HEADER TRANSFERASE 31-OCT-07 3B7L TITLE HUMAN FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH MG AND 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 [INCLUDES: DIMETHYLALLYLTRANSTRANSFERASE (EC 2.5.1.1) AND COMPND 6 GERANYLTRANSTRANSFERASE (EC 2.5.1.10)]; COMPND 7 EC: 2.5.1.10; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: FDPS, FPS, KIAA1293; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11 DERIVATIVE KEYWDS ISOPRENOID PATHWAY, CHOLESTEROL SYNTHESIS, BISPHOSPHONATE, STRUCTURAL KEYWDS 2 GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, CHOLESTEROL KEYWDS 3 BIOSYNTHESIS, HOST-VIRUS INTERACTION, ISOPRENE BIOSYNTHESIS, LIPID KEYWDS 4 SYNTHESIS, STEROID BIOSYNTHESIS, STEROL BIOSYNTHESIS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR E.S.PILKA,J.E.DUNFORD,K.GUO,A.C.W.PIKE,K.L.KAVANAGH,F.VON DELFT, AUTHOR 2 F.H.EBETINO,C.H.ARROWSMITH,A.M.EDWARDS,R.G.G.RUSSELL,U.OPPERMANN, AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 6 30-AUG-23 3B7L 1 REMARK SEQADV LINK REVDAT 5 31-JAN-18 3B7L 1 AUTHOR JRNL REVDAT 4 13-JUL-11 3B7L 1 VERSN REVDAT 3 24-FEB-09 3B7L 1 VERSN REVDAT 2 29-APR-08 3B7L 1 REMARK REVDAT 1 13-NOV-07 3B7L 0 JRNL AUTH E.S.PILKA,J.E.DUNFORD,K.GUO,A.C.W.PIKE,K.L.KAVANAGH, JRNL AUTH 2 F.VON DELFT,F.H.EBETINO,C.H.ARROWSMITH,A.M.EDWARDS, JRNL AUTH 3 R.G.G.RUSSELL,U.OPPERMANN JRNL TITL HUMAN FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH MG AND JRNL TITL 2 MINODRONATE. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 29320 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1573 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1939 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.19 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE SET COUNT : 83 REMARK 3 BIN FREE R VALUE : 0.4230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2718 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 268 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.92000 REMARK 3 B22 (A**2) : -0.92000 REMARK 3 B33 (A**2) : 1.84000 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): 0.142 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.130 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.094 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.165 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2831 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1875 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3847 ; 1.470 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4574 ; 1.353 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 342 ; 5.726 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 136 ;35.415 ;24.412 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 476 ;13.610 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;17.959 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 420 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3145 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 583 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 659 ; 0.208 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1903 ; 0.179 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1390 ; 0.183 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1301 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 198 ; 0.180 ; 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): 7 ; 0.045 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 49 ; 0.196 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.131 ; 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): 