HEADER TRANSFERASE 06-AUG-04 1W57 TITLE STRUCTURE OF THE BIFUNCTIONAL ISPDF FROM CAMPYLOBACTER JEJUNI TITLE 2 CONTAINING ZN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISPD/ISPF BIFUNCTIONAL ENZYME; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, 4- COMPND 5 DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHASE, MEP COMPND 6 CYTIDYLYLTRANSFERASE, MCT, 2-C-METHYL-D-ERYTHRITOL 2,4- COMPND 7 CYCLODIPHOSPHATE SYNTHASE, MECPS, MECDP-SYNTHASE, METHYLERYTHRITOL 4- COMPND 8 PHOSPHATE CYTIDYLYLTRANSFERASE, METHYLERYTHRITOL 2,4-CYCLODIPHOSPHATE COMPND 9 SYNTHASE; COMPND 10 EC: 2.7.7.60, 4.6.1.12; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAMPYLOBACTER JEJUNI; SOURCE 3 ORGANISM_TAXID: 197; SOURCE 4 STRAIN: JEJUNI NTCT 11168; SOURCE 5 ATCC: 33560; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET15B KEYWDS BIFUNCTIONAL ENZYME, BIOSYNTHETIC PATHWAY, ISOPRENOIDS, BIFUNCTIONAL, KEYWDS 2 NONMEVALONATE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.GABRIELSEN,C.S.BOND,W.N.HUNTER REVDAT 4 13-DEC-23 1W57 1 LINK REVDAT 3 24-FEB-09 1W57 1 VERSN REVDAT 2 08-DEC-04 1W57 1 JRNL REVDAT 1 04-OCT-04 1W57 0 JRNL AUTH M.GABRIELSEN,C.S.BOND,I.HALLYBURTON,S.HECHT,A.BACHER, JRNL AUTH 2 W.EISENREICH,F.ROHDICH,W.N.HUNTER JRNL TITL HEXAMERIC ASSEMBLY OF THE BIFUNCTIONAL METHYLERYTHRITOL JRNL TITL 2 2,4-CYCLODIPHOSPHATE SYNTHASE AND PROTEIN-PROTEIN JRNL TITL 3 ASSOCIATIONS IN THE DEOXY-XYLULOSE-DEPENDENT PATHWAY OF JRNL TITL 4 ISOPRENOID PRECURSOR BIOSYNTHESIS JRNL REF J.BIOL.CHEM. V. 279 52753 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 15466439 JRNL DOI 10.1074/JBC.M408895200 REMARK 2 REMARK 2 RESOLUTION. 3.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 3.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 95.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 367588 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.830 REMARK 3 FREE R VALUE TEST SET COUNT : 509 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.09 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.17 REMARK 3 REFLECTION IN BIN (WORKING SET) : 732 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE SET COUNT : 38 REMARK 3 BIN FREE R VALUE : 0.2520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2908 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 57 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 81.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.78900 REMARK 3 B22 (A**2) : 4.78900 REMARK 3 B33 (A**2) : -7.18300 REMARK 3 B12 (A**2) : 2.39400 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.511 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.299 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.409 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.913 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.858 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3019 ; 0.038 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2771 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4073 ; 2.128 ; 1.993 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6483 ; 2.124 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 465 ; 0.142 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3257 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 576 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 610 ; 0.232 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3158 ; 0.268 