PDB Short entry for 2VF6 HEADER TRANSFERASE 31-OCT-07 2VF6 TITLE HUMAN FDPS SYNTHASE IN COMPLEX WITH MINODRONATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FARNESYL PYROPHOSPHATE SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FPP SYNTHETASE, FPS, FARNESYL DIPHOSPHATE SYNTHETASE, COMPND 5 DIMETHYLALLYLTRANSTRANSFERASE; COMPND 6 EC: 2.5.1.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET15 DERIVATIVE; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBR KEYWDS SGC, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, TRANS- KEYWDS 2 PRENYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.G.EVDOKIMOV,B.L.BARNETT,F.H.EBETINO,M.POKROSS REVDAT 4 13-DEC-23 2VF6 1 LINK REVDAT 3 27-FEB-19 2VF6 1 REMARK REVDAT 2 24-FEB-09 2VF6 1 VERSN REVDAT 1 06-NOV-07 2VF6 0 JRNL AUTH A.G.EVDOKIMOV,B.L.BARNETT,F.H.EBETINO,M.POKROSS JRNL TITL HUMAN FDPS SYNTHASE IN COMPLEX WITH NOVEL INHIBITOR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 78.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 23948 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1288 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1701 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2460 REMARK 3 BIN FREE R VALUE SET COUNT : 82 REMARK 3 BIN FREE R VALUE : 0.3270 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2727 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 171 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.96000 REMARK 3 B22 (A**2) : -1.96000 REMARK 3 B33 (A**2) : 3.92000 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): 0.212 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.196 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.147 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.642 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2853 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3879 ; 1.117 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 347 ;11.038 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 143 ;39.259 ;24.825 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 501 ;18.642 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;22.088 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 421 ; 0.240 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2171 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1488 ; 0.248 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1996 ; 0.326 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 157 ; 0.289 ; 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): 55 ; 0.227 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.196 ; 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): 1737 ; 2.401 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2733 ; 3.528 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1287 ; 5.426 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1140 ; 7.476 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2VF6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-OCT-07. REMARK 100 THE DEPOSITION ID IS D_1290034287. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : CRYSTAL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25378 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 74.