HEADER LYASE 05-JAN-09 3FPI TITLE CRYSTAL STRUCTURE OF 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE TITLE 2 SYNTHASE ISPF COMPLEXED WITH CYTIDINE TRIPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MECPS, MECDP-SYNTHASE; COMPND 5 EC: 4.6.1.12; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA PESTIS; SOURCE 3 ORGANISM_TAXID: 214092; SOURCE 4 STRAIN: CO92; SOURCE 5 GENE: ISPF, Y0829, YPO3360, YPTB0771, YP_0327; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG19C KEYWDS CSGID, ALPHA-BETA SANDWICH, ISOPRENE BIOSYNTHESIS, LYASE, METAL- KEYWDS 2 BINDING, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS OF NATIONAL KEYWDS 3 INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES, CENTER FOR STRUCTURAL KEYWDS 4 GENOMICS OF INFECTIOUS DISEASES EXPDTA X-RAY DIFFRACTION AUTHOR Y.KIM,N.MALTSEVA,J.STAM,W.F.ANDERSON,A.JOACHIMIAK,CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS OF INFECTIOUS DISEASES (CSGID) REVDAT 3 22-NOV-23 3FPI 1 REMARK REVDAT 2 06-SEP-23 3FPI 1 REMARK SEQADV LINK REVDAT 1 03-FEB-09 3FPI 0 JRNL AUTH Y.KIM,N.MALTSEVA,J.STAM,W.F.ANDERSON,A.JOACHIMIAK JRNL TITL CRYSTAL STRUCTURE OF 2-C-METHYL-D-ERYTHRITOL JRNL TITL 2 2,4-CYCLODIPHOSPHATE SYNTHASE ISPF COMPLEXED WITH CYTIDINE JRNL TITL 3 TRIPHOSPHATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0053 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 12006 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) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 616 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) : 2.81 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.88 REMARK 3 REFLECTION IN BIN (WORKING SET) : 869 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.49 REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 REMARK 3 BIN FREE R VALUE SET COUNT : 44 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1197 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 76 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 83.86 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.78 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): 0.219 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.190 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.129 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.153 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1284 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1746 ; 1.745 ; 2.017 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 164 ; 8.492 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 52 ;38.572 ;24.231 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 206 ;21.045 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;17.763 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 194 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 948 ; 0.006 ; 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): 803 ; 0.901 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1277 ; 1.797 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 481 ; 2.702 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 469 ; 4.710 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -2 A 160 REMARK 3 ORIGIN FOR THE GROUP (A): 27.0826 8.7153 11.2289 REMARK 3 T TENSOR REMARK 3 T11: 0.0315 T22: 0.0298 REMARK 3 T33: 0.0806 T12: 0.0209 REMARK 3 T13: 0.0396 T23: 0.0236 REMARK 3 L TENSOR REMARK 3 L11: 1.5563 L22: 1.8095 REMARK 3 L33: 1.8703 L12: 0.1711 REMARK 3 L13: -0.4290 L23: 0.4238 REMARK 3 S TENSOR REMARK 3 S11: -0.0144 S12: -0.0939 S13: -0.1863 REMARK 3 S21: -0.1066 S22: -0.0184 S23: -0.1889 REMARK 3 S31: 0.0791 S32: 0.1869 S33: 0.0328 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: NULL REMARK 4 REMARK 4 3FPI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000050880. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-3 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12751 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 34.