HEADER ISOMERASE/DNA 02-JUN-06 2H7F TITLE STRUCTURE OF VARIOLA TOPOISOMERASE COVALENTLY BOUND TO DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*TP*TP*GP*TP*CP*GP*CP*CP*CP*TP*T)-3'; COMPND 3 CHAIN: Y; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*TP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*AP*CP*A)-3'; COMPND 7 CHAIN: Z; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA TOPOISOMERASE 1; COMPND 11 CHAIN: X; COMPND 12 SYNONYM: DNA TOPOISOMERASE I; COMPND 13 EC: 5.99.1.2; COMPND 14 ENGINEERED: YES; COMPND 15 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: VARIOLA VIRUS; SOURCE 7 ORGANISM_TAXID: 10255; SOURCE 8 GENE: TOP1; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS TYPE IB TOPOISOMERASE, DNA BINDING, PROTEIN-DNA COMPLEX, ISOMERASE, KEYWDS 2 ISOMERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.PERRY,Y.HWANG,F.D.BUSHMAN,G.D.VAN DUYNE REVDAT 6 20-NOV-24 2H7F 1 REMARK REVDAT 5 20-OCT-21 2H7F 1 SEQADV LINK REVDAT 4 18-OCT-17 2H7F 1 REMARK REVDAT 3 13-JUL-11 2H7F 1 VERSN REVDAT 2 24-FEB-09 2H7F 1 VERSN REVDAT 1 15-AUG-06 2H7F 0 JRNL AUTH K.PERRY,Y.HWANG,F.D.BUSHMAN,G.D.VAN DUYNE JRNL TITL STRUCTURAL BASIS FOR SPECIFICITY IN THE POXVIRUS JRNL TITL 2 TOPOISOMERASE. JRNL REF MOL.CELL V. 23 343 2006 JRNL REFN ISSN 1097-2765 JRNL PMID 16885024 JRNL DOI 10.1016/J.MOLCEL.2006.06.015 REMARK 2 REMARK 2 RESOLUTION. 2.70 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 WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 15090 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 770 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1047 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.3150 REMARK 3 BIN FREE R VALUE SET COUNT : 56 REMARK 3 BIN FREE R VALUE : 0.3700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2585 REMARK 3 NUCLEIC ACID ATOMS : 505 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 54 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) : 68.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.30000 REMARK 3 B22 (A**2) : 4.04000 REMARK 3 B33 (A**2) : -2.74000 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): 0.725 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.307 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.234 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 24.213 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3231 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4469 ; 1.530 ; 2.171 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 313 ; 5.721 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 119 ;37.073 ;23.697 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 505 ;20.164 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;20.930 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 500 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2200 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1323 ; 0.225 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2174 ; 0.312 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 94 ; 0.122 ; 0.200 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): 23 ; 0.235 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.154 ; 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): 1610 ; 0.520 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2566 ; 0.915 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1989 ; 1.229 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1903 ; 1.982 ; 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 : 3 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 : X 1 X 74 REMARK 3 ORIGIN FOR THE GROUP (A): -9.5229 -2.6204 14.7187 REMARK 3 T TENSOR REMARK 3 T11: 0.4163 T22: -0.1459 REMARK 3 T33: 0.1603 T12: -0.3041 REMARK 3 T13: 0.1107 T23: -0.1391 REMARK 3 L TENSOR REMARK 3 L11: 8.0003 L22: 10.4924 REMARK 3 L33: 6.5469 L12: 2.6217 REMARK 3 L13: -2.1735 L23: 2.3476 REMARK 3 S TENSOR REMARK 3 S11: -0.2087 S12: 0.0486 S13: -1.1335 REMARK 3 S21: 0.0759 S22: -0.1824 S23: 0.4188 REMARK 3 S31: 1.7735 S32: -0.4414 S33: 0.3911 