HEADER HYDROLASE/DNA 05-APR-07 2PFJ TITLE CRYSTAL STRUCTURE OF T7 ENDO I RESOLVASE IN COMPLEX WITH A HOLLIDAY TITLE 2 JUNCTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 27-MER; COMPND 3 CHAIN: Z; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: DNA HOLLIDAY JUNCTION; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 27-MER; COMPND 8 CHAIN: Y; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: DNA HOLLIDAY JUNCTION; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: ENDODEOXYRIBONUCLEASE 1; COMPND 13 CHAIN: A, B; COMPND 14 SYNONYM: ENDODEOXYRIBONUCLEASE I, ENDONUCLEASE; COMPND 15 EC: 3.1.21.2; COMPND 16 ENGINEERED: YES; COMPND 17 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: ENTEROBACTERIA PHAGE T7; SOURCE 7 ORGANISM_TAXID: 10760; SOURCE 8 GENE: 3; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 (PLYSS); SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS HYDROLASE, HOLLIDAY JUNCTION RESOLVASE, HOMODIMER, DOMAIN SWAPPED, KEYWDS 2 COMPOSITE ACTIVE SITE, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.M.HADDEN,A.C.DECLAIS,S.B.CARR,D.M.LILLEY,S.E.PHILLIPS REVDAT 4 20-OCT-21 2PFJ 1 SEQADV SHEET LINK REVDAT 3 13-JUL-11 2PFJ 1 VERSN REVDAT 2 24-FEB-09 2PFJ 1 VERSN REVDAT 1 30-OCT-07 2PFJ 0 JRNL AUTH J.M.HADDEN,A.C.DECLAIS,S.B.CARR,D.M.LILLEY,S.E.PHILLIPS JRNL TITL THE STRUCTURAL BASIS OF HOLLIDAY JUNCTION RESOLUTION BY T7 JRNL TITL 2 ENDONUCLEASE I. JRNL REF NATURE V. 449 621 2007 JRNL REFN ISSN 0028-0836 JRNL PMID 17873858 JRNL DOI 10.1038/NATURE06158 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 11.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 10851 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) : 0.268 REMARK 3 R VALUE (WORKING SET) : 0.267 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 538 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) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 748 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3870 REMARK 3 BIN FREE R VALUE SET COUNT : 27 REMARK 3 BIN FREE R VALUE : 0.5130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2139 REMARK 3 NUCLEIC ACID ATOMS : 1098 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 0 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) : 96.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.04000 REMARK 3 B12 (A**2) : -0.01000 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): 0.520 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.542 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 41.864 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.909 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3599 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5141 ; 1.893 ; 2.408 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 257 ; 5.743 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 101 ;35.712 ;23.663 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 411 ;19.532 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;10.965 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 537 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3489 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1392 ; 0.229 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2132 ; 0.313 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 85 ; 0.177 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.193 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 19 ; 0.190 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.094 ; 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): 1334 ; 0.640 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2108 ; 1.085 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4698 ; 1.172 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3033 ; 2.598 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 4 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 17 A 77 1 REMARK 3 1 B 17 B 77 1 REMARK 3 2 A 78 A 78 3 REMARK 3 2 B 78 B 78 3 REMARK 3 3 A 79 A 145 1 REMARK 3 3 B 79 B 145 1 REMARK 3 4 A 150 Y 30 1 REMARK 3 4 B 150 Z 30 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 1060 ; 0.05 ; 0.05 REMARK 3 LOOSE POSITIONAL 1 A (A): 6 ; 1.86 ; 5.00 REMARK 3 TIGHT THERMAL 1 A (A**2): 1060 ; 0.09 ; 0.50 REMARK 3 LOOSE THERMAL 1 A (A**2): 6 ; 1.63 ; 10.00 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 : A 17 A 145 REMARK 3 ORIGIN FOR THE GROUP (A): 32.0990 1.5810 -27.0230 REMARK 3 T TENSOR REMARK 3 T11: -0.2240 T22: 0.5872 REMARK 3 T33: -0.0144 T12: -0.4915 REMARK 3 T13: -0.2993 T23: 0.3800 REMARK 3 L TENSOR REMARK 3 L11: 3.6229 L22: 4.7778 REMARK 3 L33: 4.6715 L12: -0.5248 REMARK 3 L13: -0.7993 L23: -2.0248 REMARK 3 S TENSOR REMARK 3 S11: -0.0619 S12: -0.4985 S13: 0.1566 REMARK 3 S21: 0.6371 S22: -0.9775 S23: -1.0436 REMARK 3 S31: -0.7336 S32: 2.2821 S33: 1.0394 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 : B 17 B 145 REMARK 3 ORIGIN FOR THE GROUP (A): 26.5870 -17.3260 -19.2310 REMARK 3 T TENSOR REMARK 3 T11: -0.1628 T22: 0.4781 REMARK 3 T33: 0.1819 T12: 0.1401 REMARK 3 T13: 0.1077 T23: 0.5065 REMARK 3 L TENSOR REMARK 3 L11: 2.4986 L22: 2.5943 REMARK 3 L33: 5.2469 L12: 1.1279 REMARK 3 L13: -0.3042 L23: -2.2075 REMARK 3 S TENSOR REMARK 3 S11: -0.0914 S12: -0.8896 S13: -0.8223 REMARK 3 S21: 0.1573 S22: -0.7089 S23: -0.6707 REMARK 3 S31: 0.8113 S32: 1.7026 S33: 0.8003 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : Z 1 Z 8 REMARK 3 RESIDUE RANGE : Y 22 Y 29 REMARK 3 ORIGIN FOR THE GROUP (A): 44.4780 -10.8660 -22.2450 REMARK 3 T TENSOR REMARK 3 T11: -0.3059 T22: 0.7462 REMARK 3 T33: 0.4499 T12: 0.0281 REMARK 3 T13: 0.0857 T23: 0.6278 REMARK 3 L TENSOR REMARK 3 L11: 5.3504 L22: 3.5595 REMARK 3 L33: 5.9545 L12: 3.1942 REMARK 3 L13: -1.1286 L23: -3.7473 REMARK 3 S TENSOR REMARK 3 S11: -0.3192 S12: -0.0973 S13: -0.3535 REMARK 3 S21: -0.3026 S22: -0.1549 S23: -1.2923 REMARK 3 S31: -0.5706 S32: 1.4623 S33: 0.4740 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 2PFJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-APR-07. REMARK 100 THE DEPOSITION ID IS D_1000042321. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726 REMARK 200 MONOCHROMATOR : SI (111) MONOCHROMATOR REMARK 200 OPTICS : PT COATED SI MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11577 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05200 REMARK 200 FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.34400 REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: GLOBULAR DOMAIN FROM PDB FILE 1FZR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM CACL2, PH 6.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 82.84333 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 41.42167 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 41.42167 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 82.84333 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 PROTEIN HOMODIMER BOUND TO A REMARK 300 FOUR STRANDED DNA JUNCTION. THIS IS REPRESENTED BY THE CONTENTS OF REMARK 300 THE ASYMMTERIC UNIT. 