PDB Short entry for 1YV5 HEADER TRANSFERASE 15-FEB-05 1YV5 TITLE HUMAN FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH MG AND RISEDRONATE 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 GERANYLTRANSTRANSFERASE; 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,F.VON DELFT,C.ARROWSMITH,M.SUNDSTROM,A.EDWARDS, AUTHOR 2 U.OPPERMANN,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 7 25-OCT-23 1YV5 1 REMARK SEQADV LINK REVDAT 6 04-OCT-17 1YV5 1 HETSYN REVDAT 5 13-JUL-11 1YV5 1 VERSN REVDAT 4 12-JAN-10 1YV5 1 JRNL REVDAT 3 24-FEB-09 1YV5 1 VERSN REVDAT 2 28-JUN-05 1YV5 1 KEYWDS AUTHOR REVDAT 1 01-MAR-05 1YV5 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 28467 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) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1529 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2098 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2980 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2650 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 82 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 34.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.20000 REMARK 3 B22 (A**2) : -3.20000 REMARK 3 B33 (A**2) : 6.41000 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): 0.168 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.158 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.158 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.697 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2758 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2491 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3739 ; 1.531 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5762 ; 0.824 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 340 ; 5.484 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 125 ;34.077 ;24.480 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 455 ;14.515 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;18.511 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 416 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3049 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 563 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 643 ; 0.218 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2423 ; 0.170 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1386 ; 0.195 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1532 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 91 ; 0.159 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.142 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 5 ; 0.163 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 43 ; 0.151 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.132 ; 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): 1746 ; 2.122 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 683 ; 0.540 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2699 ; 3.248 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1194 ; 5.361 ; 7.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1037 ; 6.838 ;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 364 REMARK 3 ORIGIN FOR THE GROUP (A): 9.7683 30.1995 -7.1343 REMARK 3 T TENSOR REMARK 3 T11: -0.1019 T22: -0.0899 REMARK 3 T33: -0.1783 T12: 0.0121 REMARK 3 T13: -0.0255 T23: -0.0057 REMARK 3 L TENSOR REMARK 3 L11: 2.2139 L22: 1.5406 REMARK 3 L33: 0.6826 L12: -0.0305 REMARK 3 L13: 0.4095 L23: -0.2513 REMARK 3 S TENSOR REMARK 3 S11: 0.0061 S12: -0.1069 S13: 0.0058 REMARK 3 S21: 0.0044 S22: 0.0459 S23: 0.3184 REMARK 3 S31: -0.0340 S32: -0.0651 S33: -0.0519 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, RESTRAINTS ON MAGNESIUM TO OXYGEN DISTANCES HAVE BEEN REMARK 3 USED, DENSITY NEAR THE N- AND C-TERMINI AND THE SIDE-CHAIN OF REMARK 3 RESIDUE 34 WAS NOT INTERPRETABLE AND WAS LEFT UNMODELLED. REMARK 4 REMARK 4 1YV5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1000031954. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JAN-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.16 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30212 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 70.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : 0.09200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1UBV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% PEG 300, 0.1M PHOSPHATE-CITRATE, REMARK 280 PH 4.2, 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 35.13200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 55.47300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 55.47300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.56600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 55.47300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 55.47300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 52.69800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 55.47300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.47300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.56600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 55.47300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.47300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 52.69800 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 35.13200 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: 6860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -111.0 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 -6 REMARK 465 SER A -5 REMARK 465 SER A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 REMARK 465 HIS A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 GLY A 5 REMARK 465 ARG A 6 REMARK 465 GLU A 7 REMARK 465 ASN A 8 REMARK 465 LEU A 9 REMARK 465 TYR A 10 REMARK 465 PHE A 11 REMARK 465 GLN A 12 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 465 ARG A 365 REMARK 465 ARG A 366 REMARK 465 LYS A 367 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 CG CD CE NZ REMARK 470 GLN A 29 CG CD OE1 NE2 REMARK 470 GLN A 37 CD OE1 NE2 REMARK 470 ASP A 45 CG OD1 OD2 REMARK 470 ILE A 52 CG1 CG2 CD1 REMARK 470 GLU A 87 CG CD OE1 OE2 REMARK 470 ARG A 89 NE CZ NH1 NH2 REMARK 470 LYS A 90 CD CE NZ REMARK 470 GLN A 194 CD OE1 NE2 REMARK 470 ASP A 198 CG OD1 OD2 REMARK 470 ARG A 201 NE CZ NH1 NH2 REMARK 470 LYS A 205 CD CE NZ REMARK 470 GLU A 236 CD OE1 OE2 REMARK 470 LYS A 237 CD CE NZ REMARK 470 LYS A 243 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 GLU A 321 CD OE1 OE2 REMARK 470 GLU A 333 OE1 OE2 REMARK 470 GLU A 344 CD OE1 OE2 REMARK 470 LYS A 364 CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 131 CB CYS A 131 SG -0.096 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 54 CB - CG - OD1 ANGL. DEV. = -6.9 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 138 -76.63 -108.76 REMARK 500 THR A 215 -44.75 -131.53 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 92.7 REMARK 620 3 RIS A 901 O15 86.6 90.4 REMARK 620 4 RIS A 901 O12 96.7 165.7 79.4 REMARK 620 5 MG A 909 MG 68.1 48.8 49.3 125.9 REMARK 620 6 HOH A1009 O 167.7 91.3 105.0 81.8 122.6 REMARK 