HEADER TRANSFERASE 01-AUG-08 3E12 TITLE CU2+ SUBSTITUTED AQUIFEX AEOLICUS KDO8PS IN COMPLEX WITH KDO8P COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: KDO8PS; COMPND 5 SYNONYM: PHOSPHO-2-DEHYDRO-3-DEOXYOCTONATE ALDOLASE, 3-DEOXY-D-MANNO- COMPND 6 OCTULOSONIC ACID 8-PHOSPHATE SYNTHETASE, KDO-8-PHOSPHATE SYNTHETASE, COMPND 7 KDO 8-P SYNTHASE, KDOPS; COMPND 8 EC: 2.5.1.55; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 63363; SOURCE 4 GENE: KDSA, AQ_085; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS KDO, KDO8PS, COPPER, PEP, METAL GEOMETRY, CYTOPLASM, KEYWDS 2 LIPOPOLYSACCHARIDE BIOSYNTHESIS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.L.GATTI REVDAT 2 30-AUG-23 3E12 1 REMARK REVDAT 1 12-MAY-09 3E12 0 JRNL AUTH F.KONA,P.TAO,P.MARTIN,X.XU,D.L.GATTI JRNL TITL ELECTRONIC STRUCTURE OF THE METAL CENTER IN THE CD(2+), JRNL TITL 2 ZN(2+), AND CU(2+) SUBSTITUTED FORMS OF KDO8P SYNTHASE: JRNL TITL 3 IMPLICATIONS FOR CATALYSIS. JRNL REF BIOCHEMISTRY V. 48 3610 2009 JRNL REFN ISSN 0006-2960 JRNL PMID 19228070 JRNL DOI 10.1021/BI801955H REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 69526 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3697 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4625 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE SET COUNT : 273 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4047 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 543 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.66000 REMARK 3 B22 (A**2) : 0.66000 REMARK 3 B33 (A**2) : -1.00000 REMARK 3 B12 (A**2) : 0.33000 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): 0.090 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.089 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.053 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.567 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4387 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5970 ; 1.524 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 570 ; 5.317 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 190 ;34.482 ;24.316 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 811 ;14.151 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;15.278 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 680 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3258 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2651 ; 0.872 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4309 ; 1.564 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1736 ; 2.549 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1634 ; 4.139 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL 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 3E12 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-AUG-08. REMARK 100 THE DEPOSITION ID IS D_1000048740. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73254 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 22.