HEADER TRANSFERASE 11-MAY-11 3RYE TITLE HUMAN FDPS SYNTHASE IN COMPLEX WITH A N-METHYL PYRIDINUM TITLE 2 BISPHOSPHONATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FARNESYL PYROPHOSPHATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FPP SYNTHASE, FPS, (2E,6E)-FARNESYL DIPHOSPHATE SYNTHASE, COMPND 5 DIMETHYLALLYLTRANSTRANSFERASE, FARNESYL DIPHOSPHATE SYNTHASE, COMPND 6 GERANYLTRANSTRANSFERASE; COMPND 7 EC: 2.5.1.10, 2.5.1.1; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: P11 KEYWDS MAINLY ALPHA HELIX, ISOPRENE, LIPID, STEROID BIOSYNTHESIS, MAGNESIUM KEYWDS 2 BINDING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.G.EVDOKIMOV,B.L.BARNETT,F.H.EBETINO,M.POKROSS REVDAT 2 13-SEP-23 3RYE 1 REMARK SEQADV LINK REVDAT 1 01-JUN-11 3RYE 0 JRNL AUTH A.G.EVDOKIMOV,B.L.BARNETT,F.H.EBETINO,M.POKROSS JRNL TITL HUMAN FDPS SYNTHASE IN COMPLEX WITH A N-METHYL PYRIDINUM JRNL TITL 2 BISPHOSPHONATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 23382 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1262 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1321 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE SET COUNT : 60 REMARK 3 BIN FREE R VALUE : 0.2460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2762 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 151 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.29000 REMARK 3 B22 (A**2) : -0.29000 REMARK 3 B33 (A**2) : 0.57000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.184 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2842 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3854 ; 1.980 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 339 ; 5.000 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 141 ;24.750 ;24.752 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 496 ;15.000 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;15.000 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 420 ; 0.200 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2153 ; 0.021 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1697 ; 2.016 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2730 ; 3.185 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1145 ; 5.142 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1124 ; 7.956 ; 4.500 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3RYE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1000065530. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 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) : 1.0 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : MIRROR/SLIT REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23382 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 35.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 65.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.20000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.700 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 (%): 54.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 15% REMARK 280 ISOPROPANOL, 15% ETHYLENE GLYCOL, PH 4.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K 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 34.85650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 55.65550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 55.65550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.42825 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 55.65550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 55.65550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 52.28475 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 55.65550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.65550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.42825 