HEADER TRANSFERASE 30-OCT-07 2VF3 TITLE AQUIFEX AEOLICUS ISPE IN COMPLEX WITH LIGAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL KINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CMK , 4-CYTIDINE-5'-DIPHOSPHO-2-C-METHYL-D COMPND 5 -ERYTHRITOL KINASE; COMPND 6 EC: 2.7.1.148; COMPND 7 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: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS ISPE, KINASE, AQUIFEX, TRANSFERASE, ATP-BINDING, ISOPRENE KEYWDS 2 BIOSYNTHESIS, NON-MEVALONATE, NUCLEOTIDE-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.S.ALPHEY,W.N.HUNTER REVDAT 2 24-FEB-09 2VF3 1 VERSN REVDAT 1 25-NOV-08 2VF3 0 JRNL AUTH A.K.HIRSCH,M.S.ALPHEY,S.LAUW,M.SEET,L.BARANDUN, JRNL AUTH 2 W.EISENREICH,F.ROHDICH,W.N.HUNTER,A.BACHER, JRNL AUTH 3 F.DIEDERICH JRNL TITL INHIBITORS OF THE KINASE ISPE: STRUCTURE-ACTIVITY JRNL TITL 2 RELATIONSHIPS AND CO-CRYSTAL STRUCTURE ANALYSIS. JRNL REF ORG.BIOMOL.CHEM. V. 6 2719 2008 JRNL REFN ISSN 1477-0520 JRNL PMID 18633530 JRNL DOI 10.1039/B804375B REMARK 2 REMARK 2 RESOLUTION. 2.2 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 97.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 41732 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) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2212 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3077 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2980 REMARK 3 BIN FREE R VALUE SET COUNT : 160 REMARK 3 BIN FREE R VALUE : 0.3800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4323 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 82 REMARK 3 SOLVENT ATOMS : 156 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.10 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.224 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.204 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.156 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.093 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4498 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6116 ; 1.585 ; 2.012 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 566 ; 8.867 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 200 ;36.526 ;24.500 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 804 ;17.234 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;21.334 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 675 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3377 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2014 ; 0.219 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2998 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 232 ; 0.181 ; 0.200 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): 80 ; 0.282 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.211 ; 0.200 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): 2814 ; 0.810 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4412 ; 1.374 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1956 ; 1.729 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1679 ; 2.630 ; 4.500 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 0 A 2001 4 REMARK 3 1 B 0 B 2001 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 2077 ; 0.44 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 2077 ; 1.47 ; 2.00 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 REMARK 3 RIDING POSITIONS. CL 6 HAS BEEN ADDED UNREFINED WITH AN REMARK 3 OCCUPANCY OF 0.25 IN A POSITION PARTIALLY OCCUPIED BY LIGAND REMARK 3 RESIDUES 22-25 NEAR THE ACTIVE SITE IN BOTH CHAINS APPEARS REMARK 3 FLEXIBLE. ELECTRON DENSITY IS NOT WELL-DEFINED AND THIS IS REMARK 3 REFLECTED IN THE GEOMETRY OF THE REGION. REMARK 4 REMARK 4 2VF3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-OCT-07. REMARK 100 THE PDBE ID CODE IS EBI-34200. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43998 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.20 REMARK 200 RESOLUTION RANGE LOW (A) : 68.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.2 REMARK 200 R MERGE (I) : 0.06 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.40 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.1 REMARK 200 R MERGE FOR SHELL (I) : 0.69 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.50 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: REFMAC5 REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.8 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.6 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 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 68.65900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.65900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 68.65900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 68.65900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 68.65900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 68.65900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 68.65900 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 68.65900 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 68.65900 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 68.65900 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 68.65900 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 68.65900 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 68.65900 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 68.65900 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 68.65900 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 68.65900 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 68.65900 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 68.65900 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 GENERATING THE BIOMOLECULE 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 GLY B -2 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 OG SER A 128 - OD1 ASP A 130 2.00 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 HIS B 25 N - CA - C ANGL. DEV. = 26.4 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 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 TYR A 24 153.75 166.73 REMARK 500 ASN A 78 64.57 -114.06 REMARK 500 ASP A 130 -74.88 -5.65 REMARK 500 LYS A 138 -126.40 54.54 REMARK 500 ASN A 206 105.32 -161.83 REMARK 500 HIS B 25 111.81 -5.29 REMARK 500 LEU B 47 99.43 -59.35 REMARK 500 ASN B 78 61.57 -101.30 REMARK 500 LYS B 138 -130.80 58.03 REMARK 500 ASN B 206 106.72 -162.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 23 TYR A 24 -30.66 REMARK 500 ALA A 129 ASP A 130 104.04 REMARK 500 TYR B 24 HIS B 25 87.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASP A 130 16.0 L L OUTSIDE RANGE REMARK 500 HIS B 25 12.1 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP A1270 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GVS A1269 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GVS B1269 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP B1270 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1271 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1272 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1273 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A1274 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B1271 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B1272 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR B1274 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2V2V RELATED DB: PDB REMARK 900 ISPE IN COMPLEX WITH LIGAND REMARK 900 RELATED ID: 2V2Q