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.2200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.31000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.570 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 2RAH REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SULFATE, 15% REMARK 280 ISOPROPANOL, 15% ETHYLENE GLYCOL, 0.1M SODIUM ACETATE PH 4.5, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 298K, PH 4.6 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 34.52950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 55.60350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 55.60350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.26475 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 55.60350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 55.60350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 51.79425 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 55.60350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.60350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.26475 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 55.60350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.60350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 51.79425 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 34.52950 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 4430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.5 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 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 34.52950 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 -24 REMARK 465 GLY A -23 REMARK 465 SER A -22 REMARK 465 SER A -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 SER A -14 REMARK 465 SER A -13 REMARK 465 GLY A -12 REMARK 465 ARG A -11 REMARK 465 GLU A -10 REMARK 465 ASN A -9 REMARK 465 LEU A -8 REMARK 465 TYR A -7 REMARK 465 PHE A -6 REMARK 465 GLN A -5 REMARK 465 GLY A -4 REMARK 465 HIS A -3 REMARK 465 MET A -2 REMARK 465 GLY A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 GLY A 3 REMARK 465 ASP A 4 REMARK 465 GLN A 5 REMARK 465 ASN A 6 REMARK 465 SER A 7 REMARK 465 ASP A 8 REMARK 465 ASP A 31 REMARK 465 GLU A 32 REMARK 465 MET A 33 REMARK 465 GLY A 34 REMARK 465 HIS A 35 REMARK 465 ARG A 351 REMARK 465 ARG A 352 REMARK 465 LYS A 353 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 O HOH A 2131 O HOH A 2132 2.15 REMARK 500 O HOH A 2043 O HOH A 2132 2.16 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 2005 O HOH A 2037 8555 0.00 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 GLU A 13 -15.21 -154.09 REMARK 500 LYS A 14 -90.44 -52.94 REMARK 500 GLN A 15 -35.32 -27.62 REMARK 500 VAL A 124 -74.11 -99.94 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 VAL A 183 ASP A 184 145.71 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 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2005 DISTANCE = 6.34 ANGSTROMS 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 A1353 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 103 OD2 REMARK 620 2 ASP A 107 OD2 82.8 REMARK 620 3 M0N A1351 O5 95.2 173.6 REMARK 620 4 M0N A1351 O2 96.1 81.6 92.6 REMARK 620 5 HOH A2044 O 77.5 96.7 88.8 173.5 REMARK 620 6 HOH A2049 O 156.6 88.8 95.3 104.2 82.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1354 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 103 OD1 REMARK 620 2 ASP A 107 OD2 81.7 REMARK 620 3 M0N A1351 O2 94.4 78.2 REMARK 620 4 HOH A2050 O 91.2 97.6 172.4 REMARK 620 5 HOH A2169 O 95.4 167.3 89.7 94.9 REMARK 620 6 HOH A2170 O 176.6 95.0 86.0 88.1 88.