HEADER TRANSFERASE 09-JAN-05 1YHL TITLE STRUCTURE OF THE COMPLEX OF TRYPANOSOMA CRUZI FARNESYL DIPHOSPHATE TITLE 2 SYNTHASE WITH RISEDRONATE, DMAPP AND MG+2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: FARNESYL PYROPHOSPHATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA CRUZI; SOURCE 3 ORGANISM_TAXID: 5693; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PET28 KEYWDS FARNESYL DIPHOSPHATE SYNTHASE, BISPHOSPHONATE, DIMETHYL ALLYL KEYWDS 2 PYROPHOSPHATE SULFATE, FPPS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.B.GABELLI,J.S.MCLELLAN,A.MONTALVETTI,E.OLDFIELD,R.DOCAMPO,L.M.AMZEL REVDAT 6 14-FEB-24 1YHL 1 REMARK LINK REVDAT 5 04-OCT-17 1YHL 1 REMARK HETSYN REVDAT 4 13-JUL-11 1YHL 1 VERSN REVDAT 3 24-FEB-09 1YHL 1 VERSN REVDAT 2 23-MAY-06 1YHL 1 KEYWDS REVDAT 1 20-DEC-05 1YHL 0 JRNL AUTH S.B.GABELLI,J.S.MCLELLAN,A.MONTALVETTI,E.OLDFIELD,R.DOCAMPO, JRNL AUTH 2 L.M.AMZEL JRNL TITL STRUCTURE AND MECHANISM OF THE FARNESYL DIPHOSPHATE SYNTHASE JRNL TITL 2 FROM TRYPANOSOMA CRUZI: IMPLICATIONS FOR DRUG DESIGN. JRNL REF PROTEINS V. 62 80 2005 JRNL REFN ISSN 0887-3585 JRNL PMID 16288456 JRNL DOI 10.1002/PROT.20754 REMARK 2 REMARK 2 RESOLUTION. 1.95 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 64.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 27981 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1497 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1768 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.38 REMARK 3 BIN R VALUE (WORKING SET) : 0.2220 REMARK 3 BIN FREE R VALUE SET COUNT : 109 REMARK 3 BIN FREE R VALUE : 0.3270 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 : 39 REMARK 3 SOLVENT ATOMS : 392 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.39000 REMARK 3 B22 (A**2) : 0.39000 REMARK 3 B33 (A**2) : -0.58000 REMARK 3 B12 (A**2) : 0.19000 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): 0.165 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.160 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.105 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.621 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2990 ; 0.027 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4056 ; 2.248 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 361 ; 6.525 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 137 ;40.558 ;24.307 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 513 ;15.473 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;22.245 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 446 ; 0.280 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2239 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1708 ; 0.256 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2137 ; 0.312 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 350 ; 0.232 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.035 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 97 ; 0.286 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 37 ; 0.378 ; 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): 1871 ; 1.580 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2912 ; 2.069 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1316 ; 3.547 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1144 ; 5.113 ; 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 : 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: NULL REMARK 4 REMARK 4 1YHL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000031519. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-04 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 : X25 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 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29502 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 64.