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1402 ; 0.201 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1979 ; 0.105 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 66 ; 0.193 ; 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): 24 ; 0.238 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 135 ; 0.368 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.316 ; 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): 1828 ; 1.134 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2946 ; 2.007 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1191 ; 2.462 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1127 ; 3.787 ; 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 : BABINET MODEL PLUS MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 1W57 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-AUG-04. REMARK 100 THE DEPOSITION ID IS D_1290020675. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 160.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : DIAMOND (111), GE(220) REMARK 200 OPTICS : TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 367588 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 31.40 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 41.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.52000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1W55 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35 % ETHYLENE GLYCOL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+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 -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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 80.50200 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 80.50200 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 80.50200 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 80.50200 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 80.50200 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 80.50200 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC 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 BIOMT1 2 -0.500000 0.866025 0.000000 53.88000 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 93.32290 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 107.76000 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 4 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 -80.50200 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 107.76000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 -80.50200 REMARK 350 BIOMT1 6 0.500000 -0.866025 0.000000 53.88000 REMARK 350 BIOMT2 6 -0.866025 -0.500000 0.000000 93.32290 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 -80.50200 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 PA GPP A1374 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2038 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 CATALYTIC ACTIVITY: 2-PHOSPHO-4-(CYTIDINE 5'-DIPHOSPHO)-2-C- REMARK 400 METHYL-D-ERYTHRITOL = 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE REMARK 400 + CMP. 