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 55.65550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.65550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 52.28475 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 34.85650 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: 5090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -117.0 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 34.85650 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 SER A 5 REMARK 465 ASN A 6 REMARK 465 SER A 7 REMARK 465 MET A 33 REMARK 465 GLY A 34 REMARK 465 ARG A 351 REMARK 465 ARG A 352 REMARK 465 LYS A 353 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 OD2 ASP A 184 CG1 VAL A 186 1.98 REMARK 500 OE2 GLU A 13 NH1 ARG A 69 1.99 REMARK 500 O HOH A 428 O HOH A 478 2.02 REMARK 500 O HOH A 447 O HOH A 468 2.12 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 395 O HOH A 395 8555 1.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLN A 77 51.09 -93.04 REMARK 500 VAL A 124 -72.38 -96.97 REMARK 500 VAL A 183 -93.85 -50.04 REMARK 500 PHE A 206 -54.59 -124.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP A 8 VAL A 9 -144.62 REMARK 500 VAL A 183 ASP A 184 -109.11 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 909 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 3 O REMARK 620 2 ASP A 103 OD2 178.5 REMARK 620 3 ASP A 107 OD2 95.5 83.2 REMARK 620 4 HOH A 433 O 86.7 92.6 94.0 REMARK 620 5 HOH A 501 O 93.9 87.5 166.5 96.2 REMARK 620 6 UNR A 901 O5 89.6 91.0 81.7 174.0 88.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 907 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 103 OD1 REMARK 620 2 ASP A 107 OD2 86.1 REMARK 620 3 HOH A 497 O 79.3 99.3 REMARK 620 4 HOH A 500 O 161.3 90.1 83.2 REMARK 620 5 UNR A 901 O9 95.1 172.8 87.9 90.9 REMARK 620 6 UNR A 901 O5 95.2 82.3 174.1 102.5 90.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 908 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 243 OD2 REMARK 620 2 HOH A 476 O 172.1 REMARK 620 3 HOH A 496 O 90.0 85.5 REMARK 620 4 HOH A 499 O 85.9 87.6 89.9 REMARK 620 5 UNR A 901 O8 89.9 94.7 178.7 91.4 REMARK 620 6 UNR A 901 O6 94.4 92.4 94.3 175.7 84.4 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 UNR A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 907 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 908 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 909 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YV5 RELATED DB: PDB REMARK 900 FDPS WITH RISEDRONATE REMARK 900 RELATED ID: 2RAH RELATED DB: PDB REMARK 900 FDPS WITH NOVEL INHIBITOR REMARK 900 RELATED ID: 2VF6 RELATED DB: PDB REMARK 900 FDPS WITH MINODRONATE DBREF 3RYE A 5 353 UNP P14324 FPPS_HUMAN 71 419 SEQADV 3RYE SER A 5 UNP P14324 GLN 71 ENGINEERED MUTATION SEQRES 1 A 349 SER ASN SER ASP VAL TYR ALA GLN GLU LYS GLN ASP PHE SEQRES 2 A 349 VAL GLN HIS PHE SER GLN ILE VAL ARG VAL LEU THR GLU SEQRES 3 A 349 ASP GLU MET GLY HIS PRO GLU ILE GLY ASP ALA ILE ALA SEQRES 4 A 349 ARG LEU LYS GLU VAL LEU GLU TYR ASN ALA ILE GLY GLY SEQRES 5 A 349 LYS TYR ASN ARG GLY LEU THR VAL VAL VAL ALA PHE ARG SEQRES 6 A 349 GLU LEU VAL GLU PRO ARG LYS GLN ASP ALA ASP SER LEU SEQRES 7 A 349 GLN ARG ALA TRP THR VAL GLY TRP CYS VAL GLU LEU LEU SEQRES 8 A 349 GLN ALA PHE PHE LEU VAL ALA ASP ASP ILE MET ASP SER SEQRES 9 A 349 SER LEU THR ARG ARG GLY GLN ILE CYS TRP TYR GLN LYS SEQRES 10 A 349 PRO GLY VAL GLY LEU ASP ALA ILE ASN ASP ALA ASN LEU SEQRES 11 A 349 LEU GLU ALA CYS ILE TYR ARG LEU LEU LYS LEU TYR CYS SEQRES 12 A 349 ARG GLU GLN PRO TYR TYR LEU ASN LEU ILE GLU LEU PHE SEQRES 13 A 349 LEU GLN SER SER TYR GLN THR GLU ILE GLY GLN THR LEU SEQRES 14 A 349 ASP LEU LEU THR ALA PRO GLN GLY ASN VAL