1784 ; 2.740 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 692 ; 0.827 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2742 ; 3.637 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1252 ; 6.085 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1105 ; 7.711 ;11.000 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 8 A 350 REMARK 3 ORIGIN FOR THE GROUP (A): 9.4768 29.9560 -7.0509 REMARK 3 T TENSOR REMARK 3 T11: -0.1397 T22: -0.1527 REMARK 3 T33: -0.0998 T12: 0.0238 REMARK 3 T13: -0.0171 T23: -0.0116 REMARK 3 L TENSOR REMARK 3 L11: 1.6547 L22: 1.2258 REMARK 3 L33: 1.0441 L12: 0.2294 REMARK 3 L13: 0.5811 L23: -0.1531 REMARK 3 S TENSOR REMARK 3 S11: -0.0141 S12: -0.0184 S13: 0.1353 REMARK 3 S21: -0.0313 S22: 0.0437 S23: 0.1997 REMARK 3 S31: -0.0678 S32: -0.1509 S33: -0.0296 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 3B7L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1000045178. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-AUG-07 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS HTC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30937 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 20.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : 0.02700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.60600 REMARK 200 R SYM FOR SHELL (I) : 0.27000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1YV5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NH4CL, 20% PEG 6000, 10% ETHYLENE REMARK 280 GLYCOL, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 33.65400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 55.46100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 55.46100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 16.82700 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 55.46100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 55.46100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 50.48100 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 55.46100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.46100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 16.82700 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 55.46100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.46100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 50.48100 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 33.65400 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4040 ANGSTROM**2 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 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 HOH A1178 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 GLY A -2 REMARK 465 HIS A -1 REMARK 465 MET 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 ARG A 351 REMARK 465 ARG A 352 REMARK 465 LYS A 353 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A 8 CG OD1 OD2 REMARK 470 GLN A 12 CG CD OE1 NE2 REMARK 470 GLN A 15 CG CD OE1 NE2 REMARK 470 ASP A 16 CG OD1 OD2 REMARK 470 GLN A 23 OE1 NE2 REMARK 470 MET A 33 CG SD CE REMARK 470 LYS A 57 CE NZ REMARK 470 ARG A 75 CZ NH1 NH2 REMARK 470 LYS A 76 CG CD CE NZ REMARK 470 GLN A 180 CG CD OE1 NE2 REMARK 470 VAL A 183 CG1 CG2 REMARK 470 GLU A 222 CG CD OE1 OE2 REMARK 470 LYS A 223 CG CD CE NZ REMARK 470 LYS A 293 NZ REMARK 470 GLU A 296 CD OE1 OE2 REMARK 470 ARG A 346 NE CZ NH1 NH2 REMARK 470 LYS A 347 CE NZ REMARK 470 LYS A 350 CG CD CE NZ 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 ASP A 16 ND1 HIS A 20 2.18 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 131 CB - CG - OD1 ANGL. DEV. = 5.8 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 GLN A 77 54.41 -92.35 REMARK 500 VAL A 124 -74.75 -91.83 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 907 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 103 OD2 REMARK 620 2 ASP A 107 OD2 89.3 REMARK 620 3 M0N A 901 O3 89.7 81.3 REMARK 620 4 M0N A 901 O4 88.3 170.0 89.0 REMARK 620 5 HOH A1131 O 172.6 88.9 97.1 94.7 REMARK 620 6 HOH A1136 O 82.2 98.1 171.9 91.2 91.