PDB Short entry for 1YQ7 HEADER TRANSFERASE 01-FEB-05 1YQ7 TITLE HUMAN FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH RISEDRONATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FARNESYL PYROPHOSPHATE SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FARNESYL DIPHOSPHATE, FPP SYNTHETASE, FPS, FARNESYL COMPND 5 DIPHOSPHATE SYNTHETASE, 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 BIOSYNTHESIS, BISPHOSPHONATE KEYWDS 2 INHIBITOR, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, KEYWDS 3 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 6 25-OCT-23 1YQ7 1 REMARK SEQADV LINK REVDAT 5 04-OCT-17 1YQ7 1 HETSYN REVDAT 4 13-JUL-11 1YQ7 1 VERSN REVDAT 3 24-FEB-09 1YQ7 1 VERSN REVDAT 2 28-JUN-05 1YQ7 1 KEYWDS AUTHOR REVDAT 1 22-FEB-05 1YQ7 0 JRNL AUTH K.L.KAVANAGH,K.GUO,U.OPPERMANN JRNL TITL HUMAN FARNESYL DIPHOSPHATE COMPLEXED WITH CLINICAL INHIBITOR JRNL TITL 2 RISEDRONATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 21373 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) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1155 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1390 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.07 REMARK 3 BIN R VALUE (WORKING SET) : 0.3290 REMARK 3 BIN FREE R VALUE SET COUNT : 77 REMARK 3 BIN FREE R VALUE : 0.4270 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2654 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 52 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) : 19.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.70000 REMARK 3 B22 (A**2) : -3.70000 REMARK 3 B33 (A**2) : 7.39000 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): 0.257 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.221 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.215 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.360 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2767 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2494 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3751 ; 1.574 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5784 ; 0.834 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 340 ; 6.078 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 130 ;37.994 ;24.769 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 463 ;17.242 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;19.521 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 416 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3059 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 561 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 709 ; 0.237 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2537 ; 0.176 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1375 ; 0.195 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1566 ; 0.089 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 91 ; 0.211 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.049 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 12 ; 0.118 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 62 ; 0.146 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 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): 1816 ; 2.215 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 680 ; 0.528 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2693 ; 3.258 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1223 ; 5.326 ; 7.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1054 ; 6.640 ;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 363 REMARK 3 ORIGIN FOR THE GROUP (A): 9.7940 30.1365 -7.1528 REMARK 3 T TENSOR REMARK 3 T11: -0.0757 T22: -0.0937 REMARK 3 T33: -0.1653 T12: 0.0296 REMARK 3 T13: -0.0240 T23: -0.0342 REMARK 3 L TENSOR REMARK 3 L11: 2.0848 L22: 0.7794 REMARK 3 L33: 0.9300 L12: 0.0431 REMARK 3 L13: 0.4112 L23: -0.0448 REMARK 3 S TENSOR REMARK 3 S11: 0.0508 S12: -0.0089 S13: -0.0706 REMARK 3 S21: 0.0106 S22: 0.0710 S23: 0.4652 REMARK 3 S31: -0.0717 S32: -0.0268 S33: -0.1217 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 1YQ7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1000031801. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-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) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MULTI-LAYER OPTICS REMARK 200 OPTICS : NULL 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 : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21912 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 55.