PDB Short entry for 1PVY HEADER ISOMERASE 29-JUN-03 1PVY TITLE 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE FROM M. JANNASCHII IN TITLE 2 COMPLEX WITH RIBULOSE 5-PHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DHBP SYNTHASE; COMPND 5 EC: 5.4.99.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 2190; SOURCE 4 GENE: MJ0055; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: XL1; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNCO-MJ KEYWDS RIBOFLAVIN BIOSYNTHESIS, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.STEINBACHER,S.SCHIFFMANN,G.RICHTER,R.HUBER,A.BACHER,M.FISCHER REVDAT 3 10-NOV-21 1PVY 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1PVY 1 VERSN REVDAT 1 04-NOV-03 1PVY 0 JRNL AUTH S.STEINBACHER,S.SCHIFFMANN,G.RICHTER,R.HUBER,A.BACHER, JRNL AUTH 2 M.FISCHER JRNL TITL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE JRNL TITL 2 FROM METHANOCOCCUS JANNASCHII IN COMPLEX WITH DIVALENT METAL JRNL TITL 3 IONS AND THE SUBSTRATE RIBULOSE 5-PHOSPHATE: IMPLICATIONS JRNL TITL 4 FOR THE CATALYTIC MECHANISM JRNL REF J.BIOL.CHEM. V. 278 42256 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12904291 JRNL DOI 10.1074/JBC.M307301200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.FISCHER,W.ROMISCH,S.SCHIFFMANN,M.KELLY,H.OSCHKINAT, REMARK 1 AUTH 2 S.STEINBACHER,R.HUBER,W.EISENREICH,G.RICHTER,A.BACHER REMARK 1 TITL BIOSYNTHESIS OF RIBOFLAVIN IN ARCHAEA STUDIES ON THE REMARK 1 TITL 2 MECHANISM OF 3,4-DIHYDROXY-2-BUTANONE-4-PHOSPHATE SYNTHASE REMARK 1 TITL 3 OF METHANOCOCCUS JANNASCHII REMARK 1 REF J.BIOL.CHEM. V. 277 41410 2002 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.M206863200 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 42562 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) : 0.213 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2141 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3470 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 352 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.480 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 1PVY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1000019617. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-01 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) : 1.542 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42575 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.47600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1PVW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG1000, PH 7.