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.70 REMARK 200 R MERGE FOR SHELL (I) : 0.96800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD/MR REMARK 200 SOFTWARE USED: HKL-3000, MLPHARE, SHELXD, BALBES, DM, RESOLVE REMARK 200 STARTING MODEL: 3F6M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M AMMONIUM SULFATE, 0.1M HEPES PH REMARK 280 7.0, 0.5 % W/V PEG 8000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X,-Y+1/2,Z REMARK 290 15555 -X+1/2,Y,-Z REMARK 290 16555 X,-Y,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z,-X,-Y+1/2 REMARK 290 19555 -Z,-X+1/2,Y REMARK 290 20555 -Z+1/2,X,-Y REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z,-X REMARK 290 23555 Y,-Z,-X+1/2 REMARK 290 24555 -Y,-Z+1/2,X 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 72.81950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.81950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 72.81950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.81950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 72.81950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 72.81950 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 72.81950 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 72.81950 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 72.81950 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 72.81950 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 72.81950 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 72.81950 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 72.81950 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 72.81950 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 72.81950 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 72.81950 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 72.81950 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 72.81950 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 72.81950 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 72.81950 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 72.81950 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 72.81950 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 72.81950 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 72.81950 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 72.81950 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 72.81950 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 72.81950 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 72.81950 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 72.81950 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 72.81950 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 72.81950 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 72.81950 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 72.81950 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 72.81950 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 72.81950 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 72.81950 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 0.00000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.0 KCAL/MOL 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 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 3 1.000000 0.000000 0.000000 0.00000 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 CL CL A 165 LIES ON A SPECIAL POSITION. REMARK 375 MG MG A 168 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 244 LIES ON A SPECIAL POSITION. 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 SER A -2 REMARK 465 GLU A 160 REMARK 465 GLN A 161 REMARK 465 GLY A 162 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 PRO A 19 -169.71 -59.97 REMARK 500 ASP A 38 -7.56 -55.95 REMARK 500 PRO A 64 128.34 -35.34 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 16 SER A 17 -145.95 REMARK 500 GLY A 18 PRO A 19 -113.96 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 MG A 167 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 37 OG REMARK 620 2 CTP A 163 O3G 146.6 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 CTP A 163 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A 