HEADER LYASE 17-MAY-03 1PCW TITLE AQUIFEX AEOLICUS KDO8PS IN COMPLEX WITH CADMIUM AND APP, A BISUBSTRATE TITLE 2 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PHOSPHO-2- DEHYDRO-3-DEOXYOCTONATE ALDOLASE, 3-DEOXY-D- COMPND 5 MANNO-OCTULOSONIC ACID 8-PHOSPHATE SYNTHETASE, KDO-8-PHOSPHATE COMPND 6 SYNTHETASE, KDO 8-P SYNTHASE; COMPND 7 EC: 4.1.2.16; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 63363; SOURCE 4 GENE: KDSA OR AQ_085; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PAAKDSA KEYWDS BETA(8)/ALPHA(8) BARREL, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR X.XU,J.WANG,C.GRISON,S.PETEK,P.COUTROT,M.BIRCK,R.W.WOODARD,D.L.GATTI REVDAT 4 16-AUG-23 1PCW 1 REMARK LINK REVDAT 3 13-JUL-11 1PCW 1 VERSN REVDAT 2 24-FEB-09 1PCW 1 VERSN REVDAT 1 17-FEB-04 1PCW 0 JRNL AUTH X.XU,J.WANG,C.GRISON,S.PETEK,P.COUTROT,M.R.BIRCK, JRNL AUTH 2 R.W.WOODARD,D.L.GATTI JRNL TITL STRUCTURE-BASED DESIGN OF NOVEL INHIBITORS OF JRNL TITL 2 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE. JRNL REF DRUG DES.DISCOVERY V. 18 91 2003 JRNL REFN ISSN 1055-9612 JRNL PMID 14675946 REMARK 2 REMARK 2 RESOLUTION. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.47 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) (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 54587 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) : 0.196 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 5551 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7531 REMARK 3 BIN R VALUE (WORKING SET) : 0.3280 REMARK 3 BIN FREE R VALUE : 0.3540 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 814 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.012 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4035 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.75000 REMARK 3 B22 (A**2) : 1.61000 REMARK 3 B33 (A**2) : -5.35000 REMARK 3 B12 (A**2) : 2.56000 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.19 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) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810 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) : 1.280 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.940 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.110 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.170 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 54.73 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : PEP_A5P_MOD5.PARAM REMARK 3 PARAMETER FILE 4 : APP_MOD1.PARAM REMARK 3 PARAMETER FILE 5 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : PEP_A5P.TOPH REMARK 3 TOPOLOGY FILE 4 : APP_MOD1.TOPH REMARK 3 TOPOLOGY FILE 5 : WATER.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PCW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAY-03. REMARK 100 THE DEPOSITION ID IS D_1000019238. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JAN-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.8 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC CONFOCAL MIRRORS REMARK 200 OPTICS : OSMIC CONFOCAL MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54587 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 21.