HEADER TRANSFERASE 03-FEB-06 2DDW TITLE CRYSTAL STRUCTURE OF PYRIDOXAL KINASE FROM THE ESCHERICHIA COLI PDXK TITLE 2 GENE COMPLEXED WITH PYRIDOXAL AT 3.2 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRIDOXINE KINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PYRIDOXAL KINASE, VITAMIN B6 KINASE, PYRIDOXAMINE KINASE, COMPND 5 PN/PL/PM KINASE; COMPND 6 EC: 2.7.1.35; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: HMS 174(DE3); SOURCE 5 GENE: PDXK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HMS 174(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22(+) KEYWDS PYRIDOXAL KINASE, RIBOKINASE, PYRIDOXAL 5'-PHOSPHATE, VITAMIN B6, KEYWDS 2 PHOSPHORYLATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.K.SAFO,F.N.MUSAYEV,M.L.DI SALVO,S.HUNT,J.B.CLAUDE,V.SCHIRCH REVDAT 3 11-OCT-17 2DDW 1 REMARK REVDAT 2 24-FEB-09 2DDW 1 VERSN REVDAT 1 15-AUG-06 2DDW 0 JRNL AUTH M.K.SAFO,F.N.MUSAYEV,M.L.DI SALVO,S.HUNT,J.B.CLAUDE, JRNL AUTH 2 V.SCHIRCH JRNL TITL CRYSTAL STRUCTURE OF PYRIDOXAL KINASE FROM THE ESCHERICHIA JRNL TITL 2 COLI PDXK GENE: IMPLICATIONS FOR THE CLASSIFICATION OF JRNL TITL 3 PYRIDOXAL KINASES. JRNL REF J.BACTERIOL. V. 188 4542 2006 JRNL REFN ISSN 0021-9193 JRNL PMID 16740960 JRNL DOI 10.1128/JB.00122-06 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.500 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 38298.440 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.4 REMARK 3 NUMBER OF REFLECTIONS : 8329 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 SET) : 0.237 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 401 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.013 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.40 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1194 REMARK 3 BIN R VALUE (WORKING SET) : 0.3140 REMARK 3 BIN FREE R VALUE : 0.3540 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 57 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.047 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4010 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 49 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -21.02000 REMARK 3 B22 (A**2) : 54.17000 REMARK 3 B33 (A**2) : -33.16000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.36 REMARK 3 ESD FROM SIGMAA (A) : 0.60 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.40 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.57 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.820 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.25 REMARK 3 BSOL : 37.65 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DDW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-FEB-06. REMARK 100 THE DEPOSITION ID IS D_1000025301. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-APR-04 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : CONFOCAL MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BIOTEX REMARK 200 DATA SCALING SOFTWARE : BIOTEX REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8990 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 52.