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 SER A 2 REMARK 465 LEU A 371 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 A 217 O HOH A 2041 1.99 REMARK 500 O3P C5P A 1372 O HOH A 2041 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2045 O HOH A 2054 3665 1.66 REMARK 500 O HOH A 2016 O HOH A 2040 2655 2.02 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 ASP A 255 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 316 CB - CG - OD2 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 ASN A 13 136.87 167.59 REMARK 500 THR A 15 32.04 -82.96 REMARK 500 ARG A 16 -74.57 -67.79 REMARK 500 THR A 19 -106.91 -145.22 REMARK 500 TYR A 45 140.56 -174.04 REMARK 500 ASN A 56 43.81 -151.08 REMARK 500 LEU A 101 42.50 -94.98 REMARK 500 ASP A 133 60.91 61.47 REMARK 500 ASN A 134 12.82 53.41 REMARK 500 GLN A 138 98.11 -69.89 REMARK 500 GLN A 146 -149.72 -111.37 REMARK 500 GLN A 162 -74.78 -98.42 REMARK 500 LEU A 192 98.13 -68.57 REMARK 500 ASP A 202 49.92 -75.49 REMARK 500 SER A 244 -149.27 -126.16 REMARK 500 ASP A 247 87.46 -63.08 REMARK 500 ASN A 279 -73.56 -46.91 REMARK 500 ALA A 280 102.04 36.28 REMARK 500 LYS A 352 23.15 80.30 REMARK 500 THR A 369 27.56 -76.84 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 PHE A 17 ASN A 18 -149.00 REMARK 500 MET A 275 LYS A 276 146.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1371 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 217 OD2 REMARK 620 2 HIS A 219 NE2 100.6 REMARK 620 3 HIS A 251 ND1 112.3 91.3 REMARK 620 4 HOH A2057 O 108.6 131.8 110.9 REMARK 620 N 1 2 3 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 ZN A1371 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C5P A1372 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C5P A1373 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GPP A1374 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1W55 RELATED DB: PDB REMARK 900 STRUCTURE OF THE BIFUNCTIONAL ISPDF FROM CAMPYLOBACTER JEJUNI DBREF 1W57 A 1 371 UNP Q9PM68 ISDF_CAMJE 1 371 SEQRES 1 A 371 MET SER GLU MET SER LEU ILE MET LEU ALA ALA GLY ASN SEQRES 2 A 371 SER THR ARG PHE ASN THR LYS VAL LYS LYS GLN PHE LEU SEQRES 3 A 371 ARG LEU GLY ASN ASP PRO LEU TRP LEU TYR ALA THR LYS SEQRES 4 A 371 ASN LEU SER SER PHE TYR PRO PHE LYS LYS ILE VAL VAL SEQRES 5 A 371 THR SER SER ASN ILE THR TYR MET LYS LYS PHE THR LYS SEQRES 6 A 371 ASN TYR GLU PHE ILE GLU GLY GLY ASP THR ARG ALA GLU SEQRES 7 A 371 SER LEU LYS LYS ALA LEU GLU LEU ILE ASP SER GLU PHE SEQRES 8 A 371 VAL MET VAL SER ASP VAL ALA ARG VAL LEU VAL SER LYS SEQRES 9 A 371 ASN LEU PHE ASP ARG LEU ILE GLU ASN LEU ASP LYS ALA SEQRES 10 A 371 ASP CYS ILE THR PRO ALA LEU LYS VAL ALA ASP THR THR SEQRES 11 A 371 LEU PHE ASP ASN GLU ALA LEU GLN ARG GLU LYS ILE LYS SEQRES 12 A 371 LEU ILE GLN THR PRO GLN ILE SER LYS THR LYS LEU LEU SEQRES 13 A 371 LYS LYS ALA LEU ASP GLN ASN LEU GLU PHE THR ASP ASP SEQRES 14 A 371 SER THR ALA ILE ALA ALA MET GLY GLY LYS ILE TRP PHE SEQRES 15 A 371 VAL GLU GLY GLU GLU ASN ALA ARG LYS LEU THR PHE LYS SEQRES 16 A 371 GLU ASP LEU LYS LYS LEU ASP LEU PRO THR PRO SER PHE SEQRES 17 A 371 GLU ILE PHE THR GLY ASN GLY PHE ASP VAL HIS GLU PHE SEQRES 18 A 371 GLY GLU ASN ARG PRO LEU LEU LEU ALA GLY VAL GLN ILE SEQRES 19 A 371 HIS PRO THR MET GLY LEU LYS ALA HIS SER ASP GLY ASP SEQRES 20 A 371 VAL LEU ALA HIS SER LEU THR ASP ALA ILE LEU GLY ALA SEQRES 21 A 371 ALA GLY LEU GLY ASP ILE GLY GLU LEU TYR PRO ASP THR SEQRES 22 A 371 ASP MET LYS PHE LYS ASN ALA ASN SER MET GLU LEU LEU SEQRES 23 A 371 LYS GLN ALA TYR ASP LYS VAL ARG GLU ILE GLY PHE GLU SEQRES 24 A 371 LEU ILE ASN ILE ASP ILE CYS VAL MET ALA GLN SER PRO SEQRES 25 A 371 LYS LEU LYS ASP PHE LYS GLN ALA MET GLN SER ASN ILE SEQRES 26 A 371 ALA HIS THR LEU ASP LEU ASP GLU PHE ARG ILE ASN VAL SEQRES 27 A 371 LYS ALA THR THR THR