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 11.34 REMARK 200 R MERGE (I) : 0.11700 REMARK 200 R SYM (I) : 0.11700 REMARK 200 FOR THE DATA SET : 15.0600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.59800 REMARK 200 R SYM FOR SHELL (I) : 0.59800 REMARK 200 FOR SHELL : 2.270 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: 1JCX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM ACETATE, PH 4.8, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 281K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.02333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 106.04667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 106.04667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 53.02333 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 SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED REMARK 300 BY THE SYMMETRY OPERATION: REMARK 300 X=Y, Y=X, Z=-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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 16470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -114.0 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 1001 REMARK 465 LEU A 1193 REMARK 465 GLY A 1194 REMARK 465 ASP A 1195 REMARK 465 LYS A 1196 REMARK 465 SER A 1197 REMARK 465 GLY A 1198 REMARK 465 PRO A 1265 REMARK 465 VAL A 1266 REMARK 465 LYS A 1267 REMARK 465 MET B 2001 REMARK 465 GLU B 2002 REMARK 465 GLY B 2191 REMARK 465 GLY B 2192 REMARK 465 LEU B 2193 REMARK 465 GLY B 2194 REMARK 465 ASP B 2195 REMARK 465 LYS B 2196 REMARK 465 SER B 2197 REMARK 465 GLY B 2198 REMARK 465 PRO B 2265 REMARK 465 VAL B 2266 REMARK 465 LYS B 2267 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 GLU A1072 CD GLU A1072 OE2 0.078 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 SER A1042 136.29 -172.20 REMARK 500 SER B2015 146.81 173.98 REMARK 500 SER B2042 139.56 -170.70 REMARK 500 VAL B2187 66.67 -100.63 REMARK 500 MET B2200 106.08 -162.68 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 CD A1270 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1011 SG REMARK 620 2 HIS A1185 NE2 170.8 REMARK 620 3 GLU A1222 OE2 84.3 99.1 REMARK 620 4 GLU A1222 OE1 91.6 97.4 59.6 REMARK 620 5 ASP A1233 OD1 95.0 87.5 142.3 82.8 REMARK 620 6 H4P A1268 OA1 86.8 84.0 118.2 177.4 99.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B2270 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B2011 SG REMARK 620 2 HIS B2185 NE2 164.6 REMARK 620 3 GLU B2222 OE1 96.9 95.5 REMARK 620 4 GLU B2222 OE2 92.2 102.1 58.4 REMARK 620 5 ASP B2233 OD2 100.7 72.7 79.1 136.9 REMARK 620 6 H4P B2268 OA1 84.4 83.3 178.7 121.3 100.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 1270 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B 2270 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE H4P A 1268 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE H4P B 2268 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JCX RELATED DB: PDB REMARK 900 AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH API AND CADMIUM DBREF 1PCW A 1001 1267 UNP O66496 KDSA_AQUAE 1 267 DBREF 1PCW B 2001 2267 UNP O66496 KDSA_AQUAE 1 267 SEQRES 1 A 267 MET GLU LYS PHE LEU VAL ILE ALA GLY PRO CYS ALA ILE SEQRES 2 A 267 GLU SER GLU GLU LEU LEU LEU LYS VAL GLY GLU GLU ILE SEQRES 3 A 267 LYS ARG LEU SER GLU LYS PHE LYS GLU VAL GLU PHE VAL SEQRES 4 A 267 PHE LYS SER SER PHE ASP LYS ALA ASN ARG SER SER ILE SEQRES 5 A 267 HIS SER PHE ARG GLY HIS GLY LEU GLU TYR GLY VAL LYS SEQRES 6 A 267 ALA LEU