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 21.20 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 1FWW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, NA ACETATE, PH 4.9, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 53.43633 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 106.87267 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 106.87267 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 53.43633 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -90.0 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 1 REMARK 465 LEU A 193 REMARK 465 GLY A 194 REMARK 465 ASP A 195 REMARK 465 LYS A 196 REMARK 465 SER A 197 REMARK 465 PRO A 265 REMARK 465 VAL A 266 REMARK 465 LYS A 267 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 GLY B 192 REMARK 465 LEU B 193 REMARK 465 GLY B 194 REMARK 465 ASP B 195 REMARK 465 LYS B 196 REMARK 465 SER B 197 REMARK 465 PRO B 265 REMARK 465 VAL B 266 REMARK 465 LYS B 267 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 OD1 ASP B 133 O HOH B 1071 1.93 REMARK 500 CB GLU A 222 OE1 GLN A 237 1.96 REMARK 500 OE1 GLU B 222 OE1 GLN B 237 1.99 REMARK 500 O HOH A 1074 O HOH A 1102 2.06 REMARK 500 O HOH A 752 O HOH A 1101 2.07 REMARK 500 O HOH A 985 O HOH A 1098 2.11 REMARK 500 O HOH B 860 O HOH B 919 2.14 REMARK 500 O HOH A 855 O HOH A 1025 2.15 REMARK 500 O HOH A 1005 O HOH B 615 2.16 REMARK 500 O HOH B 728 O HOH B 1024 2.18 REMARK 500 O HOH A 723 O HOH A 1061 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 LEU B 60 CA - CB - CG ANGL. DEV. = 18.8 DEGREES REMARK 500 ASP B 133 CB - CG - OD1 ANGL. DEV. = 5.5 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 MET A 200 -57.07 -126.72 REMARK 500 MET B 200 -57.42 -136.71 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 CU A 270 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 185 NE2 REMARK 620 2 GLU A 222 OE1 96.7 REMARK 620 3 ASP A 233 OD2 83.6 128.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU B 270 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 185 NE2 REMARK 620 2 GLU B 222 OE1 95.8 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 CU A 270 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 269 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU B 270 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 269 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KD0 A 268 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KD0 B 268 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FSW RELATED DB: PDB REMARK 900 RELATED ID: 1FWW RELATED DB: PDB REMARK 900 RELATED ID: 3E0I RELATED DB: PDB DBREF 3E12 A 1 267 UNP O66496 KDSA_AQUAE 1 267 DBREF 3E12 B 1 267 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 CU A 270 1 HET PO4 A 269 5 HET KD0 A 268 20 HET CU B 270 1 HET PO4 B 269 5 HET ACT B 501 4 HET KD0 B 268 20 HETNAM CU COPPER (II) ION HETNAM PO4 PHOSPHATE ION HETNAM KD0 3-DEOXY-8-O-PHOSPHONO-D-MANNO-OCT-2-ULOSONIC ACID HETNAM ACT ACETATE ION FORMUL 3 CU 2(CU 2+) FORMUL 4 PO4 2(O4 P 3-) FORMUL 5 KD0 2(C8 H15 O11 P) FORMUL 8 ACT C2 H3 O2 1- FORMUL 10 HOH *543(H2 O) HELIX 1 1 SER A 15 PHE A 33 1 19 HELIX 2 2 GLY A 59 GLY A 75 1 17 HELIX 3 3 GLU A 84 TRP A 86 5 3 HELIX 4 4 GLN A 87 GLU A 93 1 7 HELIX 5 5 PRO A 101 CYS A 105 5 5 HELIX 6 6 GLN A 107 LYS A 116 1 10 HELIX 7 7 ALA A 130 ASP A 133 5 4 HELIX 8 8 THR A 134 GLY A 144 1 11 HELIX 9 9 ARG A 168 LYS A 174 1 7 HELIX 10 10 THR A 184 GLN A 188 5 5 HELIX 11 11 MET A 200 GLU A 202 5 3 HELIX 12 12 PHE A 203 GLY A 215 1 13 HELIX 13 13 GLU A 226 ALA A 230 5 5 HELIX 14 14 GLN A 242 LYS A 259 1 18 HELIX 15 15 SER B 15 PHE B 33 1 19 HELIX 16 16 GLY