HEADER LYASE 11-JUN-01 1JCY TITLE AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH R5P, PEP AND CADMIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: KDO8P SYNTHASE, PHOSPHO-2-DEHYDRO-3-DEOXYOCTONATE ALDOLASE, COMPND 5 3-DEOXY-D-MANNO-OCTULOSONIC ACID 8-PHOSPHATE SYNTHETASE, KDO-8- COMPND 6 PHOSPHATE SYNTHETASE; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PAAKDSA KEYWDS KDO8PS, KDO8P, KDO, R5P, PEP, BETA/ALPHA BARREL, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR J.WANG,H.S.DUEWEL,R.W.WOODARD,D.L.GATTI REVDAT 5 07-FEB-24 1JCY 1 REMARK LINK REVDAT 4 04-OCT-17 1JCY 1 REMARK REVDAT 3 13-JUL-11 1JCY 1 VERSN REVDAT 2 24-FEB-09 1JCY 1 VERSN REVDAT 1 16-JAN-02 1JCY 0 JRNL AUTH J.WANG,H.S.DUEWEL,R.W.WOODARD,D.L.GATTI JRNL TITL STRUCTURES OF AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX JRNL TITL 2 WITH R5P AND PEP, AND WITH A BISUBSTRATE INHIBITOR: ROLE OF JRNL TITL 3 ACTIVE SITE WATER IN CATALYSIS. JRNL REF BIOCHEMISTRY V. 40 15676 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11747443 JRNL DOI 10.1021/BI015568E REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 728459.560 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.8 REMARK 3 NUMBER OF REFLECTIONS : 419681 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) : 0.202 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4658 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 67.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5205 REMARK 3 BIN R VALUE (WORKING SET) : 0.3760 REMARK 3 BIN FREE R VALUE : 0.4000 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 590 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4078 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 201 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.51000 REMARK 3 B22 (A**2) : 4.51000 REMARK 3 B33 (A**2) : -9.03000 REMARK 3 B12 (A**2) : 5.05000 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) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.26 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) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.29 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.50 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) : 1.300 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.990 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.040 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.070 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 45.21 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : R5P_PEP_MIMO.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : R5P_PEP_MIMO.TOPH REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JCY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUN-01. REMARK 100 THE DEPOSITION ID IS D_1000013636. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 419681 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 27.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.8 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM NA-ACETATE, 6% PEG 4000, PH REMARK 280 4.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 278K 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 53.18967 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 106.37933 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 106.37933 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 53.18967 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 BIOLOGICAL ASSEMBLY IS A TETRAMER CONSTRUCTED FROM REMARK 300 CHAIN A AND CHAIN B AND THEIR SYMMETRY PARTNERS GENERATED BY REMARK 300 APPLICATION OF THE SYMMETRY OPERATION (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: 16810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -110.0 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 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 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 0.079 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 131.34 -174.23 REMARK 500 SER B2015 139.03 170.25 REMARK 500 PHE B2033 78.16 -116.07 REMARK 500 SER B2042 136.72 -173.03 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 173.7 REMARK 620 3 GLU A1222 OE2 77.5 105.5 REMARK 620 4 GLU A1222 OE1 88.2 89.1 53.5 REMARK 620 5 ASP A1233 OD2 73.5 100.3 123.4 77.9 REMARK 620 N 1 2 3 4 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 143.7 REMARK 620 3 GLU B2222 OE1 87.2 81.2 REMARK 620 4 GLU B2222 OE2 94.9 100.9 45.6 REMARK 620 5 ASP B2233 OD2 72.9 72.0 56.4 101.5 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 R5P A 1269 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 