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : X 75 X 314 REMARK 3 ORIGIN FOR THE GROUP (A): 9.1895 29.0344 12.2459 REMARK 3 T TENSOR REMARK 3 T11: -0.2903 T22: -0.2080 REMARK 3 T33: -0.3651 T12: -0.0979 REMARK 3 T13: -0.0619 T23: 0.0228 REMARK 3 L TENSOR REMARK 3 L11: 5.8249 L22: 3.7414 REMARK 3 L33: 4.7873 L12: -0.3012 REMARK 3 L13: -0.7778 L23: -0.2377 REMARK 3 S TENSOR REMARK 3 S11: -0.0249 S12: 0.1765 S13: 0.2524 REMARK 3 S21: -0.0167 S22: -0.2104 S23: -0.1546 REMARK 3 S31: -0.2773 S32: 0.3780 S33: 0.2353 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : Y 501 Y 511 REMARK 3 ORIGIN FOR THE GROUP (A): -8.9327 17.4861 9.3722 REMARK 3 T TENSOR REMARK 3 T11: -0.1359 T22: -0.1391 REMARK 3 T33: -0.0926 T12: -0.1469 REMARK 3 T13: 0.0225 T23: -0.1020 REMARK 3 L TENSOR REMARK 3 L11: 3.6644 L22: 3.7470 REMARK 3 L33: 6.4753 L12: -0.5193 REMARK 3 L13: 0.7915 L23: -0.3929 REMARK 3 S TENSOR REMARK 3 S11: 0.0550 S12: 0.2887 S13: -0.2132 REMARK 3 S21: -0.3867 S22: 0.1976 S23: 0.8872 REMARK 3 S31: 0.2026 S32: -0.6769 S33: -0.2526 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 2H7F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1000038023. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-APR-05; 12-APR-05 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : ALS; ALS REMARK 200 BEAMLINE : 8.2.1; 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97917; 0.97952, 0.97935, REMARK 200 0.96394 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4; ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14945 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.19900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE 2.03 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% PEG 8000, 0.1M TRIS-HCL, PH 8.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z 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 56.53950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.53950 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 34.26150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 69.11600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.26150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 69.11600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 56.53950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.26150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 69.11600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 56.53950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.26150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 69.11600 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: Y, Z, X 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 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 X 327 LIES ON A SPECIAL POSITION. 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 DT Y 502 O3' DT Y 502 C3' -0.044 REMARK 500 DG Z 521 O3' DG Z 521 C3' -0.041 REMARK 500 DC Z 524 O3' DC Z 524 C3' -0.037 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 DT Y 501 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 DT Y 504 C5' - C4' - O4' ANGL. DEV. = 7.5 DEGREES REMARK 500 DT Y 504 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 DA Z 516 O5' - C5' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 DA Z 516 O4' - C1' - N9 ANGL. DEV. = -4.7 DEGREES REMARK 500 DA Z 517 C1' - O4' - C4' ANGL. DEV. = -6.7 DEGREES REMARK 500 DA Z 517 C3' - O3' - P ANGL. DEV. = 9.6 DEGREES REMARK 500 DA Z 519 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 DA Z 520 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 DG Z 522 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG Z 522 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG Z 522 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC Z 527 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA Z 528 O4' - C1' - N9 ANGL. DEV. = 4.0 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 LYS X 7 118.30 -165.46 REMARK 500 ASN X 16 40.90 -108.52 REMARK 500 ASN X 19 74.80 60.36 REMARK 500 ASN X 25 127.95 -39.33 REMARK 500 ARG X 56 -156.84 -145.44 REMARK 500 THR X 111 40.45 -106.23 REMARK 500 TYR X 183 -71.32 -57.33 REMARK 500 SER X 194 88.14 -159.09 REMARK 500 SER X 243 137.03 -32.62 REMARK 500 PRO X 244 -75.91 7.82 REMARK 500 LEU X 245 139.79 169.52 REMARK 500 PTR X 274 -50.29 -124.28 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 SER X 243 PRO X 244 -148.