ARG LYS VAL LYS GLU GLU PHE GLY LEU LYS ILE SEQRES 7 A 267 THR THR ASP ILE HIS GLU SER TRP GLN ALA GLU PRO VAL SEQRES 8 A 267 ALA GLU VAL ALA ASP ILE ILE GLN ILE PRO ALA PHE LEU SEQRES 9 A 267 CYS ARG GLN THR ASP LEU LEU LEU ALA ALA ALA LYS THR SEQRES 10 A 267 GLY ARG ALA VAL ASN VAL LYS LYS GLY GLN PHE LEU ALA SEQRES 11 A 267 PRO TRP ASP THR LYS ASN VAL VAL GLU LYS LEU LYS PHE SEQRES 12 A 267 GLY GLY ALA LYS GLU ILE TYR LEU THR GLU ARG GLY THR SEQRES 13 A 267 THR PHE GLY TYR ASN ASN LEU VAL VAL ASP PHE ARG SER SEQRES 14 A 267 LEU PRO ILE MET LYS GLN TRP ALA LYS VAL ILE TYR ASP SEQRES 15 A 267 ALA THR HIS SER VAL GLN LEU PRO GLY GLY LEU GLY ASP SEQRES 16 A 267 LYS SER GLY GLY MET ARG GLU PHE ILE PHE PRO LEU ILE SEQRES 17 A 267 ARG ALA ALA VAL ALA VAL GLY CYS ASP GLY VAL PHE MET SEQRES 18 A 267 GLU THR HIS PRO GLU PRO GLU LYS ALA LEU SER ASP ALA SEQRES 19 A 267 SER THR GLN LEU PRO LEU SER GLN LEU GLU GLY ILE ILE SEQRES 20 A 267 GLU ALA ILE LEU GLU ILE ARG GLU VAL ALA SER LYS TYR SEQRES 21 A 267 TYR GLU THR ILE PRO VAL LYS SEQRES 1 B 267 MET GLU LYS PHE LEU VAL ILE ALA GLY PRO CYS ALA ILE SEQRES 2 B 267 GLU SER GLU GLU LEU LEU LEU LYS VAL GLY GLU GLU ILE SEQRES 3 B 267 LYS ARG LEU SER GLU LYS PHE LYS GLU VAL GLU PHE VAL SEQRES 4 B 267 PHE LYS SER SER PHE ASP LYS ALA ASN ARG SER SER ILE SEQRES 5 B 267 HIS SER PHE ARG GLY HIS GLY LEU GLU TYR GLY VAL LYS SEQRES 6 B 267 ALA LEU ARG LYS VAL LYS GLU GLU PHE GLY LEU LYS ILE SEQRES 7 B 267 THR THR ASP ILE HIS GLU SER TRP GLN ALA GLU PRO VAL SEQRES 8 B 267 ALA GLU VAL ALA ASP ILE ILE GLN ILE PRO ALA PHE LEU SEQRES 9 B 267 CYS ARG GLN THR ASP LEU LEU LEU ALA ALA ALA LYS THR SEQRES 10 B 267 GLY ARG ALA VAL ASN VAL LYS LYS GLY GLN PHE LEU ALA SEQRES 11 B 267 PRO TRP ASP THR LYS ASN VAL VAL GLU LYS LEU LYS PHE SEQRES 12 B 267 GLY GLY ALA LYS GLU ILE TYR LEU THR GLU ARG GLY THR SEQRES 13 B 267 THR PHE GLY TYR ASN ASN LEU VAL VAL ASP PHE ARG SER SEQRES 14 B 267 LEU PRO ILE MET LYS GLN TRP ALA LYS VAL ILE TYR ASP SEQRES 15 B 267 ALA THR HIS SER VAL GLN LEU PRO GLY GLY LEU GLY ASP SEQRES 16 B 267 LYS SER GLY GLY MET ARG GLU PHE ILE PHE PRO LEU ILE SEQRES 17 B 267 ARG ALA ALA VAL ALA VAL GLY CYS ASP GLY VAL PHE MET SEQRES 18 B 267 GLU THR HIS PRO GLU PRO GLU LYS ALA LEU SER ASP ALA SEQRES 19 B 267 SER THR GLN LEU PRO LEU SER GLN LEU GLU GLY ILE ILE SEQRES 20 B 267 GLU ALA ILE LEU GLU ILE ARG GLU VAL ALA SER LYS TYR SEQRES 21 B 267 TYR GLU THR ILE PRO VAL LYS HET CD A1270 1 HET H4P A1268 21 HET CD B2270 1 HET H4P B2268 42 HETNAM CD CADMIUM ION HETNAM H4P 1-DEOXY-6-O-PHOSPHONO-1-[(PHOSPHONOMETHYL)AMINO]-L- HETNAM 2 H4P THREO-HEXITOL FORMUL 3 CD 2(CD 2+) FORMUL 4 H4P 2(C7 H19 N O11 P2) FORMUL 7 HOH *340(H2 O) HELIX 1 1 SER A 1015 PHE A 1033 1 19 HELIX 2 2 GLY A 1059 GLY A 1075 1 17 HELIX 3 3 GLU A 1084 TRP A 1086 5 3 HELIX 4 4 GLN A 1087 GLU A 1093 1 7 HELIX 5 5 PRO A 1101 CYS A 1105 5 5 HELIX 6 6 GLN A 1107 LYS A 1116 1 10 HELIX 7 7 ALA A 1130 ASP A 1133 5 4 HELIX 8 8 THR A 1134 GLY A 1144 1 11 HELIX 9 9 ARG A 1168 LYS A 1174 1 7 HELIX 10 10 THR A 1184 GLN A 1188 5 5 HELIX 11 11 MET A 1200 GLU A 1202 5 3 HELIX 12 12 PHE A 1203 GLY A 1215 1 13 HELIX 13 13 GLU A 1226 ALA A 1230 5 5 HELIX 14 14 GLN A 1242 LYS A 1259 1 18 HELIX 15 15 SER B 2015 PHE B 2033 1 19 HELIX 16 16 GLY B 2059 GLY B 2075 1 17 HELIX 17 17 GLU