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 909 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 103 OD1 REMARK 620 2 ASP A 107 OD2 82.7 REMARK 620 3 M0N A 901 O3 91.3 83.6 REMARK 620 4 HOH A1128 O 86.6 91.2 174.7 REMARK 620 5 HOH A1134 O 173.1 93.5 93.9 87.7 REMARK 620 6 HOH A1135 O 90.1 170.9 91.2 93.8 94.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 908 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 243 OD2 REMARK 620 2 M0N A 901 O1 97.7 REMARK 620 3 M0N A 901 O5 92.8 89.4 REMARK 620 4 HOH A1129 O 89.7 91.7 177.1 REMARK 620 5 HOH A1130 O 90.4 171.4 87.3 91.2 REMARK 620 6 HOH A1132 O 173.7 84.1 93.3 84.1 88.2 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 MG A 907 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 908 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 909 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 910 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE M0N A 901 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YQ7 RELATED DB: PDB REMARK 900 HUMAN FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH RISEDRONATE REMARK 900 RELATED ID: 2QIS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN FARNESYL PYROPHOSPHATE SYNTHASE T210S REMARK 900 MUTANT BOUND TO RISEDRONATE REMARK 900 RELATED ID: 1ZW5 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF FARNESYL DIPHOSPHATE SYNTHASE PROTEIN REMARK 900 RELATED ID: 1YV5 RELATED DB: PDB REMARK 900 HUMAN FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH MG AND REMARK 900 RISEDRONATE DBREF 3B7L A 1 353 UNP P14324 FPPS_HUMAN 1 353 SEQADV 3B7L GLY A -2 UNP P14324 EXPRESSION TAG SEQADV 3B7L HIS A -1 UNP P14324 EXPRESSION TAG SEQADV 3B7L MET A 0 UNP P14324 EXPRESSION TAG SEQRES 1 A 356 GLY HIS MET MET ASN GLY ASP GLN ASN SER ASP VAL TYR SEQRES 2 A 356 ALA GLN GLU LYS GLN ASP PHE VAL GLN HIS PHE SER GLN SEQRES 3 A 356 ILE VAL ARG VAL LEU THR GLU ASP GLU MET GLY HIS PRO SEQRES 4 A 356 GLU ILE GLY ASP ALA ILE ALA ARG LEU LYS GLU VAL LEU SEQRES 5 A 356 GLU TYR ASN ALA ILE GLY GLY LYS TYR ASN ARG GLY LEU SEQRES 6 A 356 THR VAL VAL VAL ALA PHE ARG GLU LEU VAL GLU PRO ARG SEQRES 7 A 356 LYS GLN ASP ALA ASP SER LEU GLN ARG ALA TRP THR VAL SEQRES 8 A 356 GLY TRP CYS VAL GLU LEU LEU GLN ALA PHE PHE LEU VAL SEQRES 9 A 356 ALA ASP ASP ILE MET ASP SER SER LEU THR ARG ARG GLY SEQRES 10 A 356 GLN ILE CYS TRP TYR GLN LYS PRO GLY VAL GLY LEU ASP SEQRES 11 A 356 ALA ILE ASN ASP ALA ASN LEU LEU GLU ALA CYS ILE TYR SEQRES 12 A 356 ARG LEU LEU LYS LEU TYR CYS ARG GLU GLN PRO TYR TYR SEQRES 13 A 356 LEU ASN LEU ILE GLU LEU PHE LEU GLN SER SER TYR GLN SEQRES 14 A 356 THR GLU ILE GLY GLN THR LEU ASP LEU LEU THR ALA PRO SEQRES 15 A 356 GLN GLY ASN VAL ASP LEU VAL ARG PHE THR GLU LYS ARG SEQRES 16 A 356 TYR LYS SER ILE VAL LYS TYR LYS THR ALA PHE TYR SER SEQRES 17 A 356 PHE TYR LEU PRO ILE ALA ALA ALA MET TYR MET ALA GLY SEQRES 18 A 356 ILE ASP GLY GLU LYS GLU HIS ALA ASN ALA LYS LYS ILE SEQRES 19 A 356 LEU LEU GLU MET GLY GLU PHE PHE GLN ILE GLN ASP ASP SEQRES 20 A 356 