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z, Y, A, B 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 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 DT Z 15 REMARK 465 DT Z 16 REMARK 465 DT Y 15 REMARK 465 DT Y 16 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLY A 3 REMARK 465 TYR A 4 REMARK 465 GLY A 5 REMARK 465 ALA A 6 REMARK 465 LYS A 7 REMARK 465 GLY A 8 REMARK 465 ILE A 9 REMARK 465 ARG A 10 REMARK 465 LYS A 11 REMARK 465 VAL A 12 REMARK 465 GLY A 13 REMARK 465 ALA A 14 REMARK 465 PHE A 15 REMARK 465 ARG A 16 REMARK 465 GLY A 146 REMARK 465 GLY A 147 REMARK 465 LYS A 148 REMARK 465 LYS A 149 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLY B 3 REMARK 465 TYR B 4 REMARK 465 GLY B 5 REMARK 465 ALA B 6 REMARK 465 LYS B 7 REMARK 465 GLY B 8 REMARK 465 ILE B 9 REMARK 465 ARG B 10 REMARK 465 LYS B 11 REMARK 465 VAL B 12 REMARK 465 GLY B 13 REMARK 465 ALA B 14 REMARK 465 PHE B 15 REMARK 465 GLY B 146 REMARK 465 GLY B 147 REMARK 465 LYS B 148 REMARK 465 LYS B 149 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 DT Z 1 O5' REMARK 470 DA Y 1 O5' REMARK 470 LYS A 143 CG CD CE NZ REMARK 470 LYS B 143 CG CD CE NZ 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 DG Z 6 O3' DG Z 6 C3' -0.066 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 Z 1 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 DA Z 2 C3' - O3' - P ANGL. DEV. = 10.2 DEGREES REMARK 500 DG Z 3 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG Z 3 C3' - O3' - P ANGL. DEV. = 11.0 DEGREES REMARK 500 DC Z 4 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG Z 6 O4' - C4' - C3' ANGL. DEV. = -4.2 DEGREES REMARK 500 DG Z 6 C1' - O4' - C4' ANGL. DEV. = -7.8 DEGREES REMARK 500 DC Z 8 O4' - C1' - N1 ANGL. DEV. = -5.5 DEGREES REMARK 500 DG Z 10 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG Z 10 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 DA Z 11 C3' - O3' - P ANGL. DEV. = 9.4 DEGREES REMARK 500 DG Z 12 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 DC Z 13 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC Z 13 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DT Z 14 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG Z 17 C3' - O3' - P ANGL. DEV. = 10.1 DEGREES REMARK 500 DC Z 18 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES REMARK 500 DC Z 20 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC Z 20 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA Z 21 C1' - O4' - C4' ANGL. DEV. = -6.4 DEGREES REMARK 500 DA Z 21 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA Z 21 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA Z 22 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES REMARK 500 DC Z 23 C1' - O4' - C4' ANGL. DEV. = -6.7 DEGREES REMARK 500 DC Z 23 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 DC Z 23 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DT Z 24 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT Z 24 C5 - C4 - O4 ANGL. DEV. = -4.9 DEGREES REMARK 500 DC Z 25 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DA Z 27 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 DA Z 27 N9 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC Z 28 O5' - P - OP2 ANGL. DEV. = -6.7 DEGREES REMARK 500 DC