HEADER TRANSFERASE 10-SEP-02 1H3M TITLE STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHETASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.7.7.60; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 469008; SOURCE 4 STRAIN: BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET 15B KEYWDS TRANSFERASE, ISOPRENOID, SYNTHETASE EXPDTA X-RAY DIFFRACTION AUTHOR L.E.KEMP,C.S.BOND,W.N.HUNTER REVDAT 3 13-DEC-23 1H3M 1 REMARK REVDAT 2 24-FEB-09 1H3M 1 VERSN REVDAT 1 01-AUG-03 1H3M 0 JRNL AUTH L.E.KEMP,C.S.BOND,W.N.HUNTER JRNL TITL STRUCTURE OF A TETRAGONAL CRYSTAL FORM OF ESCHERICHIA COLI JRNL TITL 2 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 59 607 2003 JRNL REFN ISSN 0907-4449 JRNL PMID 12595740 JRNL DOI 10.1107/S090744490202365X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.B.RICHARD,M.E.BOWMAN,W.KWIATKOWSKI,C.CHOW,A.M.LILLO, REMARK 1 AUTH 2 D.E.CANE,J.P.NOEL REMARK 1 TITL STRUCTURE OF CDP-ME SYNTHETASE IN MEVALONATE-INDEPENDENT REMARK 1 TITL 2 ISOPRENOID BIOSYNTHESIS REMARK 1 REF NAT.STRUCT.BIOL. V. 8 641 2001 REMARK 1 REFN ISSN 1072-8368 REMARK 1 PMID 11427897 REMARK 1 DOI 10.1038/89691 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.19 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 18554 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) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.333 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1000 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1294 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.4150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3307 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 86 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.21000 REMARK 3 B22 (A**2) : 1.21000 REMARK 3 B33 (A**2) : -2.42000 REMARK 3 B12 (A**2) : 0.00000 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): 0.480 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.348 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.242 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.244 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.883 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3377 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4601 ; 1.668 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 429 ; 7.195 ; 5.000 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): 538 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2574 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1599 ; 0.229 ; 0.200 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): 170 ; 0.170 ; 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): 44 ; 0.280 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.267 ; 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): 2162 ; 0.944 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3470 ; 1.737 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1215 ; 2.350 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1131 ; 3.784 ; 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 WITH 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: NULL REMARK 4 REMARK 4 1H3M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-SEP-02. REMARK 100 THE DEPOSITION ID IS D_1290011398. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.00 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) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19619 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.27000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1INI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SULPHATE, 0.1M SODIUM REMARK 280 ACETATE, PH 5.6, 25% PEG 4000, PH 6.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 87.78100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.80200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.80200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 43.89050 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.80200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.80200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 131.67150 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.80200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.80200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 43.89050 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.80200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.80200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 131.67150 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 87.78100 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED MUTATION ALA 91 THR 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 ALA A 2 REMARK 465 THR A 3 REMARK 465 THR A 4 REMARK 465 HIS A 5 REMARK 465 GLY A 16 REMARK 465 PHE A 17 REMARK 465 GLY A 18 REMARK 465 ARG A 19 REMARK 465 ARG A 20 REMARK 465 MET A 21 REMARK 465 GLN A 22 REMARK 465 THR A 23 REMARK 465 GLU A 24 REMARK 465 THR A 230 REMARK 465 ILE A 231 REMARK 465 HIS A 232 REMARK 465 GLN A 233 REMARK 465 GLU A 234 REMARK 465 ASN A 235 REMARK 465 THR A 236 REMARK 465 ALA B 2 REMARK 465 THR B 3 REMARK 465 THR B 4 REMARK 465 PHE B 17 REMARK 465 GLY B 18 REMARK 465 ARG B 19 REMARK 465 ARG B 20 REMARK 465 MET B 21 REMARK 465 GLN B 22 REMARK 465 THR B 23 REMARK 465 THR B 230 REMARK 465 ILE B 231 REMARK 465 HIS B 232 REMARK 465 GLN B 233 REMARK 465 GLU B 234 REMARK 465 ASN B 235 REMARK 465 THR B 236 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 100 CG CD OE1 NE2 REMARK 480 GLU A 172 CG CD OE1 OE2 REMARK 480 GLU B 24 CG CD OE1 OE2 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 NE2 GLN A 28 O HOH A 2005 2.15 REMARK 500 O ASP A 156 NH2 ARG B 143 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 B 24 CB GLU B 24 CG 0.134 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 80 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP A 98 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 210 CB - CG - OD2 ANGL. DEV. = 6.5 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 ASP A 62 110.13 -32.82 REMARK 500 SER A 124 3.89 -64.04 REMARK 500 LEU A 164 -167.62 -117.57 REMARK 500 THR A 189 -86.77 -106.59 REMARK 500 CYS B 25 120.06 -12.12 REMARK 500 PRO B 69 -11.11 -42.01 REMARK 500 ASN B 72 16.68 -145.75 REMARK 500 THR B 189 -65.48 -108.69 REMARK 500 THR B 215 -76.79 -127.88 REMARK 500 ARG B 216 168.46 -43.88 REMARK 500 REMARK 500 REMARK: NULL 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 CL A1230 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B1230 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B1231 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B1232 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE N2P A1231 