ASP LEU VAL SEQRES 15 A 349 ARG PHE THR GLU LYS ARG TYR LYS SER ILE VAL LYS TYR SEQRES 16 A 349 LYS THR ALA PHE TYR SER PHE TYR LEU PRO ILE ALA ALA SEQRES 17 A 349 ALA MET TYR MET ALA GLY ILE ASP GLY GLU LYS GLU HIS SEQRES 18 A 349 ALA ASN ALA LYS LYS ILE LEU LEU GLU MET GLY GLU PHE SEQRES 19 A 349 PHE GLN ILE GLN ASP ASP TYR LEU ASP LEU PHE GLY ASP SEQRES 20 A 349 PRO SER VAL THR GLY LYS ILE GLY THR ASP ILE GLN ASP SEQRES 21 A 349 ASN LYS CYS SER TRP LEU VAL VAL GLN CYS LEU GLN ARG SEQRES 22 A 349 ALA THR PRO GLU GLN TYR GLN ILE LEU LYS GLU ASN TYR SEQRES 23 A 349 GLY GLN LYS GLU ALA GLU LYS VAL ALA ARG VAL LYS ALA SEQRES 24 A 349 LEU TYR GLU GLU LEU ASP LEU PRO ALA VAL PHE LEU GLN SEQRES 25 A 349 TYR GLU GLU ASP SER TYR SER HIS ILE MET ALA LEU ILE SEQRES 26 A 349 GLU GLN TYR ALA ALA PRO LEU PRO PRO ALA VAL PHE LEU SEQRES 27 A 349 GLY LEU ALA ARG LYS ILE TYR LYS ARG ARG LYS HET UNR A 901 18 HET MG A 907 1 HET MG A 908 1 HET MG A 909 1 HET SO4 A1001 5 HETNAM UNR 3-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)-1-METHYLPYRIDINIUM HETNAM MG MAGNESIUM ION HETNAM SO4 SULFATE ION FORMUL 2 UNR C8 H14 N O7 P2 1+ FORMUL 3 MG 3(MG 2+) FORMUL 6 SO4 O4 S 2- FORMUL 7 HOH *151(H2 O) HELIX 1 1 GLU A 13 HIS A 20 1 8 HELIX 2 2 HIS A 20 LEU A 28 1 9 HELIX 3 3 HIS A 35 GLU A 37 5 3 HELIX 4 4 ILE A 38 ALA A 53 1 16 HELIX 5 5 TYR A 58 VAL A 72 1 15 HELIX 6 6 GLU A 73 GLN A 77 5 5 HELIX 7 7 ASP A 78 ASP A 107 1 30 HELIX 8 8 TRP A 118 LYS A 121 5 4 HELIX 9 9 VAL A 124 LEU A 126 5 3 HELIX 10 10 ASP A 127 ARG A 148 1 22 HELIX 11 11 TYR A 152 ALA A 178 1 27 HELIX 12 12 ASP A 184 PHE A 188 5 5 HELIX 13 13 THR A 189 THR A 201 1 13 HELIX 14 14 THR A 201 PHE A 206 1 6 HELIX 15 15 PHE A 206 ALA A 217 1 12 HELIX 16 16 GLY A 221 GLY A 250 1 30 HELIX 17 17 ASP A 251 GLY A 256 1 6 HELIX 18 18 SER A 268 ALA A 278 1 11 HELIX 19 19 THR A 279 TYR A 290 1 12 HELIX 20 20 GLU A 294 LEU A 308 1 15 HELIX 21 21 ASP A 309 ALA A 333 1 25 HELIX 22 22 PRO A 337 LYS A 350 1 14 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 O HOH A 3 MG MG A 909 1555 1555 1.96 LINK OD1 ASP A 103 MG MG A 907 1555 1555 2.09 LINK OD2 ASP A 103 MG MG A 909 1555 1555 2.03 LINK OD2 ASP A 107 MG MG A 907 1555 1555 2.21 LINK OD2 ASP A 107 MG MG A 909 1555 1555 2.11 LINK OD2 ASP A 243 MG MG A 908 1555 1555 2.26 LINK O HOH A 433 MG MG A 909 1555 1555 2.07 LINK O HOH A 476 MG MG A 908 1555 1555 2.02 LINK O HOH A 496 MG MG A 908 1555 1555 2.07 LINK O HOH A 497 MG MG A 907 1555 1555 2.12 LINK O HOH A 499 MG MG A 908 1555 1555 2.23 LINK O HOH A 500 MG MG A 907 1555 1555 2.02 LINK O HOH A 501 MG MG A 909 1555 1555 2.08 LINK O9 UNR A 901 MG MG A 907 1555 1555 2.03 LINK O5 UNR A 901 MG MG A 907 1555 1555 2.07 LINK O8 UNR A 901 MG MG A 908 1555 1555 1.97 LINK O6 UNR A 901 MG MG A 908 1555 1555 2.01 LINK O5 UNR A 901 MG MG A 909 1555 1555 2.19 CISPEP 1 ALA A 334 PRO A 335 0 11.45 SITE 1 AC1 21 HOH A 3 ASP A 103 ASP A 107 ARG A 112 SITE 2 AC1 21 GLN A 171 LYS A 200 THR A 201 ASP A 243 SITE 3 AC1 21 LYS A 257 HOH A 373 HOH A 416 HOH A 417 SITE 4 AC1 21 HOH A 476 HOH A 496 HOH A 497 HOH A 499 SITE 5 AC1 21 HOH A 500 HOH A 501 MG A 907 MG A 908 SITE 6 AC1 21 MG A 909 SITE 1 AC2 6 ASP A 103 ASP A 107 HOH A 497 HOH A 500 SITE 2 AC2 6 UNR A 901 MG A 909 SITE 1 AC3 5 ASP A 243 HOH A 476 HOH A 496 HOH A 499 SITE 2 AC3 5 UNR A 901 SITE 1 AC4 7 HOH A 3 ASP A 103 ASP A 107 HOH A 433 SITE 2 AC4 7 HOH A 501 UNR A 901 MG A 907 SITE 1 AC5 7 HOH A 4 GLY A 56 LYS A 57 GLN A 96 SITE 2 AC5 7 ARG A 113 HOH A 354 HOH A 370 CRYST1 111.311 111.311 69.713 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 0.008984 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008984 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014345 0.00000