PDB Short entry for 2PFJ 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 5 30-AUG-23 2PFJ 1 REMARK 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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