HEADER TRANSFERASE 03-JUN-05 1ZW5 TITLE X-RAY STRUCTURE OF FARNESYL DIPHOSPHATE SYNTHASE PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: FARNESYL DIPHOSPHATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FARNESYL PYROPHOSPHATE SYNTHETASE, DIMETHYLALLYL COMPND 5 TRANSFERASE, GERANYL TRANSFERASE, FPPS, FDPS; COMPND 6 EC: 2.5.1.10; 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 GENE: FDPS; 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, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.L.KAVANAGH,K.GUO,X.WU,F.VON DELFT,C.ARROWSMITH,M.SUNDSTROM, AUTHOR 2 A.EDWARDS,U.OPPERMANN,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 8 23-AUG-23 1ZW5 1 REMARK SEQADV LINK REVDAT 7 31-JAN-18 1ZW5 1 AUTHOR REVDAT 6 11-OCT-17 1ZW5 1 REMARK REVDAT 5 22-MAY-13 1ZW5 1 HET HETATM HETNAM HETSYN REVDAT 4 13-JUL-11 1ZW5 1 VERSN REVDAT 3 12-JAN-10 1ZW5 1 JRNL REVDAT 2 24-FEB-09 1ZW5 1 VERSN REVDAT 1 28-JUN-05 1ZW5 0 JRNL AUTH K.L.KAVANAGH,K.GUO,J.E.DUNFORD,X.WU,S.KNAPP,F.H.EBETINO, JRNL AUTH 2 M.J.ROGERS,R.G.RUSSELL,U.OPPERMANN JRNL TITL THE MOLECULAR MECHANISM OF NITROGEN-CONTAINING JRNL TITL 2 BISPHOSPHONATES AS ANTIOSTEOPOROSIS DRUGS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 7829 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 16684881 JRNL DOI 10.1073/PNAS.0601643103 REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 16605 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 886 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1228 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE SET COUNT : 67 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2697 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 60 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 38.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.86000 REMARK 3 B22 (A**2) : -3.86000 REMARK 3 B33 (A**2) : 7.72000 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): 0.295 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.218 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.189 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.179 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2801 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2537 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3793 ; 1.504 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5865 ; 0.840 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 339 ; 5.530 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 132 ;34.947 ;24.470 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 467 ;15.640 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;16.520 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 418 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3093 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 573 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 652 ; 0.211 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2463 ; 0.172 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1380 ; 0.185 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1475 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 91 ; 0.139 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.047 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 10 ; 0.130 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 54 ; 0.239 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.203 ; 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): 1870 ; 2.427 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 687 ; 0.648 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2715 ; 3.529 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1244 ; 5.873 ; 7.