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.10600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 2DDM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% PEG 4000, 100MM TRIS-HCL, 200MM NA REMARK 280 ACETATE, 40MM MGSO4, 10% GLYCEROL, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K 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 32.83400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.68000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.51400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.68000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.83400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.51400 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 300 REMARK: THE ASYMMETRIC UNIT CONTAINS THE FUNCTIONAL DIMER 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: 4120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 SER A 2 REMARK 465 SER A 3 REMARK 465 LEU A 4 REMARK 465 LEU A 5 REMARK 465 LEU A 6 REMARK 465 PHE A 7 REMARK 465 ASN A 8 REMARK 465 ASP A 9 REMARK 465 ALA A 197 REMARK 465 SER A 198 REMARK 465 GLY A 199 REMARK 465 ASN A 200 REMARK 465 GLU A 201 REMARK 465 GLU A 202 REMARK 465 ASN A 203 REMARK 465 GLN A 204 REMARK 465 ALA A 281 REMARK 465 GLU A 282 REMARK 465 ALA A 283 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 SER B 3 REMARK 465 LEU B 4 REMARK 465 LEU B 5 REMARK 465 LEU B 6 REMARK 465 PHE B 7 REMARK 465 ASP B 130 REMARK 465 ILE B 131 REMARK 465 ASP B 132 REMARK 465 SER B 133 REMARK 465 GLY B 134 REMARK 465 ILE B 135 REMARK 465 TYR B 136 REMARK 465 VAL B 137 REMARK 465 LYS B 138 REMARK 465 ASN B 200 REMARK 465 GLU B 201 REMARK 465 GLU B 202 REMARK 465 ALA B 281 REMARK 465 GLU B 282 REMARK 465 ALA B 283 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 GLN A 269 CG CD OE1 NE2 REMARK 470 LYS B 10 CG CD CE NZ REMARK 470 GLN B 269 CG CD OE1 NE2 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 PRO A 126 C - N - CA ANGL. DEV. = 11.7 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 LEU A 14 152.53 -43.29 REMARK 500 GLN A 22 -176.45 -178.13 REMARK 500 ILE A 34 -25.16 -155.14 REMARK 500 LYS A 40 -39.99 -36.75 REMARK 500 TYR A 60 -129.51 -65.71 REMARK 500 THR A 62 -79.56 -133.53 REMARK 500 PHE A 63 121.58 61.06 REMARK 500 GLU A 71 -26.99 -166.93 REMARK 500 TRP A 72 -61.15 -91.06 REMARK 500 ASP A 84 67.20 62.87 REMARK 500 PRO A 118 -19.86 -48.77 REMARK 500 PRO A 126 24.60 -48.19 REMARK 500 VAL A 127 96.93 -25.97 REMARK 500 ILE A 128 -53.36 -146.98 REMARK 500 ASP A 130 -164.56 173.97 REMARK 500 SER A 133 138.56 -178.24 REMARK 500 TYR A 136 30.64 -72.80 REMARK 500 LYS A 138 109.91 -50.10 REMARK 500 PRO A 151 14.96 -60.49 REMARK 500 LEU A 152 -37.37 -131.57 REMARK 500 THR A 157 66.61 -116.77 REMARK 500 LYS A 169 -153.16 -115.62 REMARK 500 ASN A 170 161.98 -35.97 REMARK 500 CYS A 171 -125.95 -118.02 REMARK 500 ALA A 179 -72.64 -56.17 REMARK 500 LEU A 185 170.37 -56.86 REMARK 500 SER A 186 -158.88 175.78 REMARK 500 MET A 206 -24.20 -152.30 REMARK 500 ASP A 214 93.49 -171.58 REMARK 500 SER A 215 159.40 139.58 REMARK 500 HIS A 221 -168.93 -120.35 REMARK 500 THR A 226 148.45 -176.12 REMARK 500 LEU