HEADER TRANSFERASE 17-JUL-09 3ICM TITLE TRYPANOSOMA CRUZI FARNESYL DIPHOSPHATE SYNTHASE HOMODIMER IN COMPLEX TITLE 2 WITH ISOPENTENYL PYROPHOSPHATE, MG2+ AND 1-(2-HYDROXY-2,2-BIS- TITLE 3 PHOSPHONO-ETHYL)-3-PHENYL-PYRIDINIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: FARNESYL PYROPHOSPHATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.5.1.10; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA CRUZI; SOURCE 3 ORGANISM_TAXID: 5693; SOURCE 4 GENE: FPPS; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS FARNESYL DIPHOSPHATE SYNTHASE, FPPS, BISPHOSPHONATE, ZOLEDRONATE, KEYWDS 2 RISEDRONATE, MINODRONATE, CHAGAS DISEASE, ISOPRENE BIOSYNTHESIS, KEYWDS 3 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR L.M.AMZEL,C.H.HUANG,S.B.GABELLI,E.OLDFIELD REVDAT 4 21-FEB-24 3ICM 1 REMARK LINK REVDAT 3 01-NOV-17 3ICM 1 REMARK REVDAT 2 17-APR-13 3ICM 1 HET HETATM HETNAM VERSN REVDAT 1 09-FEB-10 3ICM 0 JRNL AUTH C.H.HUANG,S.B.GABELLI,E.OLDFIELD,L.M.AMZEL JRNL TITL BINDING OF NITROGEN-CONTAINING BISPHOSPHONATES (N-BPS) TO JRNL TITL 2 THE TRYPANOSOMA CRUZI FARNESYL DIPHOSPHATE SYNTHASE JRNL TITL 3 HOMODIMER. JRNL REF PROTEINS V. 78 888 2010 JRNL REFN ISSN 0887-3585 JRNL PMID 19876942 JRNL DOI 10.1002/PROT.22614 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 40.05 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 21540 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1077 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) : 1482 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2000 REMARK 3 BIN FREE R VALUE SET COUNT : 63 REMARK 3 BIN FREE R VALUE : 0.3280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2891 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 296 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.18000 REMARK 3 B22 (A**2) : 0.18000 REMARK 3 B33 (A**2) : -0.27000 REMARK 3 B12 (A**2) : 0.09000 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): 0.273 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.226 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.158 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.153 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2997 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4066 ; 1.814 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 361 ; 5.644 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 137 ;40.679 ;24.307 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 513 ;16.174 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;19.717 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 446 ; 0.132 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2247 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1613 ; 0.235 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2110 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 243 ; 0.233 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.092 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 85 ; 0.242 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 28 ; 0.329 ; 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): 1866 ; 1.176 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2912 ; 1.719 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1323 ; 2.872 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1154 ; 4.282 ; 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3ICM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054243. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27660 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 10.30 REMARK 200 R MERGE (I) : 0.75000 REMARK 200 R SYM (I) : 0.75000 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) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.43000 REMARK 200 R SYM FOR SHELL (I) : 0.43000 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, 200MM AMMONIUM SULFATE, PH REMARK 280 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 131.40967 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 262.81933 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 197.11450 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 328.52417 