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1077 ; 7.394 ;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 27 A 367 REMARK 3 ORIGIN FOR THE GROUP (A): 9.3239 30.1888 -6.7934 REMARK 3 T TENSOR REMARK 3 T11: -0.1421 T22: -0.0701 REMARK 3 T33: -0.1438 T12: 0.0017 REMARK 3 T13: -0.0201 T23: 0.0631 REMARK 3 L TENSOR REMARK 3 L11: 3.6652 L22: 0.9623 REMARK 3 L33: 0.8333 L12: 0.0684 REMARK 3 L13: -0.2487 L23: -0.0095 REMARK 3 S TENSOR REMARK 3 S11: 0.0141 S12: 0.3846 S13: 0.5119 REMARK 3 S21: 0.0351 S22: 0.0725 S23: 0.3939 REMARK 3 S31: -0.0320 S32: -0.2254 S33: -0.0866 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 1ZW5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1000033192. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.984 REMARK 200 MONOCHROMATOR : LN2 COOLED FIXED-EXIT SI(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17517 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 63.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : 0.11000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: DIRECT REPLACEMENT USING 1YV5 REMARK 200 STARTING MODEL: PDB ENTRY 1YV5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG 6000, 0.7 M LICL, 70 MM REMARK 280 CITRATE PH 4.0, 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 31.62250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 56.12750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 56.12750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 15.81125 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 56.12750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 56.12750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 47.43375 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 56.12750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.12750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 15.81125 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 56.12750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.12750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 47.43375 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 31.62250 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 7180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -71.0 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 0.00000 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 13 REMARK 465 HIS A 14 REMARK 465 MET A 15 REMARK 465 ASN A 16 REMARK 465 GLY A 17 REMARK 465 ASP A 18 REMARK 465 GLN A 19 REMARK 465 ASN A 20 REMARK 465 SER A 21 REMARK 465 ASP A 22 REMARK 465 VAL A 23 REMARK 465 TYR A 24 REMARK 465 ALA A 25 REMARK 465 GLN A 26 REMARK 465 MET A 47 REMARK 465 GLY A 48 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 LYS A 28 CE NZ REMARK 470 GLN A 29 CG CD OE1 NE2 REMARK 470 GLN A 37 CG CD OE1 NE2 REMARK 470 ARG A 40 CD NE CZ NH1 NH2 REMARK 470 ASP A 45 CG OD1 OD2 REMARK 470 LYS A 90 CE NZ REMARK 470 LYS A 135 NZ REMARK 470 GLN A 194 CG CD OE1 NE2 REMARK 470 LYS A 205 CD CE NZ REMARK 470 LYS A 212 NZ REMARK 470 GLU A 236 CD OE1 OE2 REMARK 470 LYS A 237 CG CD CE NZ REMARK 470 GLU A 295 CG CD OE1 OE2 REMARK 470 LYS A 301 NZ REMARK 470 GLU A 302 CG CD OE1 OE2 REMARK 470 