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 34.63600 REMARK 290 SMTRY3 2 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 MOLECULE IS A DIMER WHICH IS PRESENT IN THE ASYMMETRIC REMARK 300 UNIT 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: 6730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -170.0 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 LEU A 221 REMARK 465 ASP A 222 REMARK 465 LYS A 223 REMARK 465 TYR A 224 REMARK 465 LEU A 225 REMARK 465 LYS A 226 REMARK 465 ASP A 227 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 ASP B 222 REMARK 465 LYS B 223 REMARK 465 TYR B 224 REMARK 465 LEU B 225 REMARK 465 LYS B 226 REMARK 465 ASP B 227 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASN A 2 CG OD1 ND2 REMARK 480 LYS A 13 NZ REMARK 480 LYS A 65 CD CE NZ REMARK 480 LYS A 83 CD CE NZ REMARK 480 ARG A 86 CD NE CZ NH1 NH2 REMARK 480 ASN A 136 CB CG OD1 ND2 REMARK 480 GLU A 215 CB CG CD OE1 OE2 REMARK 480 LYS B 196 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 N ASN B 3 O HOH B 604 2.15 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 ASP A 21 -72.13 -71.51 REMARK 500 SER A 22 148.43 -173.20 REMARK 500 ARG A 25 -129.05 -131.48 REMARK 500 ALA A 50 -75.02 -106.64 REMARK 500 SER A 102 -152.55 -127.08 REMARK 500 PHE A 111 -83.05 -96.61 REMARK 500 ARG A 134 48.41 -88.37 REMARK 500 LEU A 157 -137.66 45.43 REMARK 500 VAL A 158 -4.32 -56.95 REMARK 500 GLN A 162 51.78 -110.29 REMARK 500 PRO A 179 69.79 -69.79 REMARK 500 ASP B 21 -70.26 -73.93 REMARK 500 ARG B 25 -113.48 -101.00 REMARK 500 ALA B 50 -66.95 -106.55 REMARK 500 PRO B 90 47.80 -81.53 REMARK 500 SER B 102 -150.00 -120.73 REMARK 500 PHE B 111 -84.36 -95.03 REMARK 500 ARG B 134 56.78 -91.37 REMARK 500 LEU B 157 -131.32 44.42 REMARK 500 VAL B 158 -4.41 -54.94 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 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 26 OE1 REMARK 620 2 HIS A 164 ND1 101.3 REMARK 620 3 5RP A 501 O10 103.0 93.9 REMARK 620 4 5RP A 501 O13 90.4 162.6 95.9 REMARK 620 5 5RP A 501 O14 157.6 89.6 95.7 75.2 REMARK 620 6 HOH A 852 O 71.2 88.4 174.1 83.3 89.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 503 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 26 OE2 REMARK 620 2 TYR A 95 OH 97.0 REMARK 620 3 5RP A 501 O11 86.6 100.5 REMARK 620 4 5RP A 501 O8 106.4 147.0 59.0 REMARK 620 5 5RP A 501 O13 67.8 148.0 106.3 64.5 REMARK 620 6 5RP A 501 O4 127.8 114.4 123.9 68.4 63.5 REMARK 620 7 HOH A 851 O 72.9 69.9 155.6 139.0 78.5 80.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 701 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 96 OD2 REMARK 620 2 GLU A 97 OE1 71.0 REMARK 620 3 HOH A 753 O 146.5 135.3 REMARK 620 4 HOH A 769 O 96.3 80.9 73.3 REMARK 620 5 HOH A 774 O 72.2 81.3 124.4 161.2 REMARK 620 6 HOH A 806 O 74.8 145.0 74.8 96.0 95.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 702 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 204 O REMARK 620 2 ASN A 207 OD1 86.2 REMARK 620 3 HOH A 787 O 142.1 81.1 REMARK 620 4 HOH B 613 O 146.2 108.3 71.5 REMARK 620 5 HOH B 655 O 89.3 169.3 96.7 80.