GLU LYS LEU GLY PHE ILE GLY ARG SEQRES 28 A 371 LYS GLU GLY MET ALA VAL LEU SER SER VAL ASN LEU LYS SEQRES 29 A 371 TYR PHE ASP TRP THR ARG LEU HET ZN A1371 1 HET C5P A1372 21 HET C5P A1373 21 HET GPP A1374 19 HETNAM ZN ZINC ION HETNAM C5P CYTIDINE-5'-MONOPHOSPHATE HETNAM GPP GERANYL DIPHOSPHATE FORMUL 2 ZN ZN 2+ FORMUL 3 C5P 2(C9 H14 N3 O8 P) FORMUL 5 GPP C10 H20 O7 P2 FORMUL 6 HOH *57(H2 O) HELIX 1 1 LYS A 22 PHE A 25 5 4 HELIX 2 2 LEU A 33 SER A 43 1 11 HELIX 3 3 ASN A 56 LYS A 62 1 7 HELIX 4 4 THR A 75 GLU A 85 1 11 HELIX 5 5 SER A 103 GLU A 112 1 10 HELIX 6 6 GLN A 138 ILE A 142 5 5 HELIX 7 7 THR A 153 LEU A 160 1 8 HELIX 8 8 ASP A 168 ALA A 175 1 8 HELIX 9 9 GLU A 186 ARG A 190 5 5 HELIX 10 10 PHE A 194 LEU A 201 5 8 HELIX 11 11 ASP A 247 ALA A 261 1 15 HELIX 12 12 ASP A 265 TYR A 270 1 6 HELIX 13 13 ASN A 281 ILE A 296 1 16 HELIX 14 14 LEU A 314 ASP A 316 5 3 HELIX 15 15 PHE A 317 ASP A 330 1 14 HELIX 16 16 ASP A 332 PHE A 334 5 3 HELIX 17 17 LEU A 346 LYS A 352 1 7 SHEET 1 AA 7 GLU A 68 GLU A 71 0 SHEET 2 AA 7 ILE A 50 SER A 54 1 O ILE A 50 N GLU A 68 SHEET 3 AA 7 MET A 4 LEU A 9 1 O LEU A 6 N VAL A 51 SHEET 4 AA 7 PHE A 91 ASP A 96 1 O PHE A 91 N SER A 5 SHEET 5 AA 7 GLN A 149 LYS A 152 -1 O GLN A 149 N VAL A 94 SHEET 6 AA 7 CYS A 119 LEU A 124 -1 O ILE A 120 N ILE A 150 SHEET 7 AA 7 ILE A 180 GLU A 184 1 O TRP A 181 N THR A 121 SHEET 1 AB 7 GLU A 68 GLU A 71 0 SHEET 2 AB 7 ILE A 50 SER A 54 1 O ILE A 50 N GLU A 68 SHEET 3 AB 7 MET A 4 LEU A 9 1 O LEU A 6 N VAL A 51 SHEET 4 AB 7 PHE A 91 ASP A 96 1 O PHE A 91 N SER A 5 SHEET 5 AB 7 GLN A 149 LYS A 152 -1 O GLN A 149 N VAL A 94 SHEET 6 AB 7 CYS A 119 LEU A 124 -1 O ILE A 120 N ILE A 150 SHEET 7 AB 7 LEU A 144 ILE A 145 -1 O LEU A 144 N LEU A 124 SHEET 1 AC 2 ARG A 27 LEU A 28 0 SHEET 2 AC 2 ASP A 31 PRO A 32 -1 O ASP A 31 N LEU A 28 SHEET 1 AD 2 THR A 130 LEU A 131 0 SHEET 2 AD 2 ALA A 136 LEU A 137 -1 N LEU A 137 O THR A 130 SHEET 1 AE 4 ILE A 210 GLU A 220 0 SHEET 2 AE 4 GLY A 354 TYR A 365 -1 O MET A 355 N HIS A 219 SHEET 3 AE 4 PHE A 298 MET A 308 -1 O GLU A 299 N LYS A 364 SHEET 4 AE 4 ILE A 336 THR A 341 1 O ASN A 337 N ILE A 305 SHEET 1 AF 2 GLU A 223 ASN A 224 0 SHEET 2 AF 2 MET A 238 GLY A 239 -1 O GLY A 239 N GLU A 223 SHEET 1 AG 2 LEU A 227 LEU A 229 0 SHEET 2 AG 2 VAL A 232 HIS A 235 -1 O VAL A 232 N LEU A 229 LINK OD2 ASP A 217 ZN ZN A1371 1555 1555 2.04 LINK NE2 HIS A 219 ZN ZN A1371 1555 1555 2.35 LINK ND1 HIS A 251 ZN ZN A1371 1555 1555 2.50 LINK ZN ZN A1371 O HOH A2057 1555 1555 2.59 CISPEP 1 THR A 147 PRO A 148 0 2.50 CISPEP 2 SER A 311 PRO A 312 0 -4.16 SITE 1 AC1 5 ASP A 217 HIS A 219 HIS A 243 HIS A 251 SITE 2 AC1 5 HOH A2057 SITE 1 AC2 18 ASP A 217 ASP A 265 ILE A 266 GLY A 267 SITE 2 AC2 18 GLU A 268 ALA A 309 PRO A 312 LYS A 313 SITE 3 AC2 18 LEU A 314 LYS A 315 LYS A 318 ALA A 340 SITE 4 AC2 18 THR A 341 THR A 342 GLU A 344 HOH A2041 SITE 5 AC2 18 HOH A2055 HOH A2057 SITE 1 AC3 14 LEU A 9 ALA A 10 ALA A 11 THR A 53 SITE 2 AC3 14 GLY A 73 ASP A 74 THR A 75 ARG A 76 SITE 3 AC3 14 SER A 79 ASP A 96 VAL A 97 ALA A 98 SITE 4 AC3 14 ARG A 139 LYS A 191 SITE 1 AC4 5 PHE A 216 MET A 308 GLY A 347 PHE A 348 SITE 2 AC4 5 ARG A 351 CRYST1 107.760 107.760 161.004 90.00 90.00 120.00 P 63 2 2 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 0.009280 0.005358 0.000000 0.00000 SCALE2 0.000000 0.010715 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006211 0.00000