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1352 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 243 OD2 REMARK 620 2 M0N A1351 O4 94.4 REMARK 620 3 M0N A1351 O1 99.0 92.4 REMARK 620 4 HOH A2117 O 84.5 91.5 174.6 REMARK 620 5 HOH A2119 O 86.6 177.6 85.3 90.8 REMARK 620 6 HOH A2122 O 166.7 93.9 90.9 85.0 85.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE M0N A1351 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1352 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1353 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1354 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2F92 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN FPPS IN COMPLEX WITH ALENDRONATE REMARK 900 RELATED ID: 2F8C RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FPPS IN COMPLEX WITH ZOLEDRONATE REMARK 900 RELATED ID: 2F9K RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN FPPS IN COMPLEX WITH ZOLEDRONATEAND ZN2+ REMARK 900 RELATED ID: 2F7M RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UNLIGANDED HUMAN FPPS REMARK 900 RELATED ID: 1YV5 RELATED DB: PDB REMARK 900 HUMAN FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH MG ANDRISEDRONATE REMARK 900 RELATED ID: 2F89 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN FPPS IN COMPLEX WITH PAMIDRONATE REMARK 900 RELATED ID: 2F94 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN FPPS IN COMPLEX WITH IBANDRONATE REMARK 900 RELATED ID: 1ZW5 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF FARNESYL DIPHOSPHATE SYNTHASE PROTEIN REMARK 900 RELATED ID: 1YQ7 RELATED DB: PDB REMARK 900 HUMAN FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITHRISEDRONATE REMARK 900 RELATED ID: 2F8Z RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN FPPS IN COMPLEX WITH ZOLEDRONATEAND REMARK 900 ISOPENTENYL DIPHOSPHATE DBREF 2VF6 A -24 0 PDB 2VF6 2VF6 -24 0 DBREF 2VF6 A 1 353 UNP P14324 FPPS_HUMAN 1 353 SEQRES 1 A 378 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 378 ARG GLU ASN LEU TYR PHE GLN GLY HIS MET GLY HIS MET SEQRES 3 A 378 ASN GLY ASP GLN ASN SER ASP VAL TYR ALA GLN GLU LYS SEQRES 4 A 378 GLN ASP PHE VAL GLN HIS PHE SER GLN ILE VAL ARG VAL SEQRES 5 A 378 LEU THR GLU ASP GLU MET GLY HIS PRO GLU ILE GLY ASP SEQRES 6 A 378 ALA ILE ALA ARG LEU LYS GLU VAL LEU GLU TYR ASN ALA SEQRES 7 A 378 ILE GLY GLY LYS TYR ASN ARG GLY LEU THR VAL VAL VAL SEQRES 8 A 378 ALA PHE ARG GLU LEU VAL GLU PRO ARG LYS GLN ASP ALA SEQRES 9 A 378 ASP SER LEU GLN ARG ALA TRP THR VAL GLY TRP CYS VAL SEQRES 10 A 378 GLU LEU LEU GLN ALA PHE PHE LEU VAL ALA ASP ASP ILE SEQRES 11 A 378 MET ASP SER SER LEU THR ARG ARG GLY GLN ILE CYS TRP SEQRES 12 A 378 TYR GLN LYS PRO GLY VAL GLY LEU ASP ALA ILE ASN ASP SEQRES 13 A 378 ALA ASN LEU LEU GLU ALA CYS ILE TYR ARG LEU LEU LYS SEQRES 14 A 378 LEU TYR CYS ARG GLU GLN PRO TYR TYR LEU ASN LEU ILE SEQRES 15 A 378 GLU LEU PHE LEU GLN SER SER TYR GLN THR GLU ILE GLY SEQRES 16 A 378 GLN THR LEU ASP LEU LEU THR ALA PRO GLN GLY ASN VAL SEQRES 17 A 378 ASP LEU VAL ARG PHE THR GLU LYS ARG TYR LYS SER ILE SEQRES 18 A 378 VAL LYS TYR LYS THR ALA PHE TYR SER PHE TYR LEU PRO SEQRES 19 A 378 ILE ALA ALA ALA MET TYR MET ALA GLY ILE ASP GLY GLU SEQRES 20 A 378 LYS GLU HIS ALA ASN ALA LYS LYS ILE LEU LEU GLU MET SEQRES 21 A 378 GLY GLU PHE PHE GLN ILE GLN ASP ASP TYR LEU ASP LEU SEQRES 22 A 378 PHE GLY ASP PRO SER VAL THR GLY LYS ILE GLY THR ASP SEQRES 23 A 378 ILE GLN ASP ASN LYS CYS SER TRP LEU VAL VAL GLN CYS SEQRES 24 A 378 