620 7 HOH A1017 O 89.0 110.4 158.9 80.6 145.5 78.7 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 OD2 REMARK 620 2 ASP A 117 OD1 50.5 REMARK 620 3 ASP A 121 OD2 77.7 104.9 REMARK 620 4 RIS A 901 O15 71.7 111.3 93.8 REMARK 620 5 HOH A1012 O 154.6 153.8 84.3 92.1 REMARK 620 6 HOH A1034 O 117.2 76.2 88.6 171.1 79.6 REMARK 620 7 HOH A1049 O 119.0 84.6 162.6 96.2 81.2 79.5 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 RIS A 901 O16 91.9 REMARK 620 3 RIS A 901 O11 88.5 91.4 REMARK 620 4 HOH A1045 O 86.7 83.0 172.5 REMARK 620 5 HOH A1046 O 91.3 176.6 89.8 96.0 REMARK 620 6 HOH A1080 O 159.0 89.9 112.5 72.7 86.7 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 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 PO4 A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RIS A 901 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YQ7 RELATED DB: PDB DBREF 1YV5 A 15 367 UNP P14324 FPPS_HUMAN 1 353 SEQADV 1YV5 GLY A -6 UNP P14324 CLONING ARTIFACT SEQADV 1YV5 SER A -5 UNP P14324 CLONING ARTIFACT SEQADV 1YV5 SER A -4 UNP P14324 CLONING ARTIFACT SEQADV 1YV5 HIS A -3 UNP P14324 CLONING ARTIFACT SEQADV 1YV5 HIS A -2 UNP P14324 CLONING ARTIFACT SEQADV 1YV5 HIS A -1 UNP P14324 CLONING ARTIFACT SEQADV 1YV5 HIS A 0 UNP P14324 CLONING ARTIFACT SEQADV 1YV5 HIS A 1 UNP P14324 CLONING ARTIFACT SEQADV 1YV5 HIS A 2 UNP P14324 CLONING ARTIFACT SEQADV 1YV5 SER A 3 UNP P14324 CLONING ARTIFACT SEQADV 1YV5 SER A 4 UNP P14324 CLONING ARTIFACT SEQADV 1YV5 GLY A 5 UNP P14324 CLONING ARTIFACT SEQADV 1YV5 ARG A 6 UNP P14324 CLONING ARTIFACT SEQADV 1YV5 GLU A 7 UNP P14324 CLONING ARTIFACT SEQADV 1YV5 ASN A 8 UNP P14324 CLONING ARTIFACT SEQADV 1YV5 LEU A 9 UNP P14324 CLONING ARTIFACT SEQADV 1YV5 TYR A 10 UNP P14324 CLONING ARTIFACT SEQADV 1YV5 PHE A 11 UNP P14324 CLONING ARTIFACT SEQADV 1YV5 GLN A 12 UNP P14324 CLONING ARTIFACT SEQADV 1YV5 GLY A 13 UNP P14324 CLONING ARTIFACT SEQADV 1YV5 HIS A 14 UNP P14324 CLONING ARTIFACT SEQRES 1 A 374 GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY ARG SEQRES 2 A 374 GLU ASN LEU TYR PHE GLN GLY HIS MET ASN GLY ASP GLN SEQRES 3 A 374 ASN SER ASP VAL TYR ALA GLN GLU LYS GLN ASP PHE VAL SEQRES 4 A 374 GLN HIS PHE SER GLN ILE VAL ARG VAL LEU THR GLU ASP SEQRES 5 A 374 GLU MET GLY HIS PRO GLU ILE GLY ASP ALA ILE ALA ARG SEQRES 6 A 374 LEU LYS GLU VAL LEU GLU TYR ASN ALA ILE GLY GLY LYS SEQRES 7 A 374 TYR ASN ARG GLY LEU THR VAL VAL VAL ALA PHE ARG GLU SEQRES 8 A 374 LEU VAL GLU PRO ARG LYS GLN ASP ALA ASP SER LEU GLN SEQRES 9 A 374 ARG ALA TRP THR VAL GLY TRP CYS VAL GLU LEU LEU GLN SEQRES 10 A 374 ALA PHE PHE LEU VAL ALA ASP ASP ILE MET ASP SER SER SEQRES 11 A 374 LEU THR ARG ARG GLY GLN ILE CYS TRP TYR GLN LYS PRO SEQRES 12 A 374 GLY VAL GLY LEU ASP ALA ILE ASN ASP ALA ASN LEU LEU SEQRES 13 A 374 GLU ALA CYS ILE TYR ARG LEU LEU LYS LEU TYR CYS ARG SEQRES 14 A 374 GLU GLN PRO TYR TYR LEU ASN LEU ILE GLU LEU PHE LEU SEQRES 15 A 374 GLN SER SER TYR GLN THR GLU ILE GLY GLN THR LEU ASP SEQRES 16 A 374 LEU LEU THR ALA PRO GLN GLY ASN VAL ASP LEU VAL ARG SEQRES 17 A 374 PHE THR GLU LYS ARG TYR LYS SER ILE VAL LYS TYR LYS SEQRES 18 A 374 THR ALA PHE TYR SER PHE TYR LEU PRO ILE ALA ALA ALA SEQRES 19 A 374 MET TYR MET ALA GLY ILE ASP GLY GLU LYS GLU HIS ALA SEQRES 20 A 374 ASN ALA LYS LYS ILE LEU LEU GLU MET GLY GLU PHE PHE SEQRES 21 A 374 GLN ILE GLN ASP ASP TYR LEU ASP LEU PHE GLY ASP PRO SEQRES 22 A 374 SER VAL THR GLY LYS ILE GLY THR ASP ILE GLN ASP ASN SEQRES 23 A 374 LYS CYS SER TRP LEU VAL VAL GLN