Z 28 C5' - C4' - O4' ANGL. DEV. = 6.7 DEGREES REMARK 500 DC Z 28 O4' - C1' - N1 ANGL. DEV. = -5.8 DEGREES REMARK 500 DT Z 29 O4' - C4' - C3' ANGL. DEV. = -7.4 DEGREES REMARK 500 DT Z 29 O4' - C1' - N1 ANGL. DEV. = 8.4 DEGREES REMARK 500 DA Y 1 O4' - C4' - C3' ANGL. DEV. = -4.2 DEGREES REMARK 500 DT Y 3 N1 - C2 - N3 ANGL. DEV. = 4.1 DEGREES REMARK 500 DT Y 3 N3 - C2 - O2 ANGL. DEV. = -6.7 DEGREES REMARK 500 DT Y 4 O4' - C4' - C3' ANGL. DEV. = -5.3 DEGREES REMARK 500 DT Y 4 C1' - O4' - C4' ANGL. DEV. = -7.6 DEGREES REMARK 500 DT Y 4 O4' - C1' - C2' ANGL. DEV. = -6.7 DEGREES REMARK 500 DT Y 4 O4' - C1' - N1 ANGL. DEV. = -6.1 DEGREES REMARK 500 DG Y 5 O5' - C5' - C4' ANGL. DEV. = -4.8 DEGREES REMARK 500 DG Y 5 O4' - C1' - N9 ANGL. DEV. = -7.4 DEGREES REMARK 500 DG Y 7 O3' - P - O5' ANGL. DEV. = -12.2 DEGREES REMARK 500 DG Y 7 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DT Y 8 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 DT Y 8 C4' - C3' - C2' ANGL. DEV. = -8.6 DEGREES REMARK 500 DT Y 8 O4' - C1' - N1 ANGL. DEV. = 9.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 73 ANGLE DEVIATIONS. 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 SER A 96 92.46 -166.94 REMARK 500 SER A 97 0.38 -63.80 REMARK 500 LYS A 103 114.29 -32.82 REMARK 500 LYS A 123 -25.85 52.38 REMARK 500 SER B 17 149.25 178.92 REMARK 500 SER B 96 97.59 -163.22 REMARK 500 SER B 97 0.81 -67.03 REMARK 500 LYS B 103 112.74 -31.36 REMARK 500 LYS B 123 -27.08 54.03 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 CA Z 30 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC Z 8 OP1 REMARK 620 2 ASP B 55 OD1 113.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 150 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC Z 8 OP1 REMARK 620 2 ASP B 55 OD2 129.4 REMARK 620 3 GLU B 65 OE2 88.3 101.7 REMARK 620 4 THR B 66 O 143.0 87.5 81.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA Y 30 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG Y 7 O3' REMARK 620 2 DT Y 8 OP1 57.5 REMARK 620 3 ASP A 55 OD1 126.3 78.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 150 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT Y 8 OP1 REMARK 620 2 ASP A 55 OD2 100.3 REMARK 620 3 GLU A 65 OE2 132.4 92.2 REMARK 620 4 THR A 66 O 150.1 86.7 75.6 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FZR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACTERIOPHAGE T7 ENDONUCLEASE I REMARK 900 RELATED ID: 1M0D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACTERIOPHAGE T7 ENDONUCLEASE I WITH A WILD- REMARK 900 TYPE ACTIVE SITE AND BOUND MANGANESE IONS REMARK 900 RELATED ID: 1M0I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACTERIOPHAGE T7 ENDONUCLEASE I WITH A WILD- REMARK 900 TYPE ACTIVE SITE DBREF 2PFJ A 1 149 UNP P00641 ENRN_BPT7 1 149 DBREF 2PFJ B 1 149 UNP P00641 ENRN_BPT7 1 149 DBREF 2PFJ Z 1 29 PDB 2PFJ 2PFJ 1 29 DBREF 2PFJ Y 1 29 PDB 2PFJ 2PFJ 1 29 SEQADV 2PFJ ALA A 67 UNP P00641 LYS 67 ENGINEERED MUTATION SEQADV 2PFJ ALA B 67 UNP P00641 LYS 67 ENGINEERED MUTATION SEQRES 1 Z 29 DT DA DG DC DA DG DC DC DT DG DA DG DC SEQRES 2 Z 29 DT DT DT DG DC DT DC DA DA DC DT DC DA SEQRES 3 Z 29 DA DC DT SEQRES 1 Y 29 DA DG DT DT DG DA DG DT DC DC DT DT DG SEQRES 2 Y 29 DT DT DT DC DA DA DG DG DG DG DC DT DG SEQRES 3 Y 29 DC DT DA SEQRES 1 A 149 MET ALA GLY TYR GLY ALA LYS GLY ILE ARG LYS VAL GLY SEQRES 2 A 149 ALA PHE ARG SER GLY LEU GLU ASP LYS VAL SER