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 8.900 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : 0.08700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.6, LIQUID DIFFUSION, TEMPERATURE REMARK 280 295K 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 129.83733 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 259.67467 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 194.75600 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 324.59333 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 64.91867 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 129.83733 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 259.67467 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 324.59333 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 194.75600 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 64.91867 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A DIMER THAT CAN BE GENERATED REMARK 300 WITH THE TWO FOLD AXIS. 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: 9150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27230 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 0.500000 -0.866025 0.000000 29.07600 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 50.36111 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 324.59333 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 CB MET A 1 O HOH A 1573 1.68 REMARK 500 O HOH A 1583 O HOH A 1769 1.90 REMARK 500 N MET A 1 O HOH A 1750 1.93 REMARK 500 OE1 GLN A 318 O HOH A 1539 1.95 REMARK 500 O HOH A 1551 O HOH A 1578 1.97 REMARK 500 O HOH A 1687 O HOH A 1773 1.98 REMARK 500 CB HIS A 358 O HOH A 1744 2.01 REMARK 500 O1A DMA A 1301 O HOH A 1424 2.03 REMARK 500 O HOH A 1488 O HOH A 1673 2.04 REMARK 500 O HOH A 1697 O HOH A 1780 2.07 REMARK 500 N ALA A 2 O HOH A 1586 2.08 REMARK 500 NZ LYS A 73 O HOH A 1452 2.09 REMARK 500 O HOH A 1534 O HOH A 1629 2.10 REMARK 500 O ALA A 2 O HOH A 1573 2.12 REMARK 500 O HOH A 1509 O HOH A 1688 2.13 REMARK 500 O HOH A 1545 O HOH A 1590 2.16 REMARK 500 OE1 GLU A 231 O HOH A 1636 2.17 REMARK 500 O HOH A 1488 O HOH A 1541 2.17 REMARK 500 O HOH A 1637 O HOH A 1744 2.18 REMARK 500 O HOH A 1609 O HOH A 1789 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 1441 O HOH A 1441 10665 0.98 REMARK 500 OE1 GLU A 5 OE1 GLU A 5 10555 1.70 REMARK 500 O HOH A 1729 O HOH A 1729 10555 1.93 REMARK 500 O HOH A 1469 O HOH A 1723 8566 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 175 CB CYS A 175 SG 0.109 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 MET A 1 CA - CB - CG ANGL. DEV. = 12.6 DEGREES REMARK 500 MET A 1 N - CA - C ANGL. DEV. = -21.2 DEGREES REMARK 500 ALA A 2 C - N - CA ANGL. DEV. = -18.6 DEGREES REMARK 500 ALA A 2 N - CA - CB ANGL. DEV. = 18.8 DEGREES REMARK 500 SER A 3 CA - CB - OG ANGL. DEV. = -16.3 DEGREES REMARK 500 ARG A 34 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 LEU A 36 CB - CG - CD1 ANGL. DEV. = -11.2 DEGREES REMARK 500 ARG A 51 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 MET A 168 CG - SD - CE ANGL. DEV. = -15.0 DEGREES REMARK 500 ARG A 202 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 202 NE - CZ - NH2 ANGL. DEV. = -4.4 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 ALA A 2 -149.27 -83.41 REMARK 500 SER A 3 -70.53 59.39 REMARK 500 VAL A 119 -78.33 -106.63 REMARK 500 THR A 120 166.29 76.92 REMARK 500 ASP A 181 114.59 -168.14 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 MET A 1 ALA A 2 139.48 REMARK 500 ALA A 2 SER A 3 -125.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1767 DISTANCE = 6.06 ANGSTROMS 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 A1401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 98 OD2 REMARK 620 2 ASP A 102 OD2 92.4 REMARK 620 3 RIS A1400 O12 94.3 168.5 REMARK 620 4 RIS A1400 O15 93.7 88.6 81.6 REMARK 620 5 MG A1403 MG 77.7 42.8 130.1 50.6 REMARK 620 6 HOH A1407 O 81.0 102.7 87.6 167.7 137.5 REMARK 620 7 HOH A1408 O 172.4 87.2 87.4 93.8 106.8 91.