TYR LEU ASP LEU PHE GLY ASP PRO SER VAL THR GLY LYS SEQRES 21 A 356 ILE GLY THR ASP ILE GLN ASP ASN LYS CYS SER TRP LEU SEQRES 22 A 356 VAL VAL GLN CYS LEU GLN ARG ALA THR PRO GLU GLN TYR SEQRES 23 A 356 GLN ILE LEU LYS GLU ASN TYR GLY GLN LYS GLU ALA GLU SEQRES 24 A 356 LYS VAL ALA ARG VAL LYS ALA LEU TYR GLU GLU LEU ASP SEQRES 25 A 356 LEU PRO ALA VAL PHE LEU GLN TYR GLU GLU ASP SER TYR SEQRES 26 A 356 SER HIS ILE MET ALA LEU ILE GLU GLN TYR ALA ALA PRO SEQRES 27 A 356 LEU PRO PRO ALA VAL PHE LEU GLY LEU ALA ARG LYS ILE SEQRES 28 A 356 TYR LYS ARG ARG LYS HET MG A 907 1 HET MG A 908 1 HET MG A 909 1 HET MG A 910 1 HET M0N A 901 20 HETNAM MG MAGNESIUM ION HETNAM M0N (1-HYDROXY-2-IMIDAZO[1,2-A]PYRIDIN-3-YLETHANE-1,1- HETNAM 2 M0N DIYL)BIS(PHOSPHONIC ACID) 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 MG 4(MG 2+) FORMUL 6 M0N C9 H12 N2 O7 P2 FORMUL 7 HOH *268(H2 O) HELIX 1 1 TYR A 10 HIS A 20 1 11 HELIX 2 2 HIS A 20 THR A 29 1 10 HELIX 3 3 HIS A 35 GLU A 37 5 3 HELIX 4 4 ILE A 38 ALA A 53 1 16 HELIX 5 5 TYR A 58 VAL A 72 1 15 HELIX 6 6 GLU A 73 GLN A 77 5 5 HELIX 7 7 ASP A 78 ASP A 107 1 30 HELIX 8 8 TRP A 118 LYS A 121 5 4 HELIX 9 9 VAL A 124 LEU A 126 5 3 HELIX 10 10 ASP A 127 ARG A 148 1 22 HELIX 11 11 TYR A 152 THR A 177 1 26 HELIX 12 12 ASP A 184 PHE A 188 5 5 HELIX 13 13 THR A 189 THR A 201 1 13 HELIX 14 14 THR A 201 PHE A 206 1 6 HELIX 15 15 PHE A 206 ALA A 217 1 12 HELIX 16 16 GLY A 221 GLY A 250 1 30 HELIX 17 17 ASP A 251 GLY A 256 1 6 HELIX 18 18 SER A 268 ALA A 278 1 11 HELIX 19 19 THR A 279 TYR A 290 1 12 HELIX 20 20 GLU A 294 LEU A 308 1 15 HELIX 21 21 ASP A 309 ALA A 333 1 25 HELIX 22 22 PRO A 338 LYS A 350 1 13 SHEET 1 A 2 THR A 111 ARG A 112 0 SHEET 2 A 2 GLN A 115 ILE A 116 -1 O GLN A 115 N ARG A 112 LINK OD2 ASP A 103 MG MG A 907 1555 1555 2.18 LINK OD1 ASP A 103 MG MG A 909 1555 1555 2.15 LINK OD2 ASP A 107 MG MG A 907 1555 1555 2.28 LINK OD2 ASP A 107 MG MG A 909 1555 1555 2.18 LINK OD2 ASP A 243 MG MG A 908 1555 1555 2.19 LINK O3 M0N A 901 MG MG A 907 1555 1555 2.11 LINK O4 M0N A 901 MG MG A 907 1555 1555 2.08 LINK O1 M0N A 901 MG MG A 908 1555 1555 2.08 LINK O5 M0N A 901 MG MG A 908 1555 1555 2.00 LINK O3 M0N A 901 MG MG A 909 1555 1555 2.11 LINK MG MG A 907 O HOH A1131 1555 1555 2.06 LINK MG MG A 907 O HOH A1136 1555 1555 2.14 LINK MG MG A 908 O HOH A1129 1555 1555 2.15 LINK MG MG A 908 O HOH A1130 1555 1555 2.30 LINK MG MG A 908 O HOH A1132 1555 1555 2.17 LINK MG MG A 909 O HOH A1128 1555 1555 2.14 LINK MG MG A 909 O HOH A1134 1555 1555 2.02 LINK MG MG A 909 O HOH A1135 1555 1555 2.08 CISPEP 1 ALA A 334 PRO A 335 0 7.15 SITE 1 AC1 6 ASP A 103 ASP A 107 M0N A 901 MG A 909 SITE 2 AC1 6 HOH A1131 HOH A1136 SITE 1 AC2 5 ASP A 243 M0N A 901 HOH A1129 HOH A1130 SITE 2 AC2 5 HOH A1132 SITE 1 AC3 7 ASP A 103 ASP A 107 M0N A 901 MG A 907 SITE 2 AC3 7 HOH A1128 HOH A1134 HOH A1135 SITE 1 AC4 5 THR A 260 ASP A 261 ASP A 264 LYS A 266 SITE 2 AC4 5 HOH A1131 SITE 1 AC5 25 PHE A 99 ASP A 103 ASP A 107 ARG A 112 SITE 2 AC5 25 THR A 167 GLN A 171 LYS A 200 THR A 201 SITE 3 AC5 25 GLN A 240 ASP A 243 LYS A 257 MG A 907 SITE 4 AC5 25 MG A 908 MG A 909 HOH A 937 HOH A 962 SITE 5 AC5 25 HOH A 967 HOH A1059 HOH A1129 HOH A1130 SITE 6 AC5 25 HOH A1131 HOH A1132 HOH A1134 HOH A1135 SITE 7 AC5 25 HOH A1136 CRYST1 110.922 110.922 67.308 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 0.009015 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009015 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014857 0.00000