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 26 OE1 REMARK 620 2 HIS B 164 ND1 106.3 REMARK 620 3 5RP B 601 O14 160.8 89.8 REMARK 620 4 5RP B 601 O10 98.5 102.7 87.8 REMARK 620 5 5RP B 601 O13 91.4 159.2 71.0 84.8 REMARK 620 6 HOH B 805 O 90.9 84.6 80.2 165.9 84.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 603 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 26 OE2 REMARK 620 2 5RP B 601 O8 103.0 REMARK 620 3 5RP B 601 O4 113.6 63.2 REMARK 620 4 5RP B 601 O13 62.2 55.7 57.5 REMARK 620 5 5RP B 601 O11 92.8 56.0 117.7 95.7 REMARK 620 6 HOH B 764 O 173.8 73.2 69.4 117.7 81.1 REMARK 620 7 HOH B 804 O 79.1 116.2 58.6 72.2 167.5 106.9 REMARK 620 8 HOH B 806 O 95.0 136.5 141.7 157.2 84.1 84.9 105.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5RP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5RP B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 703 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PVW RELATED DB: PDB REMARK 900 1PVW CONTAINS 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE. DBREF 1PVY A 1 227 UNP Q60364 RIBB_METJA 1 227 DBREF 1PVY B 1 227 UNP Q60364 RIBB_METJA 1 227 SEQADV 1PVY SER A 147 UNP Q60364 HIS 147 ENGINEERED MUTATION SEQADV 1PVY SER B 147 UNP Q60364 HIS 147 ENGINEERED MUTATION SEQRES 1 A 227 MET ASN ASN VAL GLU LYS ALA ILE GLU ALA LEU LYS LYS SEQRES 2 A 227 GLY GLU ILE ILE LEU VAL TYR ASP SER ASP GLU ARG GLU SEQRES 3 A 227 GLY GLU THR ASP MET VAL VAL ALA SER GLN PHE ILE THR SEQRES 4 A 227 PRO GLU HIS ILE ARG ILE MET ARG LYS ASP ALA GLY GLY SEQRES 5 A 227 LEU ILE CYS THR ALA LEU HIS PRO ASP ILE CYS ASN LYS SEQRES 6 A 227 LEU GLY ILE PRO PHE MET VAL ASP ILE LEU GLU PHE ALA SEQRES 7 A 227 SER GLN LYS PHE LYS VAL LEU ARG GLU LEU TYR PRO ASN SEQRES 8 A 227 ASP ILE PRO TYR ASP GLU LYS SER SER PHE SER ILE THR SEQRES 9 A 227 ILE ASN HIS ARG LYS THR PHE THR GLY ILE THR ASP ASN SEQRES 10 A 227 ASP ARG ALA PHE THR ILE LYS LYS LEU ALA GLU LEU VAL SEQRES 11 A 227 LYS GLU GLY ARG PHE ASN ASP PHE GLY LYS GLU PHE ARG SEQRES 12 A 227 SER PRO GLY SER VAL THR LEU LEU ARG ALA ALA GLU GLY SEQRES 13 A 227 LEU VAL LYS ASN ARG GLN GLY HIS THR GLU MET THR VAL SEQRES 14 A 227 ALA LEU ALA GLU LEU ALA ASN LEU VAL PRO ILE THR THR SEQRES 15 A 227 ILE CYS GLU MET MET GLY ASP ASP GLY ASN ALA MET SER SEQRES 16 A 227 LYS ASN GLU THR LYS ARG TYR ALA GLU LYS HIS ASN LEU SEQRES 17 A 227 ILE TYR LEU SER GLY GLU GLU ILE ILE ASN TYR TYR LEU SEQRES 18 A 227 ASP LYS TYR LEU LYS ASP SEQRES 1 B 227 MET ASN ASN VAL GLU LYS ALA ILE GLU ALA LEU LYS LYS SEQRES 2 B 227 GLY GLU ILE ILE LEU VAL TYR ASP SER ASP GLU ARG GLU SEQRES 3 B 227 GLY GLU THR ASP MET VAL VAL ALA SER GLN PHE ILE THR SEQRES 4 B 227 PRO GLU HIS ILE ARG ILE MET ARG LYS ASP ALA GLY GLY SEQRES 5 B 227 LEU ILE CYS THR ALA LEU HIS PRO ASP ILE CYS ASN LYS SEQRES 6 B 227 LEU GLY ILE PRO PHE MET VAL ASP ILE LEU GLU PHE ALA SEQRES 7 B 227 SER GLN LYS PHE LYS VAL LEU ARG GLU LEU TYR PRO ASN SEQRES 8 B 227 ASP ILE PRO TYR ASP GLU LYS SER