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 65.70483 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 131.40967 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 262.81933 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 328.52417 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 197.11450 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 65.70483 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: 8260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -124.0 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 0.500000 -0.866025 0.000000 29.16750 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 50.51959 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 328.52417 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 605 LIES ON A SPECIAL POSITION. 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 O4 SO4 A 371 O HOH A 502 1.65 REMARK 500 O HOH A 369 O HOH A 630 1.78 REMARK 500 O HOH A 386 O HOH A 609 1.95 REMARK 500 OE2 GLU A 13 O HOH A 649 2.03 REMARK 500 OE1 GLN A 157 O HOH A 647 2.10 REMARK 500 O HOH A 479 O HOH A 648 2.11 REMARK 500 OE1 GLU A 231 O HOH A 634 2.18 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 426 O HOH A 426 10665 1.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 107 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG A 107 NE - CZ - NH2 ANGL. DEV. = -7.7 DEGREES REMARK 500 ARG A 108 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 108 NE - CZ - NH2 ANGL. DEV. = -3.3 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 119 -75.45 -108.92 REMARK 500 THR A 120 161.19 67.28 REMARK 500 ASP A 181 107.04 -168.56 REMARK 500 TYR A 213 -51.88 -121.24 REMARK 500 LYS A 284 -14.49 -142.68 REMARK 500 GLN A 318 27.07 -69.61 REMARK 500 ALA A 319 -19.91 -143.76 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 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 98 OD2 REMARK 620 2 ASP A 102 OD2 89.8 REMARK 620 3 P2H A 363 O11 90.8 168.7 REMARK 620 4 P2H A 363 O15 90.5 81.2 87.5 REMARK 620 5 HOH A 492 O 178.4 91.5 88.1 90.7 REMARK 620 6 HOH A 565 O 85.0 95.3 95.9 174.3 93.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 98 OD1 REMARK 620 2 ASP A 102 OD2 83.4 REMARK 620 3 P2H A 363 O15 99.7 79.1 REMARK 620 4 HOH A 364 O 175.9 93.1 81.6 REMARK 620 5 HOH A 365 O 94.8 175.6 97.3 88.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 250 OD2 REMARK 620 2 P2H A 363 O12 97.5 REMARK 620 3 P2H A 363 O17 96.2 91.4 REMARK 620 4 HOH A 366 O 88.5 172.7 84.0 REMARK 620 5 HOH A 367 O 170.0 90.0 90.1 84.4 REMARK 620 6 HOH A 368 O 93.6 90.9 169.6 92.7 79.8 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 P2H A 363 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 371 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPE A 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IBA RELATED DB: PDB REMARK 900 RELATED ID: 3ICK RELATED DB: PDB REMARK 900 RELATED ID: 1YHL RELATED DB: PDB REMARK 900 RELATED ID: 1YKM RELATED DB: PDB REMARK 900 RELATED ID: 1YHK RELATED DB: PDB REMARK 900 RELATED ID: 3ICN RELATED DB: PDB REMARK 900 RELATED ID: 3ICZ RELATED DB: PDB REMARK 900 RELATED ID: 3ID0 RELATED DB: PDB DBREF 3ICM A 1 362 UNP Q95WL3 Q95WL3_TRYCR 1 362 SEQRES 1 A 362 MET ALA SER MET GLU ARG PHE LEU SER VAL TYR ASP GLU SEQRES 2 A 362 VAL GLN ALA PHE LEU LEU ASP GLN LEU GLN SER LYS TYR SEQRES 3 A 362 GLU ILE ASP PRO ASN ARG ALA ARG TYR LEU ARG ILE MET SEQRES 4 A 362 MET ASP THR THR CYS LEU GLY GLY LYS TYR PHE ARG GLY SEQRES 5 A 362 MET THR VAL VAL ASN VAL ALA GLU GLY PHE LEU ALA VAL SEQRES 6 A 362 THR GLN HIS ASP GLU ALA THR LYS GLU ARG ILE LEU HIS SEQRES 7 A 362 ASP ALA CYS VAL GLY GLY TRP MET ILE GLU PHE LEU GLN SEQRES 8 A 362 ALA HIS TYR LEU VAL GLU ASP ASP ILE MET ASP GLY SER SEQRES 9 A 362 VAL MET ARG ARG GLY LYS PRO CYS TRP TYR ARG PHE PRO SEQRES 10 A 362 GLY VAL THR THR GLN CYS ALA ILE ASN ASP GLY ILE ILE SEQRES 11 A 362 LEU LYS SER TRP THR GLN ILE MET ALA TRP HIS TYR PHE SEQRES 12 A 362 ALA ASP ARG PRO PHE LEU LYS ASP LEU LEU CYS LEU PHE SEQRES 13 A 362 GLN LYS VAL ASP TYR ALA THR ALA VAL GLY GLN MET TYR SEQRES 14 A 362 ASP VAL THR SER MET