LYS A 307 CD CE NZ REMARK 470 LYS A 361 CE NZ REMARK 470 ARG A 366 NE CZ NH1 NH2 REMARK 470 LYS A 367 CE NZ 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 275 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 45 14.19 -61.83 REMARK 500 GLU A 163 31.61 -91.43 REMARK 500 ASP A 198 42.42 -145.22 REMARK 500 PHE A 220 -55.24 -123.27 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 117 OD2 REMARK 620 2 ASP A 121 OD2 96.4 REMARK 620 3 ZOL A 901 O17 87.7 98.4 REMARK 620 4 ZOL A 901 O11 81.2 176.0 78.3 REMARK 620 5 MG A 909 MG 79.5 50.2 51.1 126.0 REMARK 620 6 HOH A 911 O 151.0 103.7 109.4 79.7 129.4 REMARK 620 7 HOH A 913 O 75.8 104.8 152.7 77.7 142.3 78.9 REMARK 620 N 1 2 3 4 5 6 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 117 OD1 REMARK 620 2 ASP A 117 OD2 44.2 REMARK 620 3 ASP A 121 OD2 97.0 72.1 REMARK 620 4 ZOL A 901 O17 95.8 65.4 99.7 REMARK 620 5 HOH A 912 O 161.0 154.7 93.0 98.4 REMARK 620 6 HOH A 914 O 85.7 119.7 87.3 172.6 78.6 REMARK 620 7 HOH A 916 O 80.4 113.6 165.5 94.9 85.9 78.2 REMARK 620 N 1 2 3 4 5 6 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 257 OD2 REMARK 620 2 ZOL A 901 O15 76.1 REMARK 620 3 ZOL A 901 O12 94.7 82.8 REMARK 620 4 ZOL A 901 O16 89.4 13.9 85.4 REMARK 620 5 HOH A 915 O 97.7 172.7 94.1 172.9 REMARK 620 6 HOH A 917 O 166.9 96.7 95.1 82.9 90.2 REMARK 620 7 HOH A 960 O 86.9 84.6 166.5 81.2 99.0 81.5 REMARK 620 N 1 2 3 4 5 6 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 IPE A 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZOL A 901 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YV5 RELATED DB: PDB DBREF 1ZW5 A 15 367 UNP P14324 FPPS_HUMAN 1 353 SEQADV 1ZW5 GLY A 13 UNP P14324 CLONING ARTIFACT SEQADV 1ZW5 HIS A 14 UNP P14324 CLONING ARTIFACT SEQRES 1 A 355 GLY HIS MET ASN GLY ASP GLN ASN SER ASP VAL TYR ALA SEQRES 2 A 355 GLN GLU LYS GLN ASP PHE VAL GLN HIS PHE SER GLN ILE SEQRES 3 A 355 VAL ARG VAL LEU THR GLU ASP GLU MET GLY HIS PRO GLU SEQRES 4 A 355 ILE GLY ASP ALA ILE ALA ARG LEU LYS GLU VAL LEU GLU SEQRES 5 A 355 TYR ASN ALA ILE GLY GLY LYS TYR ASN ARG GLY LEU THR SEQRES 6 A 355 VAL VAL VAL ALA PHE ARG GLU LEU VAL GLU PRO ARG LYS SEQRES 7 A 355 GLN ASP ALA ASP SER LEU GLN ARG ALA TRP THR VAL GLY SEQRES 8 A 355 TRP CYS VAL GLU LEU LEU GLN ALA PHE PHE LEU VAL ALA SEQRES 9 A 355 ASP ASP ILE MET ASP SER SER LEU THR ARG ARG GLY GLN SEQRES 10 A 355 ILE CYS TRP TYR GLN LYS PRO GLY VAL GLY LEU ASP ALA SEQRES 11 A 355 ILE ASN ASP ALA ASN LEU LEU GLU ALA CYS ILE TYR ARG SEQRES 12 A 355 LEU LEU LYS LEU TYR CYS ARG GLU GLN PRO TYR TYR LEU SEQRES 13 A 355 ASN LEU ILE GLU LEU PHE LEU GLN SER SER TYR GLN THR SEQRES 14 A 355 GLU ILE GLY GLN THR LEU ASP LEU LEU THR ALA PRO GLN SEQRES 15 A 355 GLY ASN VAL ASP LEU VAL ARG PHE THR GLU LYS ARG TYR SEQRES 16 A 355 LYS SER ILE VAL LYS TYR LYS THR ALA PHE TYR SER PHE SEQRES 17 A 355 TYR LEU PRO ILE ALA ALA ALA MET TYR MET ALA GLY ILE SEQRES 18 A 355 ASP GLY GLU LYS GLU HIS ALA ASN ALA LYS LYS ILE LEU SEQRES 19 A 355 LEU GLU MET GLY GLU PHE PHE GLN ILE GLN ASP ASP TYR SEQRES 20 A 355 LEU ASP LEU PHE GLY ASP PRO SER VAL THR GLY LYS ILE SEQRES 21 A 355 GLY THR ASP ILE GLN ASP ASN LYS CYS SER TRP LEU VAL SEQRES 22 A 355 VAL GLN CYS LEU GLN ARG ALA THR PRO GLU GLN TYR GLN SEQRES 23 A 355 ILE LEU LYS GLU ASN TYR GLY GLN LYS GLU ALA GLU LYS SEQRES 24 A 355 VAL ALA ARG VAL LYS ALA LEU TYR GLU GLU LEU ASP LEU SEQRES 25 A 355 