SER PHE SER ILE THR SEQRES 9 B 227 ILE ASN HIS ARG LYS THR PHE THR GLY ILE THR ASP ASN SEQRES 10 B 227 ASP ARG ALA PHE THR ILE LYS LYS LEU ALA GLU LEU VAL SEQRES 11 B 227 LYS GLU GLY ARG PHE ASN ASP PHE GLY LYS GLU PHE ARG SEQRES 12 B 227 SER PRO GLY SER VAL THR LEU LEU ARG ALA ALA GLU GLY SEQRES 13 B 227 LEU VAL LYS ASN ARG GLN GLY HIS THR GLU MET THR VAL SEQRES 14 B 227 ALA LEU ALA GLU LEU ALA ASN LEU VAL PRO ILE THR THR SEQRES 15 B 227 ILE CYS GLU MET MET GLY ASP ASP GLY ASN ALA MET SER SEQRES 16 B 227 LYS ASN GLU THR LYS ARG TYR ALA GLU LYS HIS ASN LEU SEQRES 17 B 227 ILE TYR LEU SER GLY GLU GLU ILE ILE ASN TYR TYR LEU SEQRES 18 B 227 ASP LYS TYR LEU LYS ASP HET 5RP A 501 14 HET ZN A 502 1 HET CA A 503 1 HET CA A 701 1 HET CA A 702 1 HET ZN A 703 1 HET 5RP B 601 14 HET ZN B 602 1 HET CA B 603 1 HETNAM 5RP RIBULOSE-5-PHOSPHATE HETNAM ZN ZINC ION HETNAM CA CALCIUM ION FORMUL 3 5RP 2(C5 H11 O8 P) FORMUL 4 ZN 3(ZN 2+) FORMUL 5 CA 4(CA 2+) FORMUL 12 HOH *352(H2 O) HELIX 1 1 ASN A 2 LYS A 13 1 12 HELIX 2 2 GLN A 36 ILE A 38 5 3 HELIX 3 3 THR A 39 ALA A 50 1 12 HELIX 4 4 HIS A 59 GLY A 67 1 9 HELIX 5 5 PHE A 70 SER A 79 1 10 HELIX 6 6 PHE A 82 GLU A 87 1 6 HELIX 7 7 THR A 115 GLU A 132 1 18 HELIX 8 8 ARG A 134 ASN A 136 5 3 HELIX 9 9 ASP A 137 GLU A 141 1 5 HELIX 10 10 GLY A 156 ASN A 160 5 5 HELIX 11 11 GLY A 163 ALA A 175 1 13 HELIX 12 12 SER A 195 HIS A 206 1 12 HELIX 13 13 GLY A 213 TYR A 220 1 8 HELIX 14 14 ASN B 3 LYS B 13 1 11 HELIX 15 15 GLN B 36 ILE B 38 5 3 HELIX 16 16 THR B 39 ALA B 50 1 12 HELIX 17 17 HIS B 59 GLY B 67 1 9 HELIX 18 18 PHE B 70 SER B 79 1 10 HELIX 19 19 GLN B 80 LYS B 81 5 2 HELIX 20 20 PHE B 82 PHE B 82 5 1 HELIX 21 21 LYS B 83 LEU B 88 1 6 HELIX 22 22 PRO B 94 LYS B 98 5 5 HELIX 23 23 THR B 115 GLY B 133 1 19 HELIX 24 24 ARG B 134 ASN B 136 5 3 HELIX 25 25 ASP B 137 GLU B 141 1 5 HELIX 26 26 GLY B 156 ASN B 160 5 5 HELIX 27 27 GLY B 163 ALA B 175 1 13 HELIX 28 28 SER B 195 HIS B 206 1 12 HELIX 29 29 GLY B 213 LEU B 221 1 9 SHEET 1 A 7 PHE A 101 HIS A 107 0 SHEET 2 A 7 PHE A 142 ARG A 152 -1 O VAL A 148 N ILE A 105 SHEET 3 A 7 GLY A 51 LEU A 58 1 N THR A 56 O LEU A 151 SHEET 4 A 7 ILE A 180 MET A 186 -1 O ILE A 183 N CYS A 55 SHEET 5 A 7 THR A 29 ALA A 34 -1 N MET A 31 O CYS A 184 SHEET 6 A 7 ILE A 17 TYR A 20 -1 N ILE A 17 O VAL A 32 SHEET 7 A 7 TYR A 210 SER A 212 1 O LEU A 211 N LEU A 18 SHEET 1 B 7 PHE B 101 HIS B 107 0 SHEET 2 B 7 PHE B 142 ARG B 152 -1 O ARG B 143 N ASN B 106 SHEET 3 B 7 GLY B 51 LEU B 58 1 N THR B 56 O THR B 149 SHEET 4 B 7 ILE B 180 MET B 186 -1 O ILE B 183 N CYS B 55 SHEET 5 B 7 THR B 29 ALA B 34 -1 N MET B 31 O CYS B 184 SHEET 6 B 7 ILE B 17 TYR B 20 -1 N ILE B 17 O VAL B 32 SHEET 7 B 7 TYR B 210 SER B 212 1 O LEU B 211 N LEU B 18 LINK OE1 GLU A 26 ZN ZN A 502 1555 1555 1.79 LINK OE2 GLU A 26 CA CA A 503 1555 1555 2.35 LINK OH TYR A 95 CA CA A 503 