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1I52 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C -METHYLERYTHRITOL (CDP- REMARK 900 ME) SYNTHASE (YGBP) INVOLVED INMEVALONATE INDEPENDENT ISOPRENOID REMARK 900 BIOSYNTHESIS REMARK 900 RELATED ID: 1INI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C -METHYLERYTHRITOL (CDP- REMARK 900 ME) SYNTHETASE (YGBP) INVOLVED INMEVALONATE INDEPENDENT ISOPRENOID REMARK 900 BIOSYNTHESIS, COMPLEXEDWITH CDP-ME AND MG2+ REMARK 900 RELATED ID: 1INJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE APO FORM OF 4- DIPHOSPHOCYTIDYL-2-C- REMARK 900 METHYLERYTHRITOL (CDP-ME ) SYNTHETASE (YGBP) INVOLVED INMEVALONATE REMARK 900 INDEPENDENT ISOPRENOID BIOSYNTHESIS DBREF 1H3M A 2 236 UNP Q46893 ISPD_ECOLI 1 235 DBREF 1H3M B 2 236 UNP Q46893 ISPD_ECOLI 1 235 SEQADV 1H3M THR A 91 UNP Q46893 ALA 90 ENGINEERED MUTATION SEQADV 1H3M THR B 91 UNP Q46893 ALA 90 ENGINEERED MUTATION SEQRES 1 A 235 ALA THR THR HIS LEU ASP VAL CYS ALA VAL VAL PRO ALA SEQRES 2 A 235 ALA GLY PHE GLY ARG ARG MET GLN THR GLU CYS PRO LYS SEQRES 3 A 235 GLN TYR LEU SER ILE GLY ASN GLN THR ILE LEU GLU HIS SEQRES 4 A 235 SER VAL HIS ALA LEU LEU ALA HIS PRO ARG VAL LYS ARG SEQRES 5 A 235 VAL VAL ILE ALA ILE SER PRO GLY ASP SER ARG PHE ALA SEQRES 6 A 235 GLN LEU PRO LEU ALA ASN HIS PRO GLN ILE THR VAL VAL SEQRES 7 A 235 ASP GLY GLY ASP GLU ARG ALA ASP SER VAL LEU THR GLY SEQRES 8 A 235 LEU LYS ALA ALA GLY ASP ALA GLN TRP VAL LEU VAL HIS SEQRES 9 A 235 ASP ALA ALA ARG PRO CYS LEU HIS GLN ASP ASP LEU ALA SEQRES 10 A 235 ARG LEU LEU ALA LEU SER GLU THR SER ARG THR GLY GLY SEQRES 11 A 235 ILE LEU ALA ALA PRO VAL ARG ASP THR MET LYS ARG ALA SEQRES 12 A 235 GLU PRO GLY LYS ASN ALA ILE ALA HIS THR VAL ASP ARG SEQRES 13 A 235 ASN GLY LEU TRP HIS ALA LEU THR PRO GLN PHE PHE PRO SEQRES 14 A 235 ARG GLU LEU LEU HIS ASP CYS LEU THR ARG ALA LEU ASN SEQRES 15 A 235 GLU GLY ALA THR ILE THR ASP GLU ALA SER ALA LEU GLU SEQRES 16 A 235 TYR CYS GLY PHE HIS PRO GLN LEU VAL GLU GLY ARG ALA SEQRES 17 A 235 ASP ASN ILE LYS VAL THR ARG PRO GLU ASP LEU ALA LEU SEQRES 18 A 235 ALA GLU PHE TYR LEU THR ARG THR ILE HIS GLN GLU ASN SEQRES 19 A 235 THR SEQRES 1 B 235 ALA THR THR HIS LEU ASP VAL CYS ALA VAL VAL PRO ALA SEQRES 2 B 235 ALA GLY PHE GLY ARG ARG MET GLN THR GLU CYS PRO LYS SEQRES 3 B 235 GLN TYR LEU SER ILE GLY ASN GLN THR ILE LEU GLU HIS SEQRES 4 B 235 SER VAL HIS ALA LEU LEU ALA HIS PRO ARG VAL LYS ARG SEQRES 5 B 235 VAL VAL ILE ALA ILE SER PRO GLY ASP SER ARG PHE ALA SEQRES 6 B 235 GLN LEU PRO LEU ALA ASN HIS PRO GLN ILE THR VAL VAL SEQRES 7 B 235 ASP GLY GLY ASP GLU ARG ALA ASP SER VAL LEU THR GLY SEQRES 8 B 235 LEU LYS ALA ALA GLY ASP ALA GLN TRP VAL LEU VAL HIS SEQRES 9 B 235 ASP ALA ALA ARG PRO CYS LEU HIS GLN ASP ASP LEU ALA SEQRES 10 B 235 ARG LEU LEU ALA LEU SER GLU THR SER ARG THR GLY GLY SEQRES 11 B 235 ILE LEU ALA ALA PRO VAL ARG ASP THR MET LYS ARG ALA SEQRES 12 B 235 GLU PRO GLY LYS ASN ALA ILE ALA HIS THR VAL ASP ARG SEQRES 13 B 235 ASN GLY LEU TRP HIS ALA LEU THR PRO GLN PHE PHE PRO SEQRES 14 B 235 ARG GLU LEU LEU HIS ASP CYS LEU THR ARG ALA LEU ASN SEQRES 15 B 235 GLU GLY ALA THR ILE THR ASP GLU ALA SER ALA LEU GLU SEQRES 16 B 235 TYR CYS GLY PHE HIS PRO GLN LEU VAL GLU GLY ARG ALA SEQRES 17 B 235 ASP ASN ILE LYS VAL THR ARG PRO GLU ASP LEU ALA LEU SEQRES 18 B 