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 98 OD1 REMARK 620 2 ASP A 102 OD2 88.5 REMARK 620 3 RIS A1400 O15 94.6 82.8 REMARK 620 4 HOH A1406 O 174.4 87.9 89.2 REMARK 620 5 HOH A1409 O 91.7 179.0 96.2 91.9 REMARK 620 6 HOH A1532 O 85.7 95.9 178.6 90.3 85.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 250 OD2 REMARK 620 2 RIS A1400 O16 96.5 REMARK 620 3 RIS A1400 O11 88.4 94.0 REMARK 620 4 HOH A1410 O 87.1 93.9 171.3 REMARK 620 5 HOH A1411 O 172.9 87.9 96.9 87.1 REMARK 620 6 HOH A1533 O 91.5 170.9 81.9 90.8 84.5 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 1401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMA A 1301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RIS A 1400 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YHK RELATED DB: PDB DBREF 1YHL A 1 362 UNP Q8WS26 Q8WS26_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 MG A1401 1 HET MG A1402 1 HET MG A1403 1 HET SO4 A1405 5 HET DMA A1301 14 HET RIS A1400 17 HETNAM MG MAGNESIUM ION HETNAM SO4 SULFATE ION HETNAM DMA DIMETHYLALLYL DIPHOSPHATE HETNAM RIS 1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID HETSYN RIS RISEDRONATE FORMUL 2 MG 3(MG 2+) FORMUL 5 SO4 O4 S 2- FORMUL 6 DMA C5 H12 O7 P2 FORMUL 7 RIS C7 H11 N O7 P2 FORMUL 8 HOH *392(H2 O) HELIX 1 1 SER A 3 GLU A 27 1 25 HELIX 2 2 ASP A 29 LEU A 45 1 17 HELIX 3 3 TYR A 49 ALA A 64 1 16 HELIX 4 4 ASP A 69 GLY A 103 1 35 HELIX 5 5 TRP A 113 PHE A 116 5 4 HELIX 6 6 VAL A 119 PHE A 143 1 25 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 SER A 224 1 12 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 SER A 275 GLY A 283 1 9 HELIX 16 16 ASN A 286 TYR A 297 1 12 HELIX 17 17 ASP A 301 ALA A 315 1 15 HELIX 18 18 ASN A 316 LYS A 340 1 25 HELIX 19 19 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 A1401 1555 1555 2.02 LINK OD1 ASP A 98 MG MG A1403 1555 1555 2.03 LINK OD2 ASP A 102 MG MG A1401 1555 1555 2.13 LINK OD2 ASP A 102 MG MG A1403 1555 1555 2.09 LINK OD2 ASP A 250 MG MG A1402 1555 1555 2.18 LINK O12 RIS A1400 MG MG A1401 1555 1555 2.14 LINK O15 RIS A1400 MG MG A1401 1555 1555 2.11 LINK O16 RIS A1400 MG MG A1402 1555 1555 1.99 LINK O11 RIS A1400 MG MG A1402 1555 1555 2.20 LINK O15 RIS A1400 MG MG A1403 1555 1555 2.38 LINK MG MG A1401 MG MG A1403 1555 1555 3.07 LINK MG MG A1401 O HOH A1407 1555 1555 2.08 LINK MG MG A1401 O HOH A1408 1555 1555 2.16 LINK MG MG A1402 O HOH A1410 1555 1555 2.02 LINK MG MG A1402 O HOH A1411 1555 1555 2.04 LINK MG MG A1402 O HOH A1533 1555 1555 2.05 LINK MG MG A1403 O HOH A1406 1555 1555 2.23 LINK MG MG A1403 O HOH A1409 1555 1555 1.99 LINK MG MG A1403 O HOH A1532 1555 1555 2.13 SITE 1 AC1 6 ASP A 98 ASP A 102 RIS A1400 MG A1403 SITE 2 AC1 6 HOH A1407 HOH A1408 SITE 1 AC2 5 ASP A 250 RIS A1400 HOH A1410 HOH A1411 SITE 2 AC2 5 HOH A1533 SITE 1 AC3 7 ASP A 98 ASP A 102 RIS A1400 MG A1401 SITE 2 AC3 7 HOH A1406 HOH A1409 HOH A1532 SITE 1 AC4 3 HIS A 141 HOH A1501 HOH A1647 SITE 1 AC5 15 GLY A 47 LYS A 48 TYR A 49 PHE A 50 SITE 2 AC5 15 ARG A 51 GLN A 91 ARG A 108 TYR A 211 SITE 3 AC5 15 PHE A 246 LYS A 264 LYS A 362 RIS A1400 SITE 4 AC5 15 HOH A1415 HOH A1424 HOH A1574 SITE 1 AC6 23 LEU A 95 ASP A 98 ASP A 102 ARG A 107 SITE 2 AC6 23 GLN A 167 LYS A 207 THR A 208 TYR A 211 SITE 3 AC6 23 ASP A 250 LYS A 264 DMA A1301 MG A1401 SITE 4 AC6 23 MG A1402 MG A1403 HOH A1407 HOH A1408 SITE 5 AC6 23 HOH A1409 HOH A1410 HOH A1411 HOH A1440 SITE 6 AC6 23 HOH A1455 HOH A1533 HOH A1663 CRYST1 58.152 58.152 389.512 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 0.017196 0.009928 0.000000 0.00000 SCALE2 0.000000 0.019857 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002567 0.00000