HEADER TRANSFERASE 23-JUN-14 4QPF TITLE NEW LOWER BONE AFFINITY BISPHOSPHONATE DRUG DESIGN FOR EFFECTIVE USE TITLE 2 IN DISEASES CHARACTERIZED BY ABNORMAL BONE RESORPTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: FARNESYL PYROPHOSPHATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 67-419; COMPND 5 SYNONYM: FPP SYNTHASE, FPS, (2E,6E)-FARNESYL DIPHOSPHATE SYNTHASE, COMPND 6 DIMETHYLALLYLTRANSTRANSFERASE, FARNESYL DIPHOSPHATE SYNTHASE, COMPND 7 GERANYLTRANSTRANSFERASE; COMPND 8 EC: 2.5.1.10, 2.5.1.1; COMPND 9 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_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11 DERIVATIVE KEYWDS ISOPRENE BIOSYNTHESIS, LIPID SYNTHESIS, STEROID BIOSYNTHESIS, KEYWDS 2 ISOPRENOID PATHWAY, CHOLESTEROL SYNTHESIS, BISPHOSPHONATE, ALL-ALPHA KEYWDS 3 HELICAL PRENYLTRANSFERASE, ISOPENTYL PYROPHOSPHATE, DIMETHYLALLYL KEYWDS 4 PYROPHOSPHATE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR F.H.EBETINO,M.LUNDY,A.A.KWAASI,J.E.DUNFORD,Z.DUAN,J.TRIFFITT,A.MAZUR, AUTHOR 2 G.JEANS,B.L.BARNETT,R.G.G.RUSSELL REVDAT 2 20-SEP-23 4QPF 1 REMARK SEQADV LINK REVDAT 1 24-JUN-15 4QPF 0 JRNL AUTH F.H.EBETINO,M.LUNDY,A.A.KWAASI,J.E.DUNFORD,Z.DUAN, JRNL AUTH 2 J.TRIFFITT,A.MAZUR,G.JEANS,B.L.BARNETT,R.G.G.RUSSELL JRNL TITL NEW LOWER BONE AFFINITY BISPHOSPHONATE DRUG DESIGN FOR JRNL TITL 2 EFFECTIVE USE IN DISEASES CHARACTERIZED BY ABNORMAL BONE JRNL TITL 3 RESORPTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 89.6 REMARK 3 NUMBER OF REFLECTIONS : 48943 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2625 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) : 1.59 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.63 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3518 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE SET COUNT : 210 REMARK 3 BIN FREE R VALUE : 0.2820 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 : 23 REMARK 3 SOLVENT ATOMS : 445 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -0.05000 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): 0.083 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.089 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.053 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.494 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2870 ; 0.021 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2742 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3907 ; 2.005 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6324 ; 0.976 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 359 ; 5.434 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 143 ;34.996 ;24.965 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 514 ;13.792 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;19.431 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 427 ; 0.122 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3265 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 663 ; 0.001 ; 0.020 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 4QPF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000086346. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 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) : 0.9796 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK DOUBLE-CRYSTAL REMARK 200 SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48943 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : 26.