235 ALA GLU PHE TYR LEU THR ARG THR ILE HIS GLN GLU ASN SEQRES 19 B 235 THR HET CL A1230 1 HET N2P A1231 7 HET CL A1232 1 HET CL B1230 1 HET CL B1231 1 HET CL B1232 1 HETNAM CL CHLORIDE ION HETNAM N2P PENTANE-1,5-DIAMINE FORMUL 3 CL 5(CL 1-) FORMUL 4 N2P C5 H14 N2 FORMUL 9 HOH *86(H2 O) HELIX 1 1 PRO A 26 TYR A 29 5 4 HELIX 2 2 ILE A 37 HIS A 48 1 12 HELIX 3 3 LEU A 68 HIS A 73 5 6 HELIX 4 4 GLU A 84 ALA A 95 1 12 HELIX 5 5 HIS A 113 ALA A 122 1 10 HELIX 6 6 LEU A 123 THR A 126 5 4 HELIX 7 7 ARG A 171 GLY A 185 1 15 HELIX 8 8 ASP A 190 CYS A 198 1 9 HELIX 9 9 ARG A 216 ARG A 229 1 14 HELIX 10 10 PRO B 26 TYR B 29 5 4 HELIX 11 11 ILE B 37 HIS B 48 1 12 HELIX 12 12 ARG B 64 LEU B 68 5 5 HELIX 13 13 LEU B 68 HIS B 73 5 6 HELIX 14 14 GLU B 84 ALA B 95 1 12 HELIX 15 15 HIS B 113 ALA B 122 1 10 HELIX 16 16 LEU B 123 THR B 126 5 4 HELIX 17 17 ARG B 171 GLU B 184 1 14 HELIX 18 18 ASP B 190 CYS B 198 1 9 HELIX 19 19 GLU B 218 ARG B 229 1 12 SHEET 1 AA 7 ILE A 76 ASP A 80 0 SHEET 2 AA 7 VAL A 51 ILE A 58 1 O VAL A 54 N THR A 77 SHEET 3 AA 7 VAL A 8 ALA A 14 1 O VAL A 8 N LYS A 52 SHEET 4 AA 7 TRP A 101 VAL A 104 1 O TRP A 101 N CYS A 9 SHEET 5 AA 7 LEU A 160 PRO A 170 -1 O GLN A 167 N VAL A 104 SHEET 6 AA 7 GLY A 131 PRO A 136 -1 O GLY A 131 N PHE A 168 SHEET 7 AA 7 GLN A 203 GLU A 206 1 O GLN A 203 N ILE A 132 SHEET 1 AB 7 ILE A 76 ASP A 80 0 SHEET 2 AB 7 VAL A 51 ILE A 58 1 O VAL A 54 N THR A 77 SHEET 3 AB 7 VAL A 8 ALA A 14 1 O VAL A 8 N LYS A 52 SHEET 4 AB 7 TRP A 101 VAL A 104 1 O TRP A 101 N CYS A 9 SHEET 5 AB 7 LEU A 160 PRO A 170 -1 O GLN A 167 N VAL A 104 SHEET 6 AB 7 MET B 141 ALA B 144 -1 O LYS B 142 N TRP A 161 SHEET 7 AB 7 ILE B 151 VAL B 155 -1 N ALA B 152 O ARG B 143 SHEET 1 AC 2 SER A 31 ILE A 32 0 SHEET 2 AC 2 GLN A 35 THR A 36 -1 O GLN A 35 N ILE A 32 SHEET 1 AD 7 ILE A 151 VAL A 155 0 SHEET 2 AD 7 THR A 140 ALA A 144 -1 O MET A 141 N VAL A 155 SHEET 3 AD 7 LEU B 160 PRO B 170 -1 O TRP B 161 N LYS A 142 SHEET 4 AD 7 TRP B 101 VAL B 104 -1 O VAL B 102 N PHE B 169 SHEET 5 AD 7 VAL B 8 ALA B 14 1 O CYS B 9 N LEU B 103 SHEET 6 AD 7 VAL B 51 ILE B 58 1 O ARG B 53 N ALA B 10 SHEET 7 AD 7 ILE B 76 ASP B 80 1 O THR B 77 N ILE B 56 SHEET 1 AE 5 ILE A 151 VAL A 155 0 SHEET 2 AE 5 THR A 140 ALA A 144 -1 O MET A 141 N VAL A 155 SHEET 3 AE 5 LEU B 160 PRO B 170 -1 O TRP B 161 N LYS A 142 SHEET 4 AE 5 GLY B 131 PRO B 136 -1 O GLY B 131 N PHE B 168 SHEET 5 AE 5 GLN B 203 GLU B 206 1 O GLN B 203 N ILE B 132 SHEET 1 BA 2 SER B 31 ILE B 32 0 SHEET 2 BA 2 GLN B 35 THR B 36 -1 O GLN B 35 N ILE B 32 SSBOND 1 CYS A 25 CYS A 25 1555 7644 2.87 CISPEP 1 THR A 165 PRO A 166 0 11.94 CISPEP 2 THR B 165 PRO B 166 0 4.24 SITE 1 AC1 2 ARG A 138 HIS A 162 SITE 1 AC2 3 HIS A 162 ASP B 139 HIS B 162 SITE 1 AC3 5 HIS B 48 ARG B 50 HOH B2011 HOH B2012 SITE 2 AC3 5 HOH B2013 SITE 1 AC4 2 GLN B 114 HOH B2027 SITE 1 AC5 6 ARG A 143 HIS A 153 HOH A2041 ARG B 143 SITE 2 AC5 6 HIS B 153 VAL B 155 CRYST1 73.604 73.604 175.562 90.00 90.00 90.00 P 41 21 2 16 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 0.013586 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013586 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005696 0.00000 MTRIX1 1 -0.752795 -0.094528 -0.651433 96.89400 1 MTRIX2 1 -0.071976 -0.971881 0.224203 105.43300 1 MTRIX3 1 -0.654309 0.215666 0.724823 23.33700 1