CYS LEU GLN ARG ALA SEQRES 24 A 374 THR PRO GLU GLN TYR GLN ILE LEU LYS GLU ASN TYR GLY SEQRES 25 A 374 GLN LYS GLU ALA GLU LYS VAL ALA ARG VAL LYS ALA LEU SEQRES 26 A 374 TYR GLU GLU LEU ASP LEU PRO ALA VAL PHE LEU GLN TYR SEQRES 27 A 374 GLU GLU ASP SER TYR SER HIS ILE MET ALA LEU ILE GLU SEQRES 28 A 374 GLN TYR ALA ALA PRO LEU PRO PRO ALA VAL PHE LEU GLY SEQRES 29 A 374 LEU ALA ARG LYS ILE TYR LYS ARG ARG LYS HET MG A 907 1 HET MG A 908 1 HET MG A 909 1 HET PO4 A1001 5 HET PO4 A1002 5 HET RIS A 901 17 HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION HETNAM RIS 1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID HETSYN RIS RISEDRONATE FORMUL 2 MG 3(MG 2+) FORMUL 5 PO4 2(O4 P 3-) FORMUL 7 RIS C7 H11 N O7 P2 FORMUL 8 HOH *82(H2 O) HELIX 1 1 GLU A 27 HIS A 34 1 8 HELIX 2 2 HIS A 34 THR A 43 1 10 HELIX 3 3 HIS A 49 GLU A 51 5 3 HELIX 4 4 ILE A 52 ALA A 67 1 16 HELIX 5 5 TYR A 72 VAL A 86 1 15 HELIX 6 6 GLU A 87 GLN A 91 5 5 HELIX 7 7 ASP A 92 ASP A 121 1 30 HELIX 8 8 TRP A 132 LYS A 135 5 4 HELIX 9 9 VAL A 138 LEU A 140 5 3 HELIX 10 10 ASP A 141 ARG A 162 1 22 HELIX 11 11 TYR A 166 ALA A 192 1 27 HELIX 12 12 ASP A 198 PHE A 202 5 5 HELIX 13 13 THR A 203 THR A 215 1 13 HELIX 14 14 THR A 215 PHE A 220 1 6 HELIX 15 15 PHE A 220 ALA A 231 1 12 HELIX 16 16 GLY A 235 GLY A 264 1 30 HELIX 17 17 ASP A 265 GLY A 270 1 6 HELIX 18 18 SER A 282 GLN A 290 1 9 HELIX 19 19 THR A 293 TYR A 304 1 12 HELIX 20 20 GLU A 308 LEU A 322 1 15 HELIX 21 21 ASP A 323 ALA A 347 1 25 HELIX 22 22 PRO A 351 TYR A 363 1 13 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 2.10 LINK OD2 ASP A 117 MG MG A 909 1555 1555 2.78 LINK OD1 ASP A 117 MG MG A 909 1555 1555 2.12 LINK OD2 ASP A 121 MG MG A 907 1555 1555 2.20 LINK OD2 ASP A 121 MG MG A 909 1555 1555 2.11 LINK OD2 ASP A 257 MG MG A 908 1555 1555 2.18 LINK O15 RIS A 901 MG MG A 907 1555 1555 2.16 LINK O12 RIS A 901 MG MG A 907 1555 1555 2.17 LINK O16 RIS A 901 MG MG A 908 1555 1555 2.15 LINK O11 RIS A 901 MG MG A 908 1555 1555 2.15 LINK O15 RIS A 901 MG MG A 909 1555 1555 2.13 LINK MG MG A 907 MG MG A 909 1555 1555 2.77 LINK MG MG A 907 O HOH A1009 1555 1555 1.79 LINK MG MG A 907 O HOH A1017 1555 1555 2.27 LINK MG MG A 908 O HOH A1045 1555 1555 2.19 LINK MG MG A 908 O HOH A1046 1555 1555 2.09 LINK MG MG A 908 O HOH A1080 1555 1555 2.01 LINK MG MG A 909 O HOH A1012 1555 1555 2.20 LINK MG MG A 909 O HOH A1034 1555 1555 1.98 LINK MG MG A 909 O HOH A1049 1555 1555 2.06 CISPEP 1 ALA A 348 PRO A 349 0 9.94 SITE 1 AC1 6 ASP A 117 ASP A 121 RIS A 901 MG A 909 SITE 2 AC1 6 HOH A1009 HOH A1017 SITE 1 AC2 5 ASP A 257 RIS A 901 HOH A1045 HOH A1046 SITE 2 AC2 5 HOH A1080 SITE 1 AC3 7 ASP A 117 ASP A 121 RIS A 901 MG A 907 SITE 2 AC3 7 HOH A1012 HOH A1034 HOH A1049 SITE 1 AC4 9 GLY A 70 LYS A 71 ARG A 74 GLN A 110 SITE 2 AC4 9 ARG A 127 PO4 A1002 HOH A1018 HOH A1026 SITE 3 AC4 9 HOH A1050 SITE 1 AC5 8 ARG A 74 GLN A 110 ARG A 126 PHE A 253 SITE 2 AC5 8 LYS A 271 RIS A 901 PO4 A1001 HOH A1050 SITE 1 AC6 22 ASP A 117 ASP A 121 ARG A 126 GLN A 185 SITE 2 AC6 22 LYS A 214 THR A 215 GLN A 254 ASP A 257 SITE 3 AC6 22 LYS A 271 MG A 907 MG A 908 MG A 909 SITE 4 AC6 22 PO4 A1002 HOH A1009 HOH A1010 HOH A1017 SITE 5 AC6 22 HOH A1044 HOH A1045 HOH A1046 HOH A1049 SITE 6 AC6 22 HOH A1076 HOH A1080 CRYST1 110.946 110.946 70.264 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 0.009013 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009013 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014232 0.00000