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 2VF6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M SODIUM CHLORIDE, 5 MM MAGNESIUM REMARK 280 CHLORIDE, 15% GLYCEROL, 100 MM SODIUM ACETATE, PH 5.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 32.98950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 56.11300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 56.11300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 16.49475 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 56.11300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 56.11300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 49.48425 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 56.11300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.11300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 16.49475 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 56.11300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.11300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 49.48425 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 32.98950 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: 4520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -85.0 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 -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 32.98950 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 -21 REMARK 465 GLY A -20 REMARK 465 SER A -19 REMARK 465 SER A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 SER A -11 REMARK 465 SER A -10 REMARK 465 GLY A -9 REMARK 465 ARG A -8 REMARK 465 GLU A -7 REMARK 465 ASN A -6 REMARK 465 LEU A -5 REMARK 465 TYR A -4 REMARK 465 PHE A -3 REMARK 465 GLN 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 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 VAL A 9 CG1 CG2 REMARK 470 TYR A 10 CG CD1 CD2 CE1 CE2 CZ OH 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 1234 O HOH A 1344 2.01 REMARK 500 O HOH A 1384 O HOH A 1408 2.07 REMARK 500 OE1 GLU A 237 O HOH A 1139 2.11 REMARK 500 NE2 GLN A 162 O HOH A 1226 2.12 REMARK 500 OE1 GLU A 306 O HOH A 1132 2.13 REMARK 500 O HOH A 1109 O HOH A 1372 2.13 REMARK 500 OD1 ASN A 133 O HOH A 1349 2.13 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 1082 O HOH A 1082 8555 1.79 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 ARG A 26 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 141 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 141 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ASP A 251 CB - CG - OD1 ANGL. DEV. = -6.0 DEGREES REMARK 500 MET A 326 CG - SD - CE ANGL. DEV. = 9.7 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 VAL A 124 -70.04 -100.58 REMARK 500 THR A 201 -38.88 -132.95 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 902 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 103 OD2 REMARK 620 2 ASP A 107 OD2 87.1 REMARK 620 3 39L A 901 O5 95.3 170.1 REMARK 620 4 39L A 901 O2 93.6 78.7 91.6 REMARK 620 5 HOH A1003 O 168.2 86.7 92.6 94.9 REMARK 620 6 HOH A1009 O 82.1 97.7 92.1 174.5 88.