164 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 165 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 166 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 167 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 168 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3F6M RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE REMARK 900 SYNTHASE ISPF FROM YERSINIA PESTIS REMARK 900 RELATED ID: IDP00520 RELATED DB: TARGETDB DBREF 3FPI A 1 162 UNP Q66EC2 ISPF_YERPE 1 162 SEQADV 3FPI SER A -2 UNP Q66EC2 EXPRESSION TAG SEQADV 3FPI ASN A -1 UNP Q66EC2 EXPRESSION TAG SEQADV 3FPI ALA A 0 UNP Q66EC2 EXPRESSION TAG SEQRES 1 A 165 SER ASN ALA MSE ARG ILE GLY HIS GLY PHE ASP VAL HIS SEQRES 2 A 165 LYS PHE GLY GLU ASN GLY SER GLY PRO LEU ILE ILE GLY SEQRES 3 A 165 GLY VAL ARG ILE PRO TYR GLU LYS GLY LEU LEU ALA HIS SEQRES 4 A 165 SER ASP GLY ASP VAL ALA LEU HIS ALA ALA THR ASP ALA SEQRES 5 A 165 LEU LEU GLY ALA ALA ALA LEU GLY ASP ILE GLY LYS LEU SEQRES 6 A 165 PHE PRO ASP THR ASP PRO ALA PHE LYS GLY ALA ASP SER SEQRES 7 A 165 ARG GLY LEU LEU ARG GLU ALA TYR ARG ARG ILE LEU ALA SEQRES 8 A 165 LYS GLY TYR LYS LEU GLY ASN LEU ASP ILE THR ILE ILE SEQRES 9 A 165 ALA GLN ALA PRO LYS MSE ALA PRO HIS ILE PRO GLN MSE SEQRES 10 A 165 ARG VAL ASN LEU ALA GLU ASP LEU GLN CYS HIS MSE ASP SEQRES 11 A 165 ASP ILE ASN VAL LYS ALA THR THR THR GLU GLN LEU GLY SEQRES 12 A 165 PHE THR GLY ARG GLY GLU GLY ILE ALA CYS GLU ALA VAL SEQRES 13 A 165 VAL LEU LEU VAL ASN VAL GLU GLN GLY MODRES 3FPI MSE A 1 MET SELENOMETHIONINE MODRES 3FPI MSE A 107 MET SELENOMETHIONINE MODRES 3FPI MSE A 114 MET SELENOMETHIONINE MODRES 3FPI MSE A 126 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 107 8 HET MSE A 114 8 HET MSE A 126 8 HET CTP A 163 29 HET EPE A 164 15 HET CL A 165 1 HET SO4 A 166 5 HET MG A 167 1 HET MG A 168 1 HETNAM MSE SELENOMETHIONINE HETNAM CTP CYTIDINE-5'-TRIPHOSPHATE HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION HETSYN EPE HEPES FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 CTP C9 H16 N3 O14 P3 FORMUL 3 EPE C8 H18 N2 O4 S FORMUL 4 CL CL 1- FORMUL 5 SO4 O4 S 2- FORMUL 6 MG 2(MG 2+) FORMUL 8 HOH *76(H2 O) HELIX 1 1 ASP A 40 ALA A 54 1 15 HELIX 2 2 ASP A 58 PHE A 63 1 6 HELIX 3 3 ASP A 67 LYS A 71 5 5 HELIX 4 4 ASP A 74 LYS A 89 1 16 HELIX 5 5 MSE A 107 PRO A 109 5 3 HELIX 6 6 HIS A 110 LEU A 122 1 13 HELIX 7 7 HIS A 125 ASP A 127 5 3 HELIX 8 8 LEU A 139 ARG A 144 1 6 SHEET 1 A 4 MSE A 1 LYS A 11 0 SHEET 2 A 4 GLY A 147 ASN A 158 -1 O LEU A 156 N ARG A 2 SHEET 3 A 4 TYR A 91 ILE A 101 -1 N ILE A 101 O ALA A 149 SHEET 4 A 4 ILE A 129 THR A 134 1 O LYS A 132 N ILE A 100 SHEET 1 B 2 LEU A 20 ILE A 22 0 SHEET 2 B 2 VAL A 25 ILE A 27 -1 O VAL A 25 N ILE A 22 LINK C ALA A 0 N MSE A 1 1555 1555 1.34 LINK C MSE A 1 N ARG A 2 1555 1555 1.32 LINK C LYS A 106 N MSE A 107 1555 1555 1.34 LINK C MSE A 107 N ALA A 108 1555 1555 1.32 LINK C GLN A 113 N MSE A 114 1555 1555 1.33 LINK C MSE A 114 N ARG A 115 1555 1555 1.33 LINK C HIS A 125 N MSE A 126 1555 1555 1.32 LINK C MSE A 126 N ASP A 127 1555 1555 1.32 LINK OG SER A 37 MG MG A 167 1555 1555 2.46 LINK O3G CTP A 163 MG MG A 167 1555 1555 2.42 CISPEP 1 ALA A 104 PRO A 105 0 2.21 SITE 1 AC1 21 ASP A 8 HIS A 10 ALA A 35 HIS A 36 SITE 2 AC1 21 ASP A 58 GLY A 60 ASP A 65 ALA A 102 SITE 3 AC1 21 PRO A 105 LYS A 106 MSE A 107 ALA A 108 SITE 4 AC1 21 ALA A 133 THR A 134 THR A 135 GLU A 137 SITE 5 AC1 21 MG A 167 HOH A 175 HOH A 178 HOH A 196 SITE 6 AC1 21 HOH A 235 SITE 1 AC2 9 PRO A 19 ARG A 26 PRO A 28 TYR A 29 SITE 2 AC2 9 LYS A 61 ARG A 115 MSE A 126 ASP A 127 SITE 3 AC2 9 HOH A 234 SITE 1 AC3 2 ARG A 144 MG A 168 SITE 1 AC4 1 ARG A 80 SITE 1 AC5 6 ALA A 35 HIS A 36 SER A 37 GLY A 39 SITE 2 AC5 6 HIS A 44 CTP A 163 SITE 1 AC6 2 CL A 165 HOH A 230 CRYST1 145.639 145.639 145.639 90.00 90.00 90.00 I 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 0.006866 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006866 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006866 0.00000