1270 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B 2270 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 2269 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEP A 1268 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEP B 2268 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FWW RELATED DB: PDB REMARK 900 AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH PEP, A5P AND CADMIUM REMARK 900 RELATED ID: 1JCX RELATED DB: PDB REMARK 900 AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH API AND CADMIUM DBREF 1JCY A 1001 1267 UNP O66496 KDSA_AQUAE 1 267 DBREF 1JCY 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 R5P A1269 14 HET CD A1270 1 HET PEP A1268 10 HET CD B2270 1 HET PO4 B2269 5 HET PEP B2268 10 HETNAM R5P RIBOSE-5-PHOSPHATE HETNAM CD CADMIUM ION HETNAM PEP PHOSPHOENOLPYRUVATE HETNAM PO4 PHOSPHATE ION FORMUL 3 R5P C5 H11 O8 P FORMUL 4 CD 2(CD 2+) FORMUL 5 PEP 2(C3 H5 O6 P) FORMUL 7 PO4 O4 P 3- FORMUL 9 HOH *201(H2 O) HELIX 1 1 SER A 1015 PHE A 1033 1 19 HELIX 2 2 HIS A 1058 GLY A 1075 1 18 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 SER A 1186 5 3 HELIX 11 11 PHE A 1203 GLY A 1215 1 13 HELIX 12 12 GLU A 1226 ALA A 1230 5 5 HELIX 13 13 GLN A 1242 LYS A 1259 1 18 HELIX 14 14 SER B 2015 PHE B 2033 1 19 HELIX 15 15 GLY B 2059 GLY B 2075 1 17 HELIX 16 16 GLU B 2084 TRP B 2086 5 3 HELIX 17 17 GLN B 2087 GLU B 2093 1 7 HELIX 18 18 PRO B 2101 CYS B 2105 5 5 HELIX 19 19 GLN B 2107 THR B 2117 1 11 HELIX 20 20 ALA B 2130 TRP B 2132 5 3 HELIX 21 21 ASP B 2133 GLY B 2144 1 12 HELIX 22 22 ARG B 2168 LYS B 2174 1 7 HELIX 23 23 MET B 2200 GLU B 2202 5 3 HELIX 24 24 PHE B 2203 GLY B 2215 1 13 HELIX 25 25 GLU B 2226 ALA B 2230 5 5 HELIX 26 26 GLN B 2242 SER B 2258 1 17 HELIX 27 27 LYS B 2259 TYR B 2261 5 3 SHEET 1 A10 LEU A1238 PRO A1239 0 SHEET 2 A10 GLY A1218 HIS A1224 1 O GLU A1222 N LEU A1238 SHEET 3 A10 PHE A1004 GLY A1009 1 O LEU A1005 N VAL A1219 SHEET 4 A10 VAL A1036 LYS A1041 1 N GLU A1037 O PHE A1004 SHEET 5 A10 LYS A1077 ASP A1081 1 O LYS A1077 N PHE A1040 SHEET 6 A10 ILE A1097 ILE A1100 1 N ILE A1097 O ILE A1078 SHEET 7 A10 ALA A1120 LYS A1124 1 O ALA A1120 N ILE A1098 SHEET 8 A10 ILE A1149 GLU A1153 1 O TYR A1150 N VAL A1123 SHEET 9 A10 LYS A1178 ASP A1182 1 O LYS A1178 N LEU A1151 SHEET 10 A10 GLY A1218 HIS A1224 1 O GLY A1218 N TYR A1181 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 C 2 GLN A1188 LEU A1189 0 SHEET 2 C 2 GLY A1198 GLY A1199 -1 N GLY A1198 O LEU A1189 SHEET 1 D10 LEU B2238 PRO B2239 0 SHEET 2 D10 GLY B2218 HIS B2224 1 O GLU B2222 N LEU B2238 SHEET 3 D10 LEU B2005 GLY B2009 1 O LEU B2005 N VAL B2219 SHEET 4 D10 GLU B2037 LYS B2041 1 O GLU B2037 N VAL B2006 SHEET 5 D10 LYS B2077 ASP B2081 1 O LYS B2077 N PHE B2040 SHEET 6 D10 ILE B2097 ILE B2100 1 N ILE B2097 O ILE B2078 SHEET 7 D10 ALA B2120 LYS B2124 1 O ALA B2120 N ILE B2098 SHEET 8 D10 ILE B2149 GLU B2153 1 N TYR B2150 O VAL B2121 SHEET 9 D10 LYS B2178 ASP B2182 1 O LYS B2178 N LEU B2151 SHEET 10 D10 GLY B2218 HIS B2224 1 O GLY B2218 N TYR B2181 SHEET 1 E 2 THR B2156 THR B2157 0 SHEET 2 E 2 LEU B2163 VAL B2164 -1 O VAL B2164 N THR B2156 LINK SG CYS A1011 CD CD A1270 1555 1555 2.63 LINK NE2 HIS A1185 CD CD A1270 1555 1555 2.29 LINK OE2 GLU A1222 CD CD A1270 1555 1555 2.39 LINK OE1 GLU A1222 CD CD A1270 1555 1555 2.52 LINK OD2 ASP A1233 CD CD A1270 1555 1555 2.45 LINK SG CYS B2011 CD CD B2270 1555 1555 2.54 LINK NE2 HIS B2185 CD CD B2270 1555 1555 2.91 LINK OE1 GLU B2222 CD CD B2270 1555 1555 3.09 LINK OE2 GLU B2222 CD CD B2270 1555 1555 2.17 LINK OD2 ASP B2233 CD CD B2270 1555 1555 2.65 SITE 1 AC1 10 ASN A1048 ARG A1049 SER A1050 ARG A1154 SITE 2 AC1 10 HIS A1185 GLN A1188 SER A1197 PEP A1268 SITE 3 AC1 10 HOH A3204 ARG B2106 SITE 1 AC2 4 CYS A1011 HIS A1185 GLU A1222 ASP A1233 SITE 1 AC3 6 CYS B2011 LYS B2046 HIS B2185 GLU B2222 SITE 2 AC3 6 ASP B2233 PEP B2268 SITE 1 AC4 4 ARG A1106 ARG B2049 SER B2050 HOH B3203 SITE 1 AC5 14 LYS A1041 SER A1043 LYS A1046 ASP A1081 SITE 2 AC5 14 GLN A1099 PRO A1101 ALA A1102 LYS A1124 SITE 3 AC5 14 ARG A1154 HIS A1185 PHE A1220 R5P A1269 SITE 4 AC5 14 HOH A3017 HOH A3021 SITE 1 AC6 14 LYS B2041 SER B2043 LYS B2046 GLN B2099 SITE 2 AC6 14 PRO B2101 ALA B2102 LYS B2124 ARG B2154 SITE 3 AC6 14 PHE B2220 CD B2270 HOH B3031 HOH B3070 SITE 4 AC6 14 HOH B3090 HOH B3205 CRYST1 84.316 84.316 159.569 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 0.011860 0.006847 0.000000 0.00000 SCALE2 0.000000 0.013695 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006267 0.00000