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 903 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 103 OD1 REMARK 620 2 ASP A 107 OD2 86.5 REMARK 620 3 39L A 901 O2 100.7 81.7 REMARK 620 4 HOH A1006 O 172.1 93.4 87.2 REMARK 620 5 HOH A1017 O 92.0 172.0 90.9 89.1 REMARK 620 6 HOH A1026 O 86.5 98.4 172.8 85.6 89.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 904 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 243 OD2 REMARK 620 2 39L A 901 O4 96.5 REMARK 620 3 39L A 901 O1 101.9 89.9 REMARK 620 4 HOH A1002 O 166.0 93.4 88.1 REMARK 620 5 HOH A1007 O 83.7 177.5 92.5 86.0 REMARK 620 6 HOH A1035 O 85.1 86.8 172.6 85.5 90.7 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 39L A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 904 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZW5 RELATED DB: PDB REMARK 900 RELATED ID: 1YQ7 RELATED DB: PDB REMARK 900 RELATED ID: 2VF6 RELATED DB: PDB REMARK 900 RELATED ID: 3B7L RELATED DB: PDB DBREF 4QPF A 1 353 UNP P14324 FPPS_HUMAN 67 419 SEQADV 4QPF MET A -21 UNP P14324 EXPRESSION TAG SEQADV 4QPF GLY A -20 UNP P14324 EXPRESSION TAG SEQADV 4QPF SER A -19 UNP P14324 EXPRESSION TAG SEQADV 4QPF SER A -18 UNP P14324 EXPRESSION TAG SEQADV 4QPF HIS A -17 UNP P14324 EXPRESSION TAG SEQADV 4QPF HIS A -16 UNP P14324 EXPRESSION TAG SEQADV 4QPF HIS A -15 UNP P14324 EXPRESSION TAG SEQADV 4QPF HIS A -14 UNP P14324 EXPRESSION TAG SEQADV 4QPF HIS A -13 UNP P14324 EXPRESSION TAG SEQADV 4QPF HIS A -12 UNP P14324 EXPRESSION TAG SEQADV 4QPF SER A -11 UNP P14324 EXPRESSION TAG SEQADV 4QPF SER A -10 UNP P14324 EXPRESSION TAG SEQADV 4QPF GLY A -9 UNP P14324 EXPRESSION TAG SEQADV 4QPF ARG A -8 UNP P14324 EXPRESSION TAG SEQADV 4QPF GLU A -7 UNP P14324 EXPRESSION TAG SEQADV 4QPF ASN A -6 UNP P14324 EXPRESSION TAG SEQADV 4QPF LEU A -5 UNP P14324 EXPRESSION TAG SEQADV 4QPF TYR A -4 UNP P14324 EXPRESSION TAG SEQADV 4QPF PHE A -3 UNP P14324 EXPRESSION TAG SEQADV 4QPF GLN A -2 UNP P14324 EXPRESSION TAG SEQADV 4QPF GLY A -1 UNP P14324 EXPRESSION TAG SEQADV 4QPF HIS A 0 UNP P14324 EXPRESSION TAG SEQRES 1 A 375 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 375 ARG GLU ASN LEU TYR PHE GLN GLY HIS MET ASN GLY ASP SEQRES 3 A 375 GLN ASN SER ASP VAL TYR ALA GLN GLU LYS GLN ASP PHE SEQRES 4 A 375 VAL GLN HIS PHE SER GLN ILE VAL ARG VAL LEU THR GLU SEQRES 5 A 375 ASP GLU MET GLY HIS PRO GLU ILE GLY ASP ALA ILE ALA SEQRES 6 A 375 ARG LEU LYS GLU VAL LEU GLU TYR ASN ALA ILE GLY GLY SEQRES 7 A 375 LYS TYR ASN ARG GLY LEU THR VAL VAL VAL ALA PHE ARG SEQRES 8 A 375 GLU LEU VAL GLU PRO ARG LYS GLN ASP ALA ASP SER LEU SEQRES 9 A 375 GLN ARG ALA TRP THR VAL GLY TRP CYS VAL GLU LEU LEU SEQRES 10 A 375 GLN ALA PHE PHE LEU VAL ALA ASP ASP ILE MET ASP SER SEQRES 11 A 375 SER LEU THR ARG ARG GLY GLN ILE CYS TRP TYR GLN LYS SEQRES 12 A 375 PRO GLY VAL GLY LEU ASP ALA ILE ASN ASP ALA ASN LEU SEQRES 13 A 375 LEU GLU ALA CYS ILE TYR ARG LEU LEU LYS LEU TYR CYS SEQRES 14 A 375 ARG GLU GLN PRO TYR TYR LEU ASN LEU ILE GLU LEU PHE SEQRES 15 A 375 LEU GLN SER SER TYR GLN THR GLU ILE GLY GLN THR LEU SEQRES 16 A 375 ASP LEU LEU THR ALA PRO GLN GLY ASN VAL ASP LEU VAL SEQRES 17 A 375 ARG PHE THR GLU LYS ARG TYR LYS SER ILE VAL LYS TYR SEQRES 18 A 375 LYS THR ALA PHE TYR SER PHE TYR LEU PRO ILE ALA ALA SEQRES 19 A 375 ALA MET