B 2084 TRP B 2086 5 3 HELIX 18 18 GLN B 2087 ALA B 2092 1 6 HELIX 19 19 PRO B 2101 CYS B 2105 5 5 HELIX 20 20 GLN B 2107 THR B 2117 1 11 HELIX 21 21 ALA B 2130 ASP B 2133 5 4 HELIX 22 22 THR B 2134 GLY B 2144 1 11 HELIX 23 23 ARG B 2168 LYS B 2174 1 7 HELIX 24 24 MET B 2200 GLU B 2202 5 3 HELIX 25 25 PHE B 2203 GLY B 2215 1 13 HELIX 26 26 GLU B 2226 ALA B 2230 5 5 HELIX 27 27 GLN B 2242 SER B 2258 1 17 HELIX 28 28 LYS B 2259 TYR B 2261 5 3 SHEET 1 A10 LEU A1238 PRO A1239 0 SHEET 2 A10 GLY A1218 HIS A1224 1 N HIS A1224 O LEU A1238 SHEET 3 A10 LYS A1178 ASP A1182 1 N TYR A1181 O PHE A1220 SHEET 4 A10 ILE A1149 GLU A1153 1 N GLU A1153 O ILE A1180 SHEET 5 A10 ALA A1120 LYS A1124 1 N VAL A1123 O THR A1152 SHEET 6 A10 ILE A1097 ILE A1100 1 N ILE A1098 O ALA A1120 SHEET 7 A10 LYS A1077 ASP A1081 1 N THR A1080 O GLN A1099 SHEET 8 A10 VAL A1036 LYS A1041 1 N PHE A1040 O LYS A1077 SHEET 9 A10 PHE A1004 GLY A1009 1 N PHE A1004 O GLU A1037 SHEET 10 A10 GLY A1218 HIS A1224 1 O VAL A1219 N ILE A1007 SHEET 1 B 2 THR A1156 THR A1157 0 SHEET 2 B 2 LEU A1163 VAL A1164 -1 O VAL A1164 N THR A1156 SHEET 1 C10 LEU B2238 PRO B2239 0 SHEET 2 C10 GLY B2218 HIS B2224 1 N HIS B2224 O LEU B2238 SHEET 3 C10 LYS B2178 ASP B2182 1 N TYR B2181 O PHE B2220 SHEET 4 C10 ILE B2149 GLU B2153 1 N GLU B2153 O ASP B2182 SHEET 5 C10 ALA B2120 LYS B2124 1 N VAL B2123 O TYR B2150 SHEET 6 C10 ILE B2097 ILE B2100 1 N ILE B2098 O ALA B2120 SHEET 7 C10 LYS B2077 ASP B2081 1 N THR B2080 O GLN B2099 SHEET 8 C10 VAL B2036 LYS B2041 1 N PHE B2040 O LYS B2077 SHEET 9 C10 PHE B2004 GLY B2009 1 N PHE B2004 O GLU B2037 SHEET 10 C10 GLY B2218 HIS B2224 1 O MET B2221 N ILE B2007 SHEET 1 D 2 THR B2156 THR B2157 0 SHEET 2 D 2 LEU B2163 VAL B2164 -1 O VAL B2164 N THR B2156 LINK SG CYS A1011 CD CD A1270 1555 1555 2.50 LINK NE2 HIS A1185 CD CD A1270 1555 1555 2.31 LINK OE2 GLU A1222 CD CD A1270 1555 1555 2.34 LINK OE1 GLU A1222 CD CD A1270 1555 1555 2.07 LINK OD1 ASP A1233 CD CD A1270 1555 1555 2.05 LINK OA1 H4P A1268 CD CD A1270 1555 1555 2.43 LINK SG CYS B2011 CD CD B2270 1555 1555 2.47 LINK NE2 HIS B2185 CD CD B2270 1555 1555 2.34 LINK OE1 GLU B2222 CD CD B2270 1555 1555 2.13 LINK OE2 GLU B2222 CD CD B2270 1555 1555 2.37 LINK OD2 ASP B2233 CD CD B2270 1555 1555 2.17 LINK OA1AH4P B2268 CD CD B2270 1555 1555 2.37 SITE 1 AC1 5 CYS A1011 HIS A1185 GLU A1222 ASP A1233 SITE 2 AC1 5 H4P A1268 SITE 1 AC2 5 CYS B2011 HIS B2185 GLU B2222 ASP B2233 SITE 2 AC2 5 H4P B2268 SITE 1 AC3 22 HOH A 13 HOH A 31 HOH A 43 HOH A 90 SITE 2 AC3 22 HOH A 201 HOH A 206 HOH A 216 HOH A 236 SITE 3 AC3 22 HOH A 359 CYS A1011 LYS A1046 ASN A1048 SITE 4 AC3 22 ARG A1049 SER A1050 PRO A1101 ALA A1102 SITE 5 AC3 22 LYS A1124 ARG A1154 HIS A1185 GLN A1188 SITE 6 AC3 22 ASP A1233 CD A1270 SITE 1 AC4 23 ARG A1106 HOH B 15 HOH B 56 HOH B 72 SITE 2 AC4 23 HOH B 93 HOH B 140 HOH B 224 HOH B 354 SITE 3 AC4 23 HOH B 373 HOH B 375 CYS B2011 LYS B2046 SITE 4 AC4 23 ASN B2048 ARG B2049 SER B2050 PRO B2101 SITE 5 AC4 23 ALA B2102 LYS B2124 ARG B2154 HIS B2185 SITE 6 AC4 23 SER B2232 ASP B2233 CD B2270 CRYST1 84.480 84.480 159.070 90.00 90.00 120.00 P 31 2 1 12 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 0.011837 0.006834 0.000000 0.00000 SCALE2 0.000000 0.013668 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006287 0.00000