B 59 GLY B 75 1 17 HELIX 17 17 GLU B 84 TRP B 86 5 3 HELIX 18 18 GLN B 87 GLU B 93 1 7 HELIX 19 19 PRO B 101 CYS B 105 5 5 HELIX 20 20 GLN B 107 THR B 117 1 11 HELIX 21 21 ALA B 130 ASP B 133 5 4 HELIX 22 22 THR B 134 GLY B 144 1 11 HELIX 23 23 ARG B 168 LYS B 174 1 7 HELIX 24 24 MET B 200 GLU B 202 5 3 HELIX 25 25 PHE B 203 GLY B 215 1 13 HELIX 26 26 GLU B 226 ALA B 230 5 5 HELIX 27 27 GLN B 242 SER B 258 1 17 HELIX 28 28 LYS B 259 TYR B 261 5 3 SHEET 1 A10 LEU A 238 PRO A 239 0 SHEET 2 A10 GLY A 218 HIS A 224 1 N GLU A 222 O LEU A 238 SHEET 3 A10 LYS A 178 ASP A 182 1 N TYR A 181 O PHE A 220 SHEET 4 A10 ILE A 149 GLU A 153 1 N GLU A 153 O ILE A 180 SHEET 5 A10 ALA A 120 LYS A 124 1 N VAL A 121 O TYR A 150 SHEET 6 A10 ILE A 97 ILE A 100 1 N ILE A 98 O ALA A 120 SHEET 7 A10 LYS A 77 ASP A 81 1 N THR A 80 O GLN A 99 SHEET 8 A10 VAL A 36 LYS A 41 1 N PHE A 40 O LYS A 77 SHEET 9 A10 PHE A 4 GLY A 9 1 N PHE A 4 O GLU A 37 SHEET 10 A10 GLY A 218 HIS A 224 1 O MET A 221 N ILE A 7 SHEET 1 B 2 THR A 156 THR A 157 0 SHEET 2 B 2 LEU A 163 VAL A 164 -1 O VAL A 164 N THR A 156 SHEET 1 C10 LEU B 238 PRO B 239 0 SHEET 2 C10 GLY B 218 HIS B 224 1 N GLU B 222 O LEU B 238 SHEET 3 C10 LYS B 178 ASP B 182 1 N TYR B 181 O PHE B 220 SHEET 4 C10 ILE B 149 GLU B 153 1 N GLU B 153 O ASP B 182 SHEET 5 C10 ALA B 120 LYS B 124 1 N VAL B 123 O TYR B 150 SHEET 6 C10 ILE B 97 ILE B 100 1 N ILE B 98 O ALA B 120 SHEET 7 C10 LYS B 77 ASP B 81 1 N THR B 80 O GLN B 99 SHEET 8 C10 VAL B 36 LYS B 41 1 N PHE B 40 O LYS B 77 SHEET 9 C10 PHE B 4 GLY B 9 1 N PHE B 4 O GLU B 37 SHEET 10 C10 GLY B 218 HIS B 224 1 O MET B 221 N ILE B 7 SHEET 1 D 2 THR B 156 THR B 157 0 SHEET 2 D 2 LEU B 163 VAL B 164 -1 O VAL B 164 N THR B 156 LINK NE2 HIS A 185 CU CU A 270 1555 1555 2.04 LINK OE1 GLU A 222 CU CU A 270 1555 1555 2.12 LINK OD2 ASP A 233 CU CU A 270 1555 1555 2.17 LINK NE2 HIS B 185 CU CU B 270 1555 1555 2.05 LINK OE1 GLU B 222 CU CU B 270 1555 1555 2.15 CISPEP 1 GLY A 198 GLY A 199 0 3.07 CISPEP 2 GLY A 199 MET A 200 0 1.33 CISPEP 3 GLY B 199 MET B 200 0 -4.99 SITE 1 AC1 5 CYS A 11 HIS A 185 GLU A 222 ASP A 233 SITE 2 AC1 5 KD0 A 268 SITE 1 AC2 8 PRO A 101 ALA A 102 LYS A 124 ARG A 154 SITE 2 AC2 8 KD0 A 268 HOH A 635 HOH A 637 HOH A 668 SITE 1 AC3 6 CYS B 11 HIS B 185 GLU B 222 ASP B 233 SITE 2 AC3 6 GLN B 237 KD0 B 268 SITE 1 AC4 8 PRO B 101 ALA B 102 LYS B 124 ARG B 154 SITE 2 AC4 8 KD0 B 268 HOH B 626 HOH B 642 HOH B 658 SITE 1 AC5 1 LYS B 174 SITE 1 AC6 23 CYS A 11 LYS A 41 SER A 43 LYS A 46 SITE 2 AC6 23 ASN A 48 ARG A 49 SER A 50 ASP A 81 SITE 3 AC6 23 GLN A 99 LYS A 124 HIS A 185 GLN A 188 SITE 4 AC6 23 PHE A 220 GLU A 222 ASP A 233 PO4 A 269 SITE 5 AC6 23 CU A 270 HOH A 853 HOH A 988 HOH A 994 SITE 6 AC6 23 HOH A1066 HOH A1134 ARG B 106 SITE 1 AC7 24 ARG A 106 CYS B 11 LYS B 41 SER B 43 SITE 2 AC7 24 LYS B 46 ASN B 48 ARG B 49 SER B 50 SITE 3 AC7 24 ASP B 81 GLN B 99 LYS B 124 ARG B 154 SITE 4 AC7 24 HIS B 185 PHE B 220 GLU B 222 ASP B 233 SITE 5 AC7 24 PO4 B 269 CU B 270 HOH B 638 HOH B 718 SITE 6 AC7 24 HOH B 764 HOH B 822 HOH B 957 HOH B1088 CRYST1 84.747 84.747 160.309 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 0.011800 0.006813 0.000000 0.00000 SCALE2 0.000000 0.013625 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006238 0.00000