RELATED DB: PDB REMARK 900 ISPE IN COMPLEX WITH LIGAND REMARK 900 RELATED ID: 2V2Y RELATED DB: PDB REMARK 900 ISPE IN COMPLEX WITH ADP AND CDP REMARK 900 RELATED ID: 2V2Z RELATED DB: PDB REMARK 900 ISPE IN COMPLEX WITH ADP AND CDPME REMARK 900 RELATED ID: 2V34 RELATED DB: PDB REMARK 900 ISPE IN COMPLEX WITH CYTIDINE AND LIGAND REMARK 900 RELATED ID: 2V8P RELATED DB: PDB REMARK 900 ISPE IN COMPLEX WITH ADP AND CDP REMARK 999 REMARK 999 SEQUENCE REMARK 999 REMNANTS OF N-TERMINAL 6HIS-TAG PRESENT IN SEQUENCE, BUT REMARK 999 ONLY PARTIALLY ORDERED IN STRUCTURE DBREF 2VF3 A -2 0 PDB 2VF3 2VF3 -2 0 DBREF 2VF3 A 1 268 UNP O67060 ISPE_AQUAE 1 268 DBREF 2VF3 B -2 0 PDB 2VF3 2VF3 -2 0 DBREF 2VF3 B 1 268 UNP O67060 ISPE_AQUAE 1 268 SEQRES 1 A 271 GLY SER HIS MET ILE LYS VAL LEU SER PRO ALA LYS ILE SEQRES 2 A 271 ASN LEU GLY LEU TRP VAL LEU GLY ARG LEU PRO SER GLY SEQRES 3 A 271 TYR HIS GLU ILE LEU THR LEU TYR GLN GLU ILE PRO PHE SEQRES 4 A 271 TYR ASP GLU ILE TYR ILE ARG GLU GLY VAL LEU ARG VAL SEQRES 5 A 271 GLU THR ASN ILE GLY ILE PRO GLN GLU GLU ASN LEU VAL SEQRES 6 A 271 TYR LYS GLY LEU ARG GLU PHE GLU ARG ILE THR GLY ILE SEQRES 7 A 271 GLU ILE ASN TYR SER ILE PHE ILE GLN LYS ASN ILE PRO SEQRES 8 A 271 PRO GLY ALA GLY LEU GLY GLY GLY SER SER ASN LEU ALA SEQRES 9 A 271 VAL VAL LEU LYS LYS VAL ASN GLU LEU LEU GLY SER PRO SEQRES 10 A 271 LEU SER GLU GLU GLU LEU ARG GLU LEU VAL GLY SER ILE SEQRES 11 A 271 SER ALA ASP ALA PRO PHE PHE LEU LEU GLY LYS SER ALA SEQRES 12 A 271 ILE GLY ARG GLY LYS GLY GLU VAL LEU GLU PRO VAL GLU SEQRES 13 A 271 THR GLU ILE SER GLY LYS ILE THR LEU VAL ILE PRO GLN SEQRES 14 A 271 VAL SER SER SER THR GLY ARG VAL TYR SER SER LEU ARG SEQRES 15 A 271 GLU GLU HIS PHE VAL THR PRO GLU TYR ALA GLU GLU LYS SEQRES 16 A 271 ILE GLN ARG ILE ILE SER GLY GLU VAL GLU GLU ILE GLU SEQRES 17 A 271 ASN VAL LEU GLY ASP ILE ALA ARG GLU LEU TYR PRO GLU SEQRES 18 A 271 ILE ASN GLU VAL TYR ARG PHE VAL GLU TYR LEU GLY PHE SEQRES 19 A 271 LYS PRO PHE VAL SER GLY SER GLY SER THR VAL TYR PHE SEQRES 20 A 271 PHE GLY GLY ALA SER GLU GLU LEU LYS LYS ALA ALA LYS SEQRES 21 A 271 MET ARG GLY TRP LYS VAL VAL GLU LEU GLU LEU SEQRES 1 B 271 GLY SER HIS MET ILE LYS VAL LEU SER PRO ALA LYS ILE SEQRES 2 B 271 ASN LEU GLY LEU TRP VAL LEU GLY ARG LEU PRO SER GLY SEQRES 3 B 271 TYR HIS GLU ILE LEU THR LEU TYR GLN GLU ILE PRO PHE SEQRES 4 B 271 TYR ASP GLU ILE TYR ILE ARG GLU GLY VAL LEU ARG VAL SEQRES 5 B 271 GLU THR ASN ILE GLY ILE PRO GLN GLU GLU ASN LEU VAL SEQRES 6 B 271 TYR LYS GLY LEU ARG GLU PHE GLU ARG ILE THR GLY ILE SEQRES 7 B 271 GLU ILE ASN TYR SER ILE PHE ILE GLN LYS ASN ILE PRO SEQRES 8 B 271 PRO GLY ALA GLY LEU GLY GLY GLY SER SER ASN LEU ALA SEQRES 9 B 271 VAL VAL LEU LYS LYS VAL ASN GLU LEU LEU GLY SER PRO SEQRES 10 B 271 LEU SER GLU GLU GLU LEU ARG GLU LEU VAL GLY SER ILE SEQRES 11 B 271 SER ALA ASP ALA PRO PHE PHE LEU LEU GLY LYS SER ALA SEQRES 12 B 271 ILE GLY ARG GLY LYS GLY GLU VAL LEU GLU PRO VAL GLU SEQRES 13 B 271 THR GLU ILE SER GLY LYS ILE THR LEU VAL ILE PRO GLN SEQRES 14 B 271 VAL SER SER SER THR GLY ARG VAL TYR SER SER LEU ARG SEQRES 15 B 271 GLU GLU HIS PHE VAL THR PRO GLU TYR ALA GLU GLU LYS SEQRES 16 B 271 ILE GLN ARG ILE ILE SER GLY GLU VAL GLU GLU ILE GLU SEQRES 17 B 271 ASN VAL LEU GLY ASP ILE ALA ARG GLU LEU TYR PRO GLU SEQRES 18 B 271 ILE ASN GLU VAL TYR ARG PHE VAL GLU TYR LEU GLY PHE SEQRES 19 B 271 LYS PRO PHE VAL SER GLY SER GLY SER THR VAL TYR PHE SEQRES 20 B 271 PHE GLY GLY ALA SER GLU GLU LEU LYS LYS ALA ALA LYS SEQRES 21 B 271 MET ARG GLY TRP LYS VAL VAL GLU LEU GLU LEU HET POP A1270 9 HET GVS A1269 28 HET GVS B1269 28 HET POP B1270 9 HET CL A1271 1 HET CL A1272 1 HET CL A1273 1 HET BR A1274 1 HET CL B1271 1 