A 249 -82.57 -49.37 REMARK 500 GLU A 262 -75.36 -58.48 REMARK 500 GLU A 271 73.45 55.41 REMARK 500 ASP A 273 34.07 -71.44 REMARK 500 PRO A 278 -165.98 -74.31 REMARK 500 PRO A 279 -158.07 -64.57 REMARK 500 ARG B 12 33.13 -79.10 REMARK 500 ALA B 20 143.77 -39.55 REMARK 500 GLN B 22 -152.42 -169.87 REMARK 500 GLN B 24 106.01 -163.51 REMARK 500 VAL B 46 142.76 -174.38 REMARK 500 HIS B 59 41.38 -76.23 REMARK 500 PHE B 73 -32.09 -39.36 REMARK 500 ALA B 79 -79.49 -43.15 REMARK 500 LEU B 80 -38.77 -26.13 REMARK 500 ARG B 90 -27.32 -148.06 REMARK 500 ALA B 91 -158.14 -129.35 REMARK 500 VAL B 92 121.02 171.59 REMARK 500 REMARK 500 THIS ENTRY HAS 70 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PXL A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PXL B 1005 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DDM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PYRIDOXAL KINASE FROM THE ESCHERICHIA COLI REMARK 900 PDXK GENE AT 2.1 A RESOLUTION REMARK 900 RELATED ID: 2DDO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PYRIDOXAL KINASE FROM THE ESCHERICHIA COLI REMARK 900 PDXK GENE COMPLEXED WITH ATP AT 2.6 A RESOLUTION DBREF 2DDW A 1 283 UNP P40191 PDXK_ECOLI 1 283 DBREF 2DDW B 1 283 UNP P40191 PDXK_ECOLI 1 283 SEQRES 1 A 283 MET SER SER LEU LEU LEU PHE ASN ASP LYS SER ARG ALA SEQRES 2 A 283 LEU GLN ALA ASP ILE VAL ALA VAL GLN SER GLN VAL VAL SEQRES 3 A 283 TYR GLY SER VAL GLY ASN SER ILE ALA VAL PRO ALA ILE SEQRES 4 A 283 LYS GLN ASN GLY LEU ASN VAL PHE ALA VAL PRO THR VAL SEQRES 5 A 283 LEU LEU SER ASN THR PRO HIS TYR ASP THR PHE TYR GLY SEQRES 6 A 283 GLY ALA ILE PRO ASP GLU TRP PHE SER GLY TYR LEU ARG SEQRES 7 A 283 ALA LEU GLN GLU ARG ASP ALA LEU ARG GLN LEU ARG ALA SEQRES 8 A 283 VAL THR THR GLY TYR MET GLY THR ALA SER GLN ILE LYS SEQRES 9 A 283 ILE LEU ALA GLU TRP LEU THR ALA LEU ARG LYS ASP HIS SEQRES 10 A 283 PRO ASP LEU LEU ILE MET VAL ASP PRO VAL ILE GLY ASP SEQRES 11 A 283 ILE ASP SER GLY ILE TYR VAL LYS PRO ASP LEU PRO GLU SEQRES 12 A 283 ALA TYR ARG GLN TYR LEU LEU PRO LEU ALA GLN GLY ILE SEQRES 13 A 283 THR PRO ASN ILE PHE GLU LEU GLU ILE LEU THR GLY LYS SEQRES 14 A 283 ASN CYS ARG ASP LEU ASP SER ALA ILE ALA ALA ALA LYS SEQRES 15 A 283 SER LEU LEU SER ASP THR LEU LYS TRP VAL VAL VAL THR SEQRES 16 A 283 SER ALA SER GLY ASN GLU GLU ASN GLN GLU MET GLN VAL SEQRES 17 A 283 VAL VAL VAL THR ALA ASP SER VAL ASN VAL ILE SER HIS SEQRES 18 A 283 SER ARG VAL LYS THR ASP LEU LYS GLY THR GLY ASP LEU SEQRES 19 A 283 PHE CYS ALA GLN LEU ILE SER GLY LEU LEU LYS GLY LYS SEQRES 20 A 283 ALA LEU THR ASP ALA VAL HIS ARG ALA GLY LEU ARG VAL SEQRES 21 A 283 LEU GLU VAL MET ARG TYR THR GLN GLN HIS GLU SER ASP SEQRES 22 A 283 GLU LEU ILE LEU PRO PRO LEU ALA GLU ALA SEQRES 1 B 283 MET SER SER LEU LEU LEU PHE ASN ASP LYS SER ARG ALA SEQRES 2 B 283 LEU GLN ALA ASP ILE VAL ALA VAL GLN SER GLN VAL VAL SEQRES 3 B 283 TYR GLY SER VAL GLY ASN SER ILE ALA VAL PRO ALA ILE SEQRES 4 B 283 LYS GLN ASN GLY LEU ASN VAL PHE ALA VAL PRO THR VAL SEQRES 5 B 283 LEU LEU SER ASN THR PRO HIS TYR ASP THR PHE TYR GLY SEQRES 6 B 283 GLY ALA ILE PRO ASP GLU TRP