIS B 294 UNP A0A0M0PWM EXPRESSION TAG SEQADV 5ZW9 HIS B 295 UNP A0A0M0PWM EXPRESSION TAG SEQADV 5ZW9 HIS B 296 UNP A0A0M0PWM EXPRESSION TAG SEQRES 1 A 296 MET GLY GLN GLU SER ASP ILE GLN SER VAL LEU PHE ASP SEQRES 2 A 296 ASP ASN HIS ARG ALA LEU GLN THR ASP ILE VAL ALA VAL SEQRES 3 A 296 GLN SER GLN VAL VAL TYR GLY SER VAL GLY ASN SER ILE SEQRES 4 A 296 ALA VAL PRO ALA ILE LYS ALA GLN GLY LEU ARG VAL THR SEQRES 5 A 296 ALA VAL PRO THR VAL LEU PHE SER ASN THR PRO HIS TYR SEQRES 6 A 296 LYS THR PHE TYR GLY GLY ILE ILE PRO ALA GLU TRP PHE SEQRES 7 A 296 ALA GLY TYR LEU THR ALA LEU ASN GLU ARG ASP ALA LEU SEQRES 8 A 296 ARG GLU LEU LYS ALA ILE THR THR GLY TYR MET GLY SER SEQRES 9 A 296 ALA ASP GLN ILE VAL LEU LEU SER LYS TRP LEU MET ALA SEQRES 10 A 296 ILE ARG ALA SER HIS PRO GLU VAL CYS ILE LEU VAL ASP SEQRES 11 A 296 PRO VAL ILE GLY ASP THR ASP SER GLY MET TYR VAL GLN SEQRES 12 A 296 ALA GLU ILE PRO GLN ALA TYR ARG THR HIS LEU LEU PRO SEQRES 13 A 296 GLN ALA GLN GLY LEU THR PRO ASN VAL PHE GLU LEU GLU SEQRES 14 A 296 MET LEU SER GLY LYS PRO CYS ARG THR LEU GLU GLU ALA SEQRES 15 A 296 VAL ALA ALA ALA GLN SER LEU LEU SER ASP THR LEU LYS SEQRES 16 A 296 TRP VAL VAL ILE THR SER ALA PRO GLY GLU SER LEU GLU SEQRES 17 A 296 THR ILE THR VAL ALA VAL VAL THR ALA GLN VAL VAL GLU SEQRES 18 A 296 VAL PHE ALA HIS PRO ARG VAL ALA THR GLU LEU LYS GLY SEQRES 19 A 296 THR GLY ASP LEU PHE CYS ALA GLU LEU VAL SER GLY ILE SEQRES 20 A 296 VAL GLN GLY LYS LYS LEU THR THR ALA ALA LYS ASP ALA SEQRES 21 A 296 ALA GLN ARG VAL LEU GLU VAL MET THR TRP THR GLN GLN SEQRES 22 A 296 CYS GLY CYS ASP GLU LEU ILE LEU PRO PRO ALA GLY GLU SEQRES 23 A 296 ALA ARG LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 296 MET GLY GLN GLU SER ASP ILE GLN SER VAL LEU PHE ASP SEQRES 2 B 296 ASP ASN HIS ARG ALA LEU GLN THR ASP ILE VAL ALA VAL SEQRES 3 B 296 GLN SER GLN VAL VAL TYR GLY SER VAL GLY ASN SER ILE SEQRES 4 B 296 ALA VAL PRO ALA ILE LYS ALA GLN GLY LEU ARG VAL THR SEQRES 5 B 296 ALA VAL PRO THR VAL LEU PHE SER ASN THR PRO HIS TYR SEQRES 6 B 296 LYS THR PHE TYR GLY GLY ILE ILE PRO ALA GLU TRP PHE SEQRES 7 B 296 ALA GLY TYR LEU THR ALA LEU ASN GLU ARG ASP ALA LEU SEQRES 8 B 296 ARG GLU LEU LYS ALA ILE THR THR GLY TYR MET GLY SER SEQRES 9 B 296 ALA ASP GLN ILE VAL LEU LEU SER LYS TRP LEU MET ALA SEQRES 10 B 296 ILE ARG ALA SER HIS PRO GLU VAL CYS ILE LEU VAL ASP SEQRES 11 B 296 PRO VAL ILE GLY ASP THR ASP SER GLY MET TYR VAL GLN SEQRES 12 B 296 ALA GLU ILE PRO GLN ALA TYR ARG THR HIS LEU LEU PRO SEQRES 13 B 296 GLN ALA GLN GLY LEU THR PRO ASN VAL PHE GLU LEU GLU SEQRES 14 B 296 MET LEU SER GLY LYS PRO CYS ARG THR LEU GLU GLU ALA SEQRES 15 B 296 VAL ALA ALA ALA GLN SER LEU LEU SER ASP THR LEU LYS SEQRES 16 B 296 TRP VAL VAL ILE THR SER ALA PRO GLY GLU SER LEU GLU SEQRES 17 B 296 THR ILE THR VAL ALA VAL VAL THR ALA GLN VAL VAL GLU SEQRES 18 B 296 VAL PHE ALA HIS PRO ARG VAL ALA THR GLU LEU LYS GLY SEQRES 19 B 296 THR GLY ASP LEU PHE CYS ALA GLU LEU VAL SER GLY ILE SEQRES 20 B 296 VAL GLN GLY LYS LYS LEU THR THR ALA ALA LYS ASP ALA SEQRES 21 B 296 ALA GLN ARG VAL LEU GLU VAL MET THR TRP THR GLN GLN SEQRES 22 B 296 CYS GLY CYS ASP GLU LEU ILE LEU PRO PRO ALA GLY GLU SEQRES 23 B 296 ALA ARG LEU GLU