1555 1555 2.43 LINK OD2 ASP A 96 CA CA A 701 1555 1555 2.57 LINK OE1 GLU A 97 CA CA A 701 1555 1555 2.33 LINK ND1 HIS A 164 ZN ZN A 502 1555 1555 2.11 LINK O GLU A 204 CA CA A 702 1555 1555 2.44 LINK ND1 HIS A 206 ZN ZN A 703 1555 1555 2.10 LINK OD1 ASN A 207 CA CA A 702 1555 1555 2.22 LINK O10 5RP A 501 ZN ZN A 502 1555 1555 2.20 LINK O13 5RP A 501 ZN ZN A 502 1555 1555 2.49 LINK O14 5RP A 501 ZN ZN A 502 1555 1555 2.16 LINK O11 5RP A 501 CA CA A 503 1555 1555 2.50 LINK O8 5RP A 501 CA CA A 503 1555 1555 2.69 LINK O13 5RP A 501 CA CA A 503 1555 1555 2.41 LINK O4 5RP A 501 CA CA A 503 1555 1555 2.67 LINK ZN ZN A 502 O HOH A 852 1555 1555 2.09 LINK CA CA A 503 O HOH A 851 1555 1555 2.07 LINK CA CA A 701 O HOH A 753 1555 1555 2.39 LINK CA CA A 701 O HOH A 769 1555 1555 2.21 LINK CA CA A 701 O HOH A 774 1555 1555 2.31 LINK CA CA A 701 O HOH A 806 1555 1555 2.36 LINK CA CA A 702 O HOH A 787 1555 1555 2.30 LINK CA CA A 702 O HOH B 613 1555 1455 2.38 LINK CA CA A 702 O HOH B 655 1555 1455 2.49 LINK OE1 GLU B 26 ZN ZN B 602 1555 1555 1.85 LINK OE2 GLU B 26 CA CA B 603 1555 1555 2.32 LINK ND1 HIS B 164 ZN ZN B 602 1555 1555 2.19 LINK O14 5RP B 601 ZN ZN B 602 1555 1555 2.44 LINK O10 5RP B 601 ZN ZN B 602 1555 1555 2.10 LINK O13 5RP B 601 ZN ZN B 602 1555 1555 2.49 LINK O8 5RP B 601 CA CA B 603 1555 1555 3.04 LINK O4 5RP B 601 CA CA B 603 1555 1555 3.00 LINK O13 5RP B 601 CA CA B 603 1555 1555 2.78 LINK O11 5RP B 601 CA CA B 603 1555 1555 2.26 LINK ZN ZN B 602 O HOH B 805 1555 1555 2.12 LINK CA CA B 603 O HOH B 764 1555 1555 2.73 LINK CA CA B 603 O HOH B 804 1555 1555 2.27 LINK CA CA B 603 O HOH B 806 1555 1555 2.19 CISPEP 1 SER A 144 PRO A 145 0 -1.50 CISPEP 2 SER B 144 PRO B 145 0 2.06 SITE 1 AC1 19 ARG A 25 GLU A 26 ASP A 30 CYS A 55 SITE 2 AC1 19 TYR A 95 LEU A 151 ARG A 161 GLY A 163 SITE 3 AC1 19 HIS A 164 THR A 165 ILE A 183 GLU A 185 SITE 4 AC1 19 ZN A 502 CA A 503 HOH A 723 HOH A 766 SITE 5 AC1 19 HOH A 847 HOH A 851 HOH A 852 SITE 1 AC2 18 ARG B 25 GLU B 26 ASP B 30 CYS B 55 SITE 2 AC2 18 PHE B 101 ARG B 161 GLY B 163 HIS B 164 SITE 3 AC2 18 THR B 165 GLU B 185 ZN B 602 CA B 603 SITE 4 AC2 18 HOH B 772 HOH B 778 HOH B 785 HOH B 804 SITE 5 AC2 18 HOH B 805 HOH B 806 SITE 1 AC3 4 GLU A 26 HIS A 164 5RP A 501 HOH A 852 SITE 1 AC4 4 GLU A 26 TYR A 95 5RP A 501 HOH A 851 SITE 1 AC5 4 GLU B 26 HIS B 164 5RP B 601 HOH B 805 SITE 1 AC6 5 GLU B 26 5RP B 601 HOH B 764 HOH B 804 SITE 2 AC6 5 HOH B 806 SITE 1 AC7 6 ASP A 96 GLU A 97 HOH A 753 HOH A 769 SITE 2 AC7 6 HOH A 774 HOH A 806 SITE 1 AC8 5 GLU A 204 ASN A 207 HOH A 787 HOH B 613 SITE 2 AC8 5 HOH B 655 SITE 1 AC9 1 HIS A 206 CRYST1 53.197 69.272 57.110 90.00 93.52 90.00 P 1 21 1 4 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 0.018798 0.000000 0.001156 0.00000 SCALE2 0.000000 0.014436 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017543 0.00000