PHE SER GLY TYR LEU ARG SEQRES 7 B 283 ALA LEU GLN GLU ARG ASP ALA LEU ARG GLN LEU ARG ALA SEQRES 8 B 283 VAL THR THR GLY TYR MET GLY THR ALA SER GLN ILE LYS SEQRES 9 B 283 ILE LEU ALA GLU TRP LEU THR ALA LEU ARG LYS ASP HIS SEQRES 10 B 283 PRO ASP LEU LEU ILE MET VAL ASP PRO VAL ILE GLY ASP SEQRES 11 B 283 ILE ASP SER GLY ILE TYR VAL LYS PRO ASP LEU PRO GLU SEQRES 12 B 283 ALA TYR ARG GLN TYR LEU LEU PRO LEU ALA GLN GLY ILE SEQRES 13 B 283 THR PRO ASN ILE PHE GLU LEU GLU ILE LEU THR GLY LYS SEQRES 14 B 283 ASN CYS ARG ASP LEU ASP SER ALA ILE ALA ALA ALA LYS SEQRES 15 B 283 SER LEU LEU SER ASP THR LEU LYS TRP VAL VAL VAL THR SEQRES 16 B 283 SER ALA SER GLY ASN GLU GLU ASN GLN GLU MET GLN VAL SEQRES 17 B 283 VAL VAL VAL THR ALA ASP SER VAL ASN VAL ILE SER HIS SEQRES 18 B 283 SER ARG VAL LYS THR ASP LEU LYS GLY THR GLY ASP LEU SEQRES 19 B 283 PHE CYS ALA GLN LEU ILE SER GLY LEU LEU LYS GLY LYS SEQRES 20 B 283 ALA LEU THR ASP ALA VAL HIS ARG ALA GLY LEU ARG VAL SEQRES 21 B 283 LEU GLU VAL MET ARG TYR THR GLN GLN HIS GLU SER ASP SEQRES 22 B 283 GLU LEU ILE LEU PRO PRO LEU ALA GLU ALA HET PXL A1003 12 HET PXL B1005 12 HETNAM PXL 3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE HETSYN PXL PYRIDOXAL FORMUL 3 PXL 2(C8 H9 N O3) FORMUL 5 HOH *49(H2 O) HELIX 1 1 GLY A 31 ASN A 42 1 12 HELIX 2 2 TRP A 72 ARG A 83 1 12 HELIX 3 3 THR A 99 ARG A 114 1 16 HELIX 4 4 ASP A 140 TYR A 148 1 9 HELIX 5 5 PHE A 161 GLY A 168 1 8 HELIX 6 6 ASP A 173 SER A 183 1 11 HELIX 7 7 GLY A 230 LEU A 244 1 15 HELIX 8 8 ALA A 248 HIS A 270 1 23 HELIX 9 9 GLY B 31 ASN B 42 1 12 HELIX 10 10 PRO B 69 ASP B 84 1 16 HELIX 11 11 ALA B 100 ARG B 114 1 15 HELIX 12 12 ASP B 140 TYR B 148 1 9 HELIX 13 13 ASN B 159 GLY B 168 1 10 HELIX 14 14 ASP B 173 SER B 183 1 11 HELIX 15 15 GLY B 230 LYS B 245 1 16 HELIX 16 16 ALA B 248 HIS B 270 1 23 SHEET 1 A 3 GLN A 24 VAL A 25 0 SHEET 2 A 3 VAL A 52 LEU A 54 1 O LEU A 54 N GLN A 24 SHEET 3 A 3 GLY A 65 ALA A 67 -1 O GLY A 66 N LEU A 53 SHEET 1 B 2 ALA A 91 THR A 94 0 SHEET 2 B 2 LEU A 121 VAL A 124 1 O LEU A 121 N VAL A 92 SHEET 1 C 4 GLY A 155 ILE A 156 0 SHEET 2 C 4 TRP A 191 THR A 195 1 O VAL A 193 N ILE A 156 SHEET 3 C 4 VAL A 208 THR A 212 -1 O VAL A 211 N VAL A 192 SHEET 4 C 4 SER A 215 ILE A 219 -1 O ASN A 217 N VAL A 210 SHEET 1 D 2 VAL B 52 LEU B 54 0 SHEET 2 D 2 GLY B 65 ALA B 67 -1 O GLY B 66 N LEU B 53 SHEET 1 E 6 ALA B 91 THR B 93 0 SHEET 2 E 6 LEU B 121 VAL B 124 1 O MET B 123 N VAL B 92 SHEET 3 E 6 GLY B 155 ILE B 156 1 O GLY B 155 N VAL B 124 SHEET 4 E 6 TRP B 191 THR B 195 1 O VAL B 193 N ILE B 156 SHEET 5 E 6 VAL B 208 THR B 212 -1 O VAL B 209 N VAL B 194 SHEET 6 E 6 SER B 215 ASN B 217 -1 O ASN B 217 N VAL B 210 SHEET 1 F 2 GLN B 204 GLU B 205 0 SHEET 2 F 2 SER B 222 ARG B 223 -1 O ARG B 223 N GLN B 204 SITE 1 AC1 4 SER A 23 PRO A 58 HIS A 59 ASP A 233 SITE 1 AC2 4 SER B 23 PRO B 58 HIS B 59 ASP B 233 CRYST1 65.668 75.028 109.360 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 0.015228 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013328 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009144 0.00000