HET CL B1272 1 HET CL B1273 1 HET BR B1274 1 HETNAM CL CHLORIDE ION HETNAM GVS ETHYL {3-[4-AMINO-5-{3-[(CYCLOPROPYLSULFONYL) HETNAM 2 GVS AMINO]PROP-1-YN-1-YL}-2-OXOPYRIMIDIN-1(2H)- HETNAM 3 GVS YL]OXETAN-3-YL}ACETATE HETNAM BR BROMIDE ION HETNAM POP PYROPHOSPHATE 2- FORMUL 3 CL 6(CL 1-) FORMUL 4 GVS 2(C17 H22 N4 O6 S1) FORMUL 5 BR 2(BR 1-) FORMUL 6 POP 2(H2 O7 P2 2-) FORMUL 7 HOH *156(H2 O1) HELIX 1 1 PRO A 56 GLU A 59 5 4 HELIX 2 2 ASN A 60 GLY A 74 1 15 HELIX 3 3 GLY A 94 LEU A 111 1 18 HELIX 4 4 SER A 116 SER A 128 1 13 HELIX 5 5 PRO A 132 GLY A 137 1 6 HELIX 6 6 SER A 170 SER A 176 1 7 HELIX 7 7 ARG A 179 PHE A 183 5 5 HELIX 8 8 THR A 185 SER A 198 1 14 HELIX 9 9 GLU A 200 ILE A 204 5 5 HELIX 10 10 ASN A 206 TYR A 216 1 11 HELIX 11 11 TYR A 216 LEU A 229 1 14 HELIX 12 12 SER A 249 GLY A 260 1 12 HELIX 13 13 PRO B 56 GLU B 59 5 4 HELIX 14 14 ASN B 60 GLY B 74 1 15 HELIX 15 15 GLY B 94 LEU B 111 1 18 HELIX 16 16 SER B 116 SER B 128 1 13 HELIX 17 17 ASP B 130 LEU B 136 5 7 HELIX 18 18 SER B 170 SER B 177 1 8 HELIX 19 19 ARG B 179 PHE B 183 5 5 HELIX 20 20 THR B 185 SER B 198 1 14 HELIX 21 21 GLU B 200 ILE B 204 5 5 HELIX 22 22 ASN B 206 TYR B 216 1 11 HELIX 23 23 TYR B 216 LEU B 229 1 14 HELIX 24 24 SER B 249 GLY B 260 1 12 SHEET 1 AA 4 ILE A 2 ARG A 19 0 SHEET 2 AA 4 HIS A 25 GLU A 44 -1 O GLU A 26 N LEU A 17 SHEET 3 AA 4 SER A 139 ARG A 143 -1 O ALA A 140 N TYR A 31 SHEET 4 AA 4 VAL A 148 PRO A 151 -1 O VAL A 148 N ARG A 143 SHEET 1 AB 4 ILE A 2 ARG A 19 0 SHEET 2 AB 4 HIS A 25 GLU A 44 -1 O GLU A 26 N LEU A 17 SHEET 3 AB 4 TYR A 79 GLN A 84 -1 O SER A 80 N ARG A 43 SHEET 4 AB 4 ARG A 48 THR A 51 1 O ARG A 48 N ILE A 81 SHEET 1 AC 4 PHE A 234 VAL A 235 0 SHEET 2 AC 4 VAL A 242 PHE A 244 -1 O TYR A 243 N PHE A 234 SHEET 3 AC 4 GLY A 158 ILE A 164 -1 O THR A 161 N PHE A 244 SHEET 4 AC 4 LYS A 262 LEU A 268 -1 O LYS A 262 N ILE A 164 SHEET 1 BA 4 ILE B 2 ARG B 19 0 SHEET 2 BA 4 HIS B 25 GLU B 44 -1 O GLU B 26 N LEU B 17 SHEET 3 BA 4 SER B 139 ARG B 143 -1 O ALA B 140 N TYR B 31 SHEET 4 BA 4 VAL B 148 PRO B 151 -1 O VAL B 148 N ARG B 143 SHEET 1 BB 4 ILE B 2 ARG B 19 0 SHEET 2 BB 4 HIS B 25 GLU B 44 -1 O GLU B 26 N LEU B 17 SHEET 3 BB 4 TYR B 79 GLN B 84 -1 O SER B 80 N ARG B 43 SHEET 4 BB 4 ARG B 48 THR B 51 1 O ARG B 48 N ILE B 81 SHEET 1 BC 4 PHE B 234 VAL B 235 0 SHEET 2 BC 4 VAL B 242 PHE B 244 -1 O TYR B 243 N PHE B 234 SHEET 3 BC 4 GLY B 158 ILE B 164 -1 O THR B 161 N PHE B 244 SHEET 4 BC 4 LYS B 262 LEU B 268 -1 O LYS B 262 N ILE B 164 CISPEP 1 SER B 22 GLY B 23 0 -11.50 CISPEP 2 GLY B 239 SER B 240 0 15.07 SITE 1 AC1 10 PRO A 89 GLY A 90 ALA A 91 GLY A 92 SITE 2 AC1 10 LEU A 93 GLY A 94 GLY A 95 GLY A 96 SITE 3 AC1 10 HOH A2084 HOH A2085 SITE 1 AC2 15 LYS A 9 ASN A 11 LEU A 14 TYR A 24 SITE 2 AC2 15 HIS A 25 ILE A 27 TYR A 31 ALA A 129 SITE 3 AC2 15 ASP A 130 LYS A 145 THR A 171 TYR A 175 SITE 4 AC2 15 GLY A 237 CL A1272 GLU B 181 SITE 1 AC3 11 ASN B 11 LEU B 14 TYR B 24 HIS B 25 SITE 2 AC3 11 ILE B 27 TYR B 31 ASP B 130 LYS B 145 SITE 3 AC3 11 THR B 171 TYR B 175 GLY B 237 SITE 1 AC4 9 GLY B 90 ALA B 91 GLY B 92 LEU B 93 SITE 2 AC4 9 GLY B 94 GLY B 95 GLY B 96 HOH B2016 SITE 3 AC4 9 HOH B2071 SITE 1 AC5 3 TYR A 216 PRO A 217 GLU A 218 SITE 1 AC6 4 TYR A 24 HIS A 25 TYR A 175 GVS A1269 SITE 1 AC7 3 ARG A 43 ASN A 220 ARG A 224 SITE 1 AC8 4 ARG A 19 GLU A 180 GLY B 18 ARG B 19 SITE 1 AC9 1 ARG B 213 SITE 1 BC1 2 ARG B 43 ILE B 55 SITE 1 BC2 3 ASN B 206 PHE B 234 VAL B 235 CRYST1 137.318 137.318 137.318 90.00 90.00 90.00 P 21 3 24 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 0.007282 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007282 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007282 0.00000