TYR MET ALA GLY ILE ASP GLY GLU LYS GLU HIS SEQRES 20 A 375 ALA ASN ALA LYS LYS ILE LEU LEU GLU MET GLY GLU PHE SEQRES 21 A 375 PHE GLN ILE GLN ASP ASP TYR LEU ASP LEU PHE GLY ASP SEQRES 22 A 375 PRO SER VAL THR GLY LYS ILE GLY THR ASP ILE GLN ASP SEQRES 23 A 375 ASN LYS CYS SER TRP LEU VAL VAL GLN CYS LEU GLN ARG SEQRES 24 A 375 ALA THR PRO GLU GLN TYR GLN ILE LEU LYS GLU ASN TYR SEQRES 25 A 375 GLY GLN LYS GLU ALA GLU LYS VAL ALA ARG VAL LYS ALA SEQRES 26 A 375 LEU TYR GLU GLU LEU ASP LEU PRO ALA VAL PHE LEU GLN SEQRES 27 A 375 TYR GLU GLU ASP SER TYR SER HIS ILE MET ALA LEU ILE SEQRES 28 A 375 GLU GLN TYR ALA ALA PRO LEU PRO PRO ALA VAL PHE LEU SEQRES 29 A 375 GLY LEU ALA ARG LYS ILE TYR LYS ARG ARG LYS HET 39L A 901 20 HET MG A 902 1 HET MG A 903 1 HET MG A 904 1 HETNAM 39L [1-FLUORO-2-(IMIDAZO[1,2-A]PYRIDIN-3-YL)ETHANE-1,1- HETNAM 2 39L DIYL]BIS(PHOSPHONIC ACID) HETNAM MG MAGNESIUM ION FORMUL 2 39L C9 H11 F N2 O6 P2 FORMUL 3 MG 3(MG 2+) FORMUL 6 HOH *445(H2 O) HELIX 1 1 TYR A 10 GLN A 19 1 10 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 GLU A 73 GLN A 77 5 5 HELIX 6 6 ASP A 78 ASP A 107 1 30 HELIX 7 7 TRP A 118 LYS A 121 5 4 HELIX 8 8 VAL A 124 LEU A 126 5 3 HELIX 9 9 ASP A 127 ARG A 148 1 22 HELIX 10 10 TYR A 152 ALA A 178 1 27 HELIX 11 11 ASP A 184 PHE A 188 5 5 HELIX 12 12 THR A 189 THR A 201 1 13 HELIX 13 13 THR A 201 PHE A 206 1 6 HELIX 14 14 PHE A 206 ALA A 217 1 12 HELIX 15 15 GLY A 221 GLY A 250 1 30 HELIX 16 16 ASP A 251 GLY A 256 1 6 HELIX 17 17 SER A 268 ALA A 278 1 11 HELIX 18 18 THR A 279 TYR A 290 1 12 HELIX 19 19 GLU A 294 LEU A 308 1 15 HELIX 20 20 ASP A 309 ALA A 333 1 25 HELIX 21 21 PRO A 337 TYR A 349 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 902 1555 1555 2.10 LINK OD1 ASP A 103 MG MG A 903 1555 1555 2.06 LINK OD2 ASP A 107 MG MG A 902 1555 1555 2.20 LINK OD2 ASP A 107 MG MG A 903 1555 1555 2.14 LINK OD2 ASP A 243 MG MG A 904 1555 1555 2.12 LINK O5 39L A 901 MG MG A 902 1555 1555 2.04 LINK O2 39L A 901 MG MG A 902 1555 1555 2.15 LINK O2 39L A 901 MG MG A 903 1555 1555 2.07 LINK O4 39L A 901 MG MG A 904 1555 1555 1.98 LINK O1 39L A 901 MG MG A 904 1555 1555 2.04 LINK MG MG A 902 O HOH A1003 1555 1555 2.09 LINK MG MG A 902 O HOH A1009 1555 1555 2.06 LINK MG MG A 903 O HOH A1006 1555 1555 2.13 LINK MG MG A 903 O HOH A1017 1555 1555 2.08 LINK MG MG A 903 O HOH A1026 1555 1555 2.11 LINK MG MG A 904 O HOH A1002 1555 1555 2.20 LINK MG MG A 904 O HOH A1007 1555 1555 2.09 LINK MG MG A 904 O HOH A1035 1555 1555 2.14 CISPEP 1 ALA A 334 PRO A 335 0 7.40 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 A 902 MG A 903 MG A 904 HOH A1002 SITE 5 AC1 26 HOH A1003 HOH A1006 HOH A1007 HOH A1009 SITE 6 AC1 26 HOH A1017 HOH A1022 HOH A1027 HOH A1035 SITE 7 AC1 26 HOH A1036 HOH A1161 SITE 1 AC2 6 ASP A 103 ASP A 107 39L A 901 MG A 903 SITE 2 AC2 6 HOH A1003 HOH A1009 SITE 1 AC3 7 ASP A 103 ASP A 107 39L A 901 MG A 902 SITE 2 AC3 7 HOH A1006 HOH A1017 HOH A1026 SITE 1 AC4 5 ASP A 243 39L A 901 HOH A1002 HOH A1007 SITE 2 AC4 5 HOH A1035 CRYST1 112.226 112.226 65.979 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 0.008911 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008911 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015156 0.00000