HIS HIS HIS HIS HIS HIS HET PO4 A 301 5 HET MG A 302 1 HET EDO A 303 4 HET PEG A 304 7 HET EDO B 301 4 HET EDO B 302 4 HET PE4 B 303 24 HETNAM PO4 PHOSPHATE ION HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}- HETNAM 2 PE4 ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL HETSYN EDO ETHYLENE GLYCOL HETSYN PE4 POLYETHYLENE GLYCOL PEG4000 FORMUL 3 PO4 O4 P 3- FORMUL 4 MG MG 2+ FORMUL 5 EDO 3(C2 H6 O2) FORMUL 6 PEG C4 H10 O3 FORMUL 9 PE4 C16 H34 O8 FORMUL 10 HOH *163(H2 O) HELIX 1 AA1 GLY A 36 GLN A 47 1 12 HELIX 2 AA2 PRO A 74 ARG A 88 1 15 HELIX 3 AA3 SER A 104 HIS A 122 1 19 HELIX 4 AA4 GLU A 145 LEU A 154 1 10 HELIX 5 AA5 LEU A 155 ALA A 158 5 4 HELIX 6 AA6 ASN A 164 GLY A 173 1 10 HELIX 7 AA7 THR A 178 LEU A 190 1 13 HELIX 8 AA8 GLY A 234 GLY A 250 1 17 HELIX 9 AA9 LYS A 252 CYS A 274 1 23 HELIX 10 AB1 GLY B 36 GLN B 47 1 12 HELIX 11 AB2 PRO B 74 ARG B 88 1 15 HELIX 12 AB3 SER B 104 HIS B 122 1 19 HELIX 13 AB4 GLU B 145 LEU B 154 1 10 HELIX 14 AB5 ASN B 164 GLY B 173 1 10 HELIX 15 AB6 THR B 178 LEU B 190 1 13 HELIX 16 AB7 GLY B 234 GLY B 250 1 17 HELIX 17 AB8 LYS B 252 GLY B 275 1 24 SHEET 1 AA1 9 GLY A 70 ILE A 72 0 SHEET 2 AA1 9 VAL A 51 PHE A 59 -1 N LEU A 58 O GLY A 71 SHEET 3 AA1 9 ILE A 23 VAL A 30 1 N ALA A 25 O VAL A 54 SHEET 4 AA1 9 ALA A 96 THR A 99 1 O THR A 98 N VAL A 26 SHEET 5 AA1 9 CYS A 126 VAL A 129 1 O LEU A 128 N ILE A 97 SHEET 6 AA1 9 GLY A 160 LEU A 161 1 O GLY A 160 N VAL A 129 SHEET 7 AA1 9 TRP A 196 ALA A 202 1 O VAL A 198 N LEU A 161 SHEET 8 AA1 9 GLU A 208 VAL A 214 -1 O VAL A 214 N VAL A 197 SHEET 9 AA1 9 GLU A 221 PRO A 226 -1 O GLU A 221 N ALA A 213 SHEET 1 AA2 2 GLY A 134 ASP A 135 0 SHEET 2 AA2 2 GLY A 139 MET A 140 -1 O GLY A 139 N ASP A 135 SHEET 1 AA3 9 GLY B 70 ILE B 72 0 SHEET 2 AA3 9 VAL B 51 PHE B 59 -1 N LEU B 58 O GLY B 71 SHEET 3 AA3 9 ILE B 23 VAL B 30 1 N ALA B 25 O VAL B 54 SHEET 4 AA3 9 ALA B 96 THR B 99 1 O THR B 98 N VAL B 26 SHEET 5 AA3 9 CYS B 126 VAL B 129 1 O LEU B 128 N ILE B 97 SHEET 6 AA3 9 GLY B 160 LEU B 161 1 O GLY B 160 N VAL B 129 SHEET 7 AA3 9 TRP B 196 ILE B 199 1 O VAL B 198 N LEU B 161 SHEET 8 AA3 9 THR B 211 VAL B 215 -1 O VAL B 214 N VAL B 197 SHEET 9 AA3 9 VAL B 219 PHE B 223 -1 O GLU B 221 N ALA B 213 SHEET 1 AA4 2 GLY B 134 ASP B 135 0 SHEET 2 AA4 2 GLY B 139 MET B 140 -1 O GLY B 139 N ASP B 135 LINK O2 PO4 A 301 MG MG A 302 1555 1555 2.30 LINK MG MG A 302 O HOH A 476 1555 1555 2.63 CISPEP 1 THR A 216 ALA A 217 0 -0.91 CISPEP 2 THR A 230 GLU A 231 0 -5.34 CISPEP 3 THR B 216 ALA B 217 0 -0.36 SITE 1 AC1 7 LYS A 233 GLY A 234 THR A 235 GLY A 236 SITE 2 AC1 7 ASP A 237 MG A 302 HOH A 409 SITE 1 AC2 2 PO4 A 301 HOH A 476 SITE 1 AC3 3 GLU A 180 VAL A 220 PE4 B 303 SITE 1 AC4 5 ALA A 224 HOH A 403 HOH A 446 HOH A 462 SITE 2 AC4 5 PE4 B 303 SITE 1 AC5 1 GLU B 76 SITE 1 AC6 5 VAL B 132 TYR B 141 GLY B 234 THR B 235 SITE 2 AC6 5 GLY B 236 SITE 1 AC7 8 LYS A 66 ALA A 224 EDO A 303 PEG A 304 SITE 2 AC7 8 GLN B 47 LYS B 251 GLN B 262 HOH B 468 CRYST1 65.110 72.890 107.520 90.00 90.00 90.00 P 21 21 21 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 0.015359 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013719 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009301 0.00000