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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: 6930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -109.0 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 HIS A 49 REMARK 465 LYS A 364 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 LYS A 71 NZ REMARK 470 ARG A 89 NE CZ NH1 NH2 REMARK 470 GLN A 194 CD OE1 NE2 REMARK 470 ARG A 201 CD NE CZ NH1 NH2 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 CD CE 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 344 CD OE1 OE2 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 92 151.27 -38.86 REMARK 500 VAL A 138 -70.05 -126.37 REMARK 500 THR A 215 -50.71 -131.17 REMARK 500 VAL A 268 -60.98 -93.34 REMARK 500 ASP A 323 55.78 70.10 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 117 OD1 58.0 REMARK 620 3 ASP A 121 OD2 115.5 74.0 REMARK 620 4 RIS A 901 O15 116.4 81.4 93.7 REMARK 620 5 RIS A 901 O12 86.9 125.1 157.2 78.8 REMARK 620 6 MG A 909 MG 107.7 50.0 51.0 50.3 128.7 REMARK 620 7 HOH A1010 O 120.5 167.9 97.8 108.4 65.1 131.1 REMARK 620 8 HOH A1019 O 62.8 115.1 112.4 151.7 72.9 157.5 59.2 REMARK 620 N 1 2 3 4 5 6 7 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 121 OD2 78.4 REMARK 620 3 RIS A 901 O15 86.4 93.8 REMARK 620 4 HOH A1014 O 153.0 75.8 87.3 REMARK 620 5 HOH A1037 O 115.9 81.0 155.1 67.8 REMARK 620 N 1 2 3 4 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 O11 81.9 REMARK 620 3 RIS A 901 O16 92.4 79.1 REMARK 620 4 HOH A1050 O 79.4 160.1 94.9 REMARK 620 5 HOH A1051 O 89.0 79.2 157.8 107.1 REMARK 620 N 1 2 3 4 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 DBREF 1YQ7 A 15 367 UNP P14324 FPPS_HUMAN 1 353 SEQADV 1YQ7 GLY A -6 UNP P14324 CLONING ARTIFACT SEQADV 1YQ7 SER A -5 UNP P14324 CLONING ARTIFACT SEQADV 1YQ7 SER A -4 UNP P14324 CLONING ARTIFACT SEQADV 1YQ7 HIS A -3 UNP P14324 CLONING ARTIFACT SEQADV 1YQ7 HIS A -2 UNP P14324 CLONING ARTIFACT SEQADV 1YQ7 HIS A -1 UNP P14324 CLONING ARTIFACT SEQADV 1YQ7 HIS A 0 UNP P14324 CLONING ARTIFACT SEQADV 1YQ7 HIS A 1 UNP P14324 CLONING ARTIFACT SEQADV 1YQ7 HIS A 2 UNP P14324 CLONING ARTIFACT SEQADV 1YQ7 SER A 3 UNP P14324 CLONING ARTIFACT SEQADV 1YQ7 SER A 4 UNP P14324 CLONING ARTIFACT SEQADV 1YQ7 GLY A 5 UNP P14324 CLONING ARTIFACT SEQADV 1YQ7 ARG A 6 UNP P14324 CLONING ARTIFACT SEQADV 1YQ7 GLU A 7 UNP P14324 CLONING ARTIFACT SEQADV 1YQ7 ASN A 8 UNP P14324 CLONING ARTIFACT SEQADV 1YQ7 LEU A 9 UNP P14324 CLONING ARTIFACT SEQADV 1YQ7 TYR A 10 UNP P14324 CLONING ARTIFACT SEQADV 1YQ7 PHE A 11 UNP P14324 CLONING ARTIFACT SEQADV 1YQ7 GLN A 12 UNP P14324 CLONING ARTIFACT SEQADV 1YQ7 GLY A 13 UNP P14324 CLONING ARTIFACT SEQADV 1YQ7 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 *52(H2 O) HELIX 1 1 GLU A 27 GLU A 44 1 18 HELIX 2 2 ILE A 52 ILE A 68 1 17 HELIX 3 3 TYR A 72 VAL A 86 1 15 HELIX 4 4 GLU A 87 GLN A 91 5 5 HELIX 5 5 ASP A 92 ASP A 121 1 30 HELIX 6 6 TRP A 132 LYS A 135 5 4 HELIX 7 7 VAL A 138 LEU A 140 5 3 HELIX 8 8 ASP A 141 ARG A 162 1 22 HELIX 9 9 TYR A 166 THR A 191 1 26 HELIX 10 10 ASP A 198 PHE A 202 5 5 HELIX 11 11 THR A 203 THR A 215 1 13 HELIX 12 12 THR A 215 PHE A 220 1 6 HELIX 13 13 PHE A 220 ALA A 231 1 12 HELIX 14 14 GLY A 235 GLY A 264 1 30 HELIX 15 15 ASP A 265 GLY A 270 1 6 HELIX 16 16 SER A 282 GLN A 290 1 9 HELIX 17 17 THR A 293 TYR A 304 1 12 HELIX 18 18 GLU A 308 ASP A 323 1 16 HELIX 19 19 ASP A 323 ALA A 347 1 25 HELIX 20 20 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 2.16 LINK OD1 ASP A 117 MG MG A 907 1555 1555 2.40 LINK OD1 ASP A 117 MG MG A 909 1555 1555 2.19 LINK OD2 ASP A 121 MG MG A 907 1555 1555 2.18 LINK OD2 ASP A 121 MG MG A 909 1555 1555 2.17 LINK OD2 ASP A 257 MG MG A 908 1555 1555 2.18 LINK O15 RIS A 901 MG MG A 907 1555 1555 2.14 LINK O12 RIS A 901 MG MG A 907 1555 1555 2.21 LINK O11 RIS A 901 MG MG A 908 1555 1555 2.14 LINK O16 RIS A 901 MG MG A 908 1555 1555 2.13 LINK O15 RIS A 901 MG MG A 909 1555 1555 2.14 LINK MG MG A 907 MG MG A 909 1555 1555 2.74 LINK MG MG A 907 O HOH A1010 1555 1555 1.92 LINK MG MG A 907 O HOH A1019 1555 1555 2.67 LINK MG MG A 908 O HOH A1050 1555 1555 1.99 LINK MG MG A 908 O HOH A1051 1555 1555 2.07 LINK MG MG A 909 O HOH A1014 1555 1555 2.08 LINK MG MG A 909 O HOH A1037 1555 1555 2.82 CISPEP 1 ALA A 348 PRO A 349 0 9.87 SITE 1 AC1 6 ASP A 117 ASP A 121 RIS A 901 MG A 909 SITE 2 AC1 6 HOH A1010 HOH A1019 SITE 1 AC2 4 ASP A 257 RIS A 901 HOH A1050 HOH A1051 SITE 1 AC3 7 ASP A 117 ASP A 121 ASP A 188 RIS A 901 SITE 2 AC3 7 MG A 907 HOH A1014 HOH A1037 SITE 1 AC4 8 GLY A 70 LYS A 71 ARG A 74 GLN A 110 SITE 2 AC4 8 ARG A 127 PO4 A1002 HOH A1020 HOH A1029 SITE 1 AC5 8 ARG A 74 GLN A 110 ARG A 126 PHE A 253 SITE 2 AC5 8 ASP A 257 LYS A 271 RIS A 901 PO4 A1001 SITE 1 AC6 19 ASP A 117 ASP A 121 ARG A 126 GLN A 185 SITE 2 AC6 19 LYS A 214 THR A 215 GLN A 254 ASP A 257 SITE 3 AC6 19 LYS A 271 MG A 907 MG A 908 MG A 909 SITE 4 AC6 19 PO4 A1002 HOH A1010 HOH A1012 HOH A1014 SITE 5 AC6 19 HOH A1019 HOH A1050 HOH A1051 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