PRO ALA VAL PHE LEU GLN TYR GLU GLU ASP SER TYR SER SEQRES 26 A 355 HIS ILE MET ALA LEU ILE GLU GLN TYR ALA ALA PRO LEU SEQRES 27 A 355 PRO PRO ALA VAL PHE LEU GLY LEU ALA ARG LYS ILE TYR SEQRES 28 A 355 LYS ARG ARG LYS HET MG A 907 1 HET MG A 908 1 HET MG A 909 1 HET IPE A 900 14 HET ZOL A 901 16 HETNAM MG MAGNESIUM ION HETNAM IPE 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE HETNAM ZOL ZOLEDRONIC ACID HETSYN IPE ISOPENTENYL PYROPHOSPHATE HETSYN ZOL (1-HYDROXY-2-IMIDAZOL-1-YLETHYLIDENE)DIPHOSPHONIC ACID FORMUL 2 MG 3(MG 2+) FORMUL 5 IPE C5 H12 O7 P2 FORMUL 6 ZOL C5 H10 N2 O7 P2 FORMUL 7 HOH *60(H2 O) HELIX 1 1 GLU A 27 HIS A 34 1 8 HELIX 2 2 HIS A 34 GLU A 44 1 11 HELIX 3 3 ILE A 52 ALA A 67 1 16 HELIX 4 4 TYR A 72 VAL A 86 1 15 HELIX 5 5 GLU A 87 GLN A 91 5 5 HELIX 6 6 ASP A 92 ASP A 121 1 30 HELIX 7 7 TRP A 132 LYS A 135 5 4 HELIX 8 8 VAL A 138 LEU A 140 5 3 HELIX 9 9 ASP A 141 ARG A 162 1 22 HELIX 10 10 TYR A 166 THR A 191 1 26 HELIX 11 11 ASP A 198 PHE A 202 5 5 HELIX 12 12 THR A 203 THR A 215 1 13 HELIX 13 13 THR A 215 PHE A 220 1 6 HELIX 14 14 PHE A 220 ALA A 231 1 12 HELIX 15 15 GLY A 235 GLY A 264 1 30 HELIX 16 16 ASP A 265 GLY A 270 1 6 HELIX 17 17 SER A 282 ALA A 292 1 11 HELIX 18 18 THR A 293 TYR A 304 1 12 HELIX 19 19 GLU A 308 LEU A 322 1 15 HELIX 20 20 ASP A 323 ALA A 347 1 25 HELIX 21 21 PRO A 352 TYR A 363 1 12 SHEET 1 A 2 THR A 125 ARG A 126 0 SHEET 2 A 2 GLN A 129 ILE A 130 -1 O GLN A 129 N ARG A 126 LINK OD2 ASP A 117 MG MG A 907 1555 1555 2.13 LINK OD1 ASP A 117 MG MG A 909 1555 1555 2.20 LINK OD2 ASP A 117 MG MG A 909 1555 1555 3.14 LINK OD2 ASP A 121 MG MG A 907 1555 1555 2.17 LINK OD2 ASP A 121 MG MG A 909 1555 1555 2.13 LINK OD2 ASP A 257 MG MG A 908 1555 1555 2.17 LINK O17 ZOL A 901 MG MG A 907 1555 1555 2.17 LINK O11 ZOL A 901 MG MG A 907 1555 1555 2.18 LINK O15 ZOL A 901 MG MG A 908 1555 1555 4.61 LINK O12 ZOL A 901 MG MG A 908 1555 1555 2.15 LINK O16 ZOL A 901 MG MG A 908 1555 1555 2.18 LINK O17 ZOL A 901 MG MG A 909 1555 1555 2.17 LINK MG MG A 907 MG MG A 909 1555 1555 2.72 LINK MG MG A 907 O HOH A 911 1555 1555 1.93 LINK MG MG A 907 O HOH A 913 1555 1555 2.31 LINK MG MG A 908 O HOH A 915 1555 1555 2.03 LINK MG MG A 908 O HOH A 917 1555 1555 2.10 LINK MG MG A 908 O HOH A 960 1555 1555 2.11 LINK MG MG A 909 O HOH A 912 1555 1555 2.32 LINK MG MG A 909 O HOH A 914 1555 1555 2.05 LINK MG MG A 909 O HOH A 916 1555 1555 1.97 CISPEP 1 ALA A 348 PRO A 349 0 -4.62 SITE 1 AC1 6 ASP A 117 ASP A 121 ZOL A 901 MG A 909 SITE 2 AC1 6 HOH A 911 HOH A 913 SITE 1 AC2 5 ASP A 257 ZOL A 901 HOH A 915 HOH A 917 SITE 2 AC2 5 HOH A 960 SITE 1 AC3 8 ASP A 117 ASP A 121 ASP A 188 ZOL A 901 SITE 2 AC3 8 MG A 907 HOH A 912 HOH A 914 HOH A 916 SITE 1 AC4 15 GLY A 70 LYS A 71 ARG A 74 GLN A 110 SITE 2 AC4 15 ARG A 127 TYR A 218 GLN A 254 ASP A 257 SITE 3 AC4 15 ZOL A 901 HOH A 946 HOH A 957 HOH A 963 SITE 4 AC4 15 HOH A 965 HOH A 966 HOH A 968 SITE 1 AC5 19 ASP A 117 ASP A 121 ARG A 126 LYS A 214 SITE 2 AC5 19 THR A 215 GLN A 254 ASP A 257 LYS A 271 SITE 3 AC5 19 IPE A 900 MG A 907 MG A 908 MG A 909 SITE 4 AC5 19 HOH A 911 HOH A 913 HOH A 915 HOH A 916 SITE 5 AC5 19 HOH A 917 HOH A 960 HOH A 961 CRYST1 112.255 112.255 63.245 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 0.008908 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008908 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015812 0.00000