LEU GLN ARG ALA THR PRO GLU GLN TYR GLN ILE LEU LYS SEQRES 25 A 378 GLU ASN TYR GLY GLN LYS GLU ALA GLU LYS VAL ALA ARG SEQRES 26 A 378 VAL LYS ALA LEU TYR GLU GLU LEU ASP LEU PRO ALA VAL SEQRES 27 A 378 PHE LEU GLN TYR GLU GLU ASP SER TYR SER HIS ILE MET SEQRES 28 A 378 ALA LEU ILE GLU GLN TYR ALA ALA PRO LEU PRO PRO ALA SEQRES 29 A 378 VAL PHE LEU GLY LEU ALA ARG LYS ILE TYR LYS ARG ARG SEQRES 30 A 378 LYS HET M0N A1351 20 HET MG A1352 1 HET MG A1353 1 HET MG A1354 1 HETNAM M0N (1-HYDROXY-2-IMIDAZO[1,2-A]PYRIDIN-3-YLETHANE-1,1- HETNAM 2 M0N DIYL)BIS(PHOSPHONIC ACID) HETNAM MG MAGNESIUM ION HETSYN M0N MINODRONATE; 1-HYDROXY-2-(5,6,7,8-TETRAHYDROIMIDAZO[1, HETSYN 2 M0N 2-A]PYRIDIN-3-YL)ETHANE-1,1-DIYLDIPHOSPONIC ACID; (1- HETSYN 3 M0N HYDROXY-2-IMIDAZO[1,2-A]PYRIDIN-3-YL-ETHYLIDENE)-1,1- HETSYN 4 M0N BISPHOSPHONIC ACID FORMUL 2 M0N C9 H12 N2 O7 P2 FORMUL 3 MG 3(MG 2+) FORMUL 6 HOH *171(H2 O) HELIX 1 1 GLU A 13 HIS A 20 1 8 HELIX 2 2 HIS A 20 THR A 29 1 10 HELIX 3 3 ILE A 38 ALA A 53 1 16 HELIX 4 4 TYR A 58 VAL A 72 1 15 HELIX 5 5 ASP A 78 ASP A 107 1 30 HELIX 6 6 TRP A 118 LYS A 121 5 4 HELIX 7 7 VAL A 124 LEU A 126 5 3 HELIX 8 8 ASP A 127 ARG A 148 1 22 HELIX 9 9 TYR A 152 ALA A 178 1 27 HELIX 10 10 ASP A 184 PHE A 188 5 5 HELIX 11 11 THR A 189 THR A 201 1 13 HELIX 12 12 THR A 201 PHE A 206 1 6 HELIX 13 13 PHE A 206 ALA A 217 1 12 HELIX 14 14 GLY A 221 GLY A 250 1 30 HELIX 15 15 ASP A 251 GLY A 256 1 6 HELIX 16 16 SER A 268 ALA A 278 1 11 HELIX 17 17 THR A 279 TYR A 290 1 12 HELIX 18 18 GLU A 294 LEU A 308 1 15 HELIX 19 19 ASP A 309 ALA A 333 1 25 HELIX 20 20 PRO A 337 LYS A 350 1 14 SHEET 1 AA 2 THR A 111 ARG A 112 0 SHEET 2 AA 2 GLN A 115 ILE A 116 -1 O GLN A 115 N ARG A 112 LINK OD2 ASP A 103 MG MG A1353 1555 1555 2.16 LINK OD1 ASP A 103 MG MG A1354 1555 1555 2.06 LINK OD2 ASP A 107 MG MG A1353 1555 1555 2.18 LINK OD2 ASP A 107 MG MG A1354 1555 1555 2.15 LINK OD2 ASP A 243 MG MG A1352 1555 1555 2.20 LINK O4 M0N A1351 MG MG A1352 1555 1555 1.90 LINK O1 M0N A1351 MG MG A1352 1555 1555 2.12 LINK O5 M0N A1351 MG MG A1353 1555 1555 2.04 LINK O2 M0N A1351 MG MG A1353 1555 1555 2.04 LINK O2 M0N A1351 MG MG A1354 1555 1555 2.23 LINK MG MG A1352 O HOH A2117 1555 1555 2.29 LINK MG MG A1352 O HOH A2119 1555 1555 2.06 LINK MG MG A1352 O HOH A2122 1555 1555 2.12 LINK MG MG A1353 O HOH A2044 1555 1555 2.03 LINK MG MG A1353 O HOH A2049 1555 1555 1.97 LINK MG MG A1354 O HOH A2050 1555 1555 2.04 LINK MG MG A1354 O HOH A2169 1555 1555 2.07 LINK MG MG A1354 O HOH A2170 1555 1555 2.02 CISPEP 1 ALA A 334 PRO A 335 0 20.32 SITE 1 AC1 26 PHE A 99 ASP A 103 ASP A 107 ARG A 112 SITE 2 AC1 26 THR A 167 GLN A 171 LYS A 200 THR A 201 SITE 3 AC1 26 TYR A 204 GLN A 240 ASP A 243 LYS A 257 SITE 4 AC1 26 MG A1352 MG A1353 MG A1354 HOH A2044 SITE 5 AC1 26 HOH A2049 HOH A2114 HOH A2117 HOH A2119 SITE 6 AC1 26 HOH A2122 HOH A2167 HOH A2168 HOH A2169 SITE 7 AC1 26 HOH A2170 HOH A2171 SITE 1 AC2 5 ASP A 243 M0N A1351 HOH A2117 HOH A2119 SITE 2 AC2 5 HOH A2122 SITE 1 AC3 6 ASP A 103 ASP A 107 M0N A1351 MG A1354 SITE 2 AC3 6 HOH A2044 HOH A2049 SITE 1 AC4 7 ASP A 103 ASP A 107 M0N A1351 MG A1353 SITE 2 AC4 7 HOH A2050 HOH A2169 HOH A2170 CRYST1 111.207 111.207 69.059 90.00 90.00 90.00 P 41 21 2 8 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 0.008992 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008992 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014480 0.00000