LYS GLN SEQRES 3 A 149 LEU GLU SER LYS GLY ILE LYS PHE GLU TYR GLU GLU TRP SEQRES 4 A 149 LYS VAL PRO TYR VAL ILE PRO ALA SER ASN HIS THR TYR SEQRES 5 A 149 THR PRO ASP PHE LEU LEU PRO ASN GLY ILE PHE VAL GLU SEQRES 6 A 149 THR ALA GLY LEU TRP GLU SER ASP ASP ARG LYS LYS HIS SEQRES 7 A 149 LEU LEU ILE ARG GLU GLN HIS PRO GLU LEU ASP ILE ARG SEQRES 8 A 149 ILE VAL PHE SER SER SER ARG THR LYS LEU TYR LYS GLY SEQRES 9 A 149 SER PRO THR SER TYR GLY GLU PHE CYS GLU LYS HIS GLY SEQRES 10 A 149 ILE LYS PHE ALA ASP LYS LEU ILE PRO ALA GLU TRP ILE SEQRES 11 A 149 LYS GLU PRO LYS LYS GLU VAL PRO PHE ASP ARG LEU LYS SEQRES 12 A 149 ARG LYS GLY GLY LYS LYS SEQRES 1 B 149 MET ALA GLY TYR GLY ALA LYS GLY ILE ARG LYS VAL GLY SEQRES 2 B 149 ALA PHE ARG SER GLY LEU GLU ASP LYS VAL SER LYS GLN SEQRES 3 B 149 LEU GLU SER LYS GLY ILE LYS PHE GLU TYR GLU GLU TRP SEQRES 4 B 149 LYS VAL PRO TYR VAL ILE PRO ALA SER ASN HIS THR TYR SEQRES 5 B 149 THR PRO ASP PHE LEU LEU PRO ASN GLY ILE PHE VAL GLU SEQRES 6 B 149 THR ALA GLY LEU TRP GLU SER ASP ASP ARG LYS LYS HIS SEQRES 7 B 149 LEU LEU ILE ARG GLU GLN HIS PRO GLU LEU ASP ILE ARG SEQRES 8 B 149 ILE VAL PHE SER SER SER ARG THR LYS LEU TYR LYS GLY SEQRES 9 B 149 SER PRO THR SER TYR GLY GLU PHE CYS GLU LYS HIS GLY SEQRES 10 B 149 ILE LYS PHE ALA ASP LYS LEU ILE PRO ALA GLU TRP ILE SEQRES 11 B 149 LYS GLU PRO LYS LYS GLU VAL PRO PHE ASP ARG LEU LYS SEQRES 12 B 149 ARG LYS GLY GLY LYS LYS HET CA Z 30 1 HET CA Y 30 1 HET CA A 150 1 HET CA B 150 1 HETNAM CA CALCIUM ION FORMUL 5 CA 4(CA 2+) HELIX 1 1 SER A 17 SER A 29 1 13 HELIX 2 2 GLU A 71 HIS A 85 1 15 HELIX 3 3 SER A 108 GLY A 117 1 10 HELIX 4 4 PRO A 126 GLU A 132 1 7 HELIX 5 5 PRO A 138 LEU A 142 5 5 HELIX 6 6 SER B 17 SER B 29 1 13 HELIX 7 7 GLU B 71 HIS B 85 1 15 HELIX 8 8 SER B 108 GLY B 117 1 10 HELIX 9 9 PRO B 126 GLU B 132 1 7 HELIX 10 10 PRO B 138 LEU B 142 5 5 SHEET 1 A 4 GLU A 35 TYR A 36 0 SHEET 2 A 4 PHE B 56 LEU B 57 -1 O LEU B 57 N GLU A 35 SHEET 3 A 4 ILE B 90 PHE B 94 1 O ARG B 91 N PHE B 63 SHEET 4 A 4 PHE B 120 ASP B 122 1 O ALA B 121 N PHE B 94 SHEET 1 B 3 SER B 48 TYR B 52 0 SHEET 2 B 3 TRP A 39 ILE A 45 -1 N VAL A 41 O TYR B 52 SHEET 3 B 3 LYS B 143 ARG B 144 -1 O LYS B 143 N LYS A 40 SHEET 1 C 3 SER A 48 TYR A 52 0 SHEET 2 C 3 TRP B 39 ILE B 45 -1 O VAL B 41 N TYR A 52 SHEET 3 C 3 LYS A 143 ARG A 144 -1 N LYS A 143 O LYS B 40 SHEET 1 D 4 PHE A 120 ASP A 122 0 SHEET 2 D 4 ILE A 90 PHE A 94 1 N PHE A 94 O ALA A 121 SHEET 3 D 4 PHE A 56 LEU A 57 -1 N PHE A 56 O VAL A 64 SHEET 4 D 4 GLU B 35 TYR B 36 -1 O GLU B 35 N LEU A 57 LINK OP1 DC Z 8 CA CA Z 30 1555 1555 2.68 LINK OP1 DC Z 8 CA CA B 150 1555 1555 2.41 LINK CA CA Z 30 OD1 ASP B 55 1555 1555 2.21 LINK O3' DG Y 7 CA CA Y 30 1555 1555 2.88 LINK OP1 DT Y 8 CA CA Y 30 1555 1555 2.15 LINK OP1 DT Y 8 CA CA A 150 1555 1555 2.43 LINK CA CA Y 30 OD1 ASP A 55 1555 1555 2.20 LINK OD2 ASP A 55 CA CA A 150 1555 1555 2.16 LINK OE2 GLU A 65 CA CA A 150 1555 1555 2.21 LINK O THR A 66 CA CA A 150 1555 1555 2.22 LINK OD2 ASP B 55 CA CA B 150 1555 1555 2.16 LINK OE2 GLU B 65 CA CA B 150 1555 1555 2.19 LINK O THR B 66 CA CA B 150 1555 1555 2.22 CRYST1 92.977 92.977 124.265 90.00 90.00 120.00 P 32 2 1 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 0.010755 0.006210 0.000000 0.00000 SCALE2 0.000000 0.012419 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008047 0.00000 MASTER 541 0 4 10 14 0 0 6 0 0 0 30 END