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2H7G RELATED DB: PDB DBREF 2H7F X 1 314 UNP P32989 TOP1_VARV 1 314 DBREF 2H7F Y 501 511 PDB 2H7F 2H7F 501 511 DBREF 2H7F Z 515 528 PDB 2H7F 2H7F 515 528 SEQADV 2H7F SER X 100 UNP P32989 CYS 100 ENGINEERED MUTATION SEQADV 2H7F SER X 211 UNP P32989 CYS 211 ENGINEERED MUTATION SEQADV 2H7F PTR X 274 UNP P32989 TYR 274 MODIFIED RESIDUE SEQRES 1 Y 11 DT DT DG DT DC DG DC DC DC DT DT SEQRES 1 Z 14 DT DA DA DT DA DA DG DG DG DC DG DA DC SEQRES 2 Z 14 DA SEQRES 1 X 314 MET ARG ALA LEU PHE TYR LYS ASP GLY LYS LEU PHE THR SEQRES 2 X 314 ASP ASN ASN PHE LEU ASN PRO VAL SER ASP ASN ASN PRO SEQRES 3 X 314 ALA TYR GLU VAL LEU GLN HIS VAL LYS ILE PRO THR HIS SEQRES 4 X 314 LEU THR ASP VAL VAL VAL TYR GLY GLN THR TRP GLU GLU SEQRES 5 X 314 ALA LEU THR ARG LEU ILE PHE VAL GLY SER ASP SER LYS SEQRES 6 X 314 GLY ARG ARG GLN TYR PHE TYR GLY LYS MET HIS VAL GLN SEQRES 7 X 314 ASN ARG ASN ALA LYS ARG ASP ARG ILE PHE VAL ARG VAL SEQRES 8 X 314 TYR ASN VAL MET LYS ARG ILE ASN SER PHE ILE ASN LYS SEQRES 9 X 314 ASN ILE LYS LYS SER SER THR ASP SER ASN TYR GLN LEU SEQRES 10 X 314 ALA VAL PHE MET LEU MET GLU THR MET PHE PHE ILE ARG SEQRES 11 X 314 PHE GLY LYS MET LYS TYR LEU LYS GLU ASN GLU THR VAL SEQRES 12 X 314 GLY LEU LEU THR LEU LYS ASN LYS HIS ILE GLU ILE SER SEQRES 13 X 314 PRO ASP LYS ILE VAL ILE LYS PHE VAL GLY LYS ASP LYS SEQRES 14 X 314 VAL SER HIS GLU PHE VAL VAL HIS LYS SER ASN ARG LEU SEQRES 15 X 314 TYR LYS PRO LEU LEU LYS LEU THR ASP ASP SER SER PRO SEQRES 16 X 314 GLU GLU PHE LEU PHE ASN LYS LEU SER GLU ARG LYS VAL SEQRES 17 X 314 TYR GLU SER ILE LYS GLN PHE GLY ILE ARG ILE LYS ASP SEQRES 18 X 314 LEU ARG THR TYR GLY VAL ASN TYR THR PHE LEU TYR ASN SEQRES 19 X 314 PHE TRP THR ASN VAL LYS SER ILE SER PRO LEU PRO SER SEQRES 20 X 314 PRO LYS LYS LEU ILE ALA LEU THR ILE LYS GLN THR ALA SEQRES 21 X 314 GLU VAL VAL GLY HIS THR PRO SER ILE SER LYS ARG ALA SEQRES 22 X 314 PTR MET ALA THR THR ILE LEU GLU MET VAL LYS ASP LYS SEQRES 23 X 314 ASN PHE LEU ASP VAL VAL SER LYS THR THR PHE ASP GLU SEQRES 24 X 314 PHE LEU SER ILE VAL VAL ASP HIS VAL LYS SER SER THR SEQRES 25 X 314 ASP GLY MODRES 2H7F PTR X 274 TYR O-PHOSPHOTYROSINE HET PTR X 274 16 HETNAM PTR O-PHOSPHOTYROSINE HETSYN PTR PHOSPHONOTYROSINE FORMUL 3 PTR C9 H12 N O6 P FORMUL 4 HOH *54(H2 O) HELIX 1 1 PRO X 26 VAL X 34 1 9 HELIX 2 2 THR X 49 LEU X 54 1 6 HELIX 3 3 GLY X 73 ILE X 106 1 34 HELIX 4 4 ASP X 112 PHE X 128 1 17 HELIX 5 5 LYS X 133 GLU X 141 1 9 HELIX 6 6 LYS X 149 LYS X 151 5 3 HELIX 7 7 LYS X 167 LYS X 169 5 3 HELIX 8 8 LEU X 182 THR X 190 1 9 HELIX 9 9 SER X 204 LYS X 213 1 10 HELIX 10 10 GLN X 214 GLY X 216 5 3 HELIX 11 11 ARG X 218 ILE X 242 1 25 HELIX 12 12 SER X 247 GLY X 264 1 18 HELIX 13 13 THR X 266 PTR X 274 1 9 HELIX 14 14 ALA X 276 VAL X 283 1 8 HELIX 15 15 LYS X 284 LYS X 286 5 3 HELIX 16 16 ASN X 287 LYS X 294 1 8 HELIX 17 17 THR X 296 THR X 312 1 17 SHEET 1 A 5 LYS X 10 PHE X 12 0 SHEET 2 A 5 ALA X 3 LYS X 7 -1 N PHE X 5 O PHE X 12 SHEET 3 A 5 THR X 41 TYR X 46 -1 O VAL X 45 N LEU X 4 SHEET 4 A 5 LEU X 57 SER X 62 -1 O VAL X 60 N VAL X 44 SHEET 5 A 5 ARG X 68 TYR X 72 -1 O GLN X 69 N GLY X 61 SHEET 1 B 3 ILE X 153 ILE X 155 0 SHEET 2 B 3 LYS X 159 VAL X 165 -1 O VAL X 161 N GLU X 154 SHEET 3 B 3 SER X 171 HIS X 177 -1 O VAL X 176 N ILE X 160 LINK C3' DT Y 511 O3P PTR X 274 1555 1555 2.12 LINK C ALA X 273 N PTR X 274 1555 1555 1.33 LINK C PTR X 274 N MET X 275 1555 1555 1.33 CRYST1 68.523 138.232 113.079 90.00 90.00 90.00 C 2 2 21 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 0.014594 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007234 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008843 0.00000