CYS ASP SER ASN LYS LEU ASP PRO SEQRES 15 A 362 GLU VAL ALA GLN PRO MET THR THR ASP PHE ALA GLU PHE SEQRES 16 A 362 THR PRO ALA ILE TYR LYS ARG ILE VAL LYS TYR LYS THR SEQRES 17 A 362 THR PHE TYR THR TYR LEU LEU PRO LEU VAL MET GLY LEU SEQRES 18 A 362 PHE VAL SER GLU ALA ALA ALA SER VAL GLU MET ASN LEU SEQRES 19 A 362 VAL GLU ARG VAL ALA HIS LEU ILE GLY GLU TYR PHE GLN SEQRES 20 A 362 VAL GLN ASP ASP VAL MET ASP CYS PHE THR PRO PRO GLU SEQRES 21 A 362 GLN LEU GLY LYS VAL GLY THR ASP ILE GLU ASP ALA LYS SEQRES 22 A 362 CYS SER TRP LEU ALA VAL THR PHE LEU GLY LYS ALA ASN SEQRES 23 A 362 ALA ALA GLN VAL ALA GLU PHE LYS ALA ASN TYR GLY ASP SEQRES 24 A 362 LYS ASP PRO ALA LYS VAL ALA VAL VAL LYS ARG LEU TYR SEQRES 25 A 362 SER GLU ALA ASN LEU GLN ALA ASP PHE ALA ALA TYR GLU SEQRES 26 A 362 ALA GLU VAL VAL ARG GLU VAL GLU SER LEU ILE GLU GLN SEQRES 27 A 362 LEU LYS VAL LYS SER PRO THR PHE ALA GLU SER VAL ALA SEQRES 28 A 362 VAL VAL TRP GLU LYS THR HIS LYS ARG LYS LYS HET P2H A 363 23 HET SO4 A 371 5 HET IPE A 900 14 HET MG A 401 1 HET MG A 402 1 HET MG A 403 1 HETNAM P2H 1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)-3-PHENYLPYRIDINIUM HETNAM SO4 SULFATE ION HETNAM IPE 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE HETNAM MG MAGNESIUM ION HETSYN IPE ISOPENTENYL PYROPHOSPHATE FORMUL 2 P2H C13 H16 N O7 P2 1+ FORMUL 3 SO4 O4 S 2- FORMUL 4 IPE C5 H12 O7 P2 FORMUL 5 MG 3(MG 2+) FORMUL 8 HOH *296(H2 O) HELIX 1 1 MET A 1 TYR A 26 1 26 HELIX 2 2 ASP A 29 LEU A 45 1 17 HELIX 3 3 TYR A 49 VAL A 65 1 17 HELIX 4 4 ASP A 69 ASP A 102 1 34 HELIX 5 5 TRP A 113 PHE A 116 5 4 HELIX 6 6 VAL A 119 ALA A 144 1 26 HELIX 7 7 PHE A 148 THR A 172 1 25 HELIX 8 8 ASP A 176 LEU A 180 5 5 HELIX 9 9 THR A 196 THR A 208 1 13 HELIX 10 10 THR A 208 TYR A 213 1 6 HELIX 11 11 TYR A 213 GLU A 225 1 13 HELIX 12 12 ALA A 226 VAL A 230 5 5 HELIX 13 13 GLU A 231 THR A 257 1 27 HELIX 14 14 PRO A 258 GLY A 263 1 6 HELIX 15 15 THR A 267 ALA A 272 1 6 HELIX 16 16 SER A 275 LEU A 282 1 8 HELIX 17 17 ASN A 286 TYR A 297 1 12 HELIX 18 18 ASP A 301 ALA A 315 1 15 HELIX 19 19 ASN A 316 VAL A 341 1 26 HELIX 20 20 SER A 343 LYS A 359 1 17 SHEET 1 A 2 MET A 106 ARG A 107 0 SHEET 2 A 2 LYS A 110 PRO A 111 -1 O LYS A 110 N ARG A 107 LINK OD2 ASP A 98 MG MG A 401 1555 1555 2.12 LINK OD1 ASP A 98 MG MG A 403 1555 1555 2.14 LINK OD2 ASP A 102 MG MG A 401 1555 1555 2.24 LINK OD2 ASP A 102 MG MG A 403 1555 1555 2.24 LINK OD2 ASP A 250 MG MG A 402 1555 1555 2.12 LINK O11 P2H A 363 MG MG A 401 1555 1555 1.90 LINK O15 P2H A 363 MG MG A 401 1555 1555 2.19 LINK O12 P2H A 363 MG MG A 402 1555 1555 2.02 LINK O17 P2H A 363 MG MG A 402 1555 1555 2.09 LINK O15 P2H A 363 MG MG A 403 1555 1555 2.29 LINK O HOH A 364 MG MG A 403 1555 1555 2.42 LINK O HOH A 365 MG MG A 403 1555 1555 2.20 LINK O HOH A 366 MG MG A 402 1555 1555 2.24 LINK O HOH A 367 MG MG A 402 1555 1555 2.37 LINK O HOH A 368 MG MG A 402 1555 1555 2.23 LINK MG MG A 401 O HOH A 492 1555 1555 2.18 LINK MG MG A 401 O HOH A 565 1555 1555 2.02 SITE 1 AC1 22 TYR A 94 ASP A 98 ASP A 102 ARG A 107 SITE 2 AC1 22 THR A 163 GLN A 167 LYS A 207 TYR A 211 SITE 3 AC1 22 ASP A 250 LYS A 264 HOH A 364 HOH A 365 SITE 4 AC1 22 HOH A 366 HOH A 368 MG A 401 MG A 402 SITE 5 AC1 22 MG A 403 HOH A 482 HOH A 492 HOH A 565 SITE 6 AC1 22 HOH A 613 IPE A 900 SITE 1 AC2 7 GLY A 47 LYS A 48 TYR A 49 ARG A 108 SITE 2 AC2 7 HOH A 387 HOH A 502 HOH A 564 SITE 1 AC3 16 LYS A 48 ARG A 51 GLN A 91 ARG A 108 SITE 2 AC3 16 THR A 208 TYR A 211 THR A 212 PHE A 246 SITE 3 AC3 16 GLN A 247 ASP A 250 P2H A 363 HOH A 387 SITE 4 AC3 16 HOH A 462 HOH A 502 HOH A 564 HOH A 593 SITE 1 AC4 6 ASP A 98 ASP A 102 P2H A 363 MG A 403 SITE 2 AC4 6 HOH A 492 HOH A 565 SITE 1 AC5 5 ASP A 250 P2H A 363 HOH A 366 HOH A 367 SITE 2 AC5 5 HOH A 368 SITE 1 AC6 6 ASP A 98 ASP A 102 P2H A 363 HOH A 364 SITE 2 AC6 6 HOH A 365 MG A 401 CRYST1 58.335 58.335 394.229 90.00 90.00 120.00 P 61 2 2 12 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 0.017142 0.009897 0.000000 0.00000 SCALE2 0.000000 0.019794 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002537 0.00000