HEADER HYDROLASE/DNA 26-SEP-06 2IHN TITLE CO-CRYSTAL OF BACTERIOPHAGE T4 RNASE H WITH A FORK DNA SUBSTRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*TP*AP*AP*CP*TP*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*CP*C) COMPND 3 -3'; COMPND 4 CHAIN: C; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*GP*GP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*TP COMPND 8 *AP*GP*TP*CP*AP*A)-3'; COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: RIBONUCLEASE H; COMPND 13 CHAIN: A; COMPND 14 SYNONYM: RNASE H; COMPND 15 EC: 3.1.26.4; COMPND 16 ENGINEERED: YES; COMPND 17 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: DNA WAS DESIGNED ACCORDING TO SEQUENCES IN SOURCE 4 HARRINGTON, J.J. AND LIEBER, M.R. EMBO J. 13, 1235-46 (1994); SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: DNA WAS DESIGNED ACCORDING TO SEQUENCES IN SOURCE 8 HARRINGTON, J.J. AND LIEBER, M.R. EMBO J. 13, 1235-46 (1994); SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE T4; SOURCE 11 ORGANISM_TAXID: 10665; SOURCE 12 STRAIN: T4D; SOURCE 13 GENE: RNH, 33.2, DAS; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-PLYSS; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PNN2202-D132N KEYWDS BPT4 RNASE H, PROTEIN:DNA COMPLEX, 5'-3' EXONUCLEASE, HYDROLASE KEYWDS 2 (NUCLEIC ACID), HELIX-HAIRPIN-HELIX MOTIF TYPE 2 (HHH2), FORK DNA, KEYWDS 3 HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.M.DEVOS,T.C.MUESER REVDAT 5 30-AUG-23 2IHN 1 REMARK REVDAT 4 20-OCT-21 2IHN 1 SEQADV REVDAT 3 24-FEB-09 2IHN 1 VERSN REVDAT 2 09-OCT-07 2IHN 1 JRNL REVDAT 1 21-AUG-07 2IHN 0 JRNL AUTH J.M.DEVOS,S.J.TOMANICEK,C.E.JONES,N.G.NOSSAL,T.C.MUESER JRNL TITL CRYSTAL STRUCTURE OF BACTERIOPHAGE T4 5' NUCLEASE IN COMPLEX JRNL TITL 2 WITH A BRANCHED DNA REVEALS HOW FEN-1 FAMILY NUCLEASES BIND JRNL TITL 3 THEIR SUBSTRATES. JRNL REF J.BIOL.CHEM. V. 282 31713 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17693399 JRNL DOI 10.1074/JBC.M703209200 REMARK 2 REMARK 2 RESOLUTION. 3.00 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 10142 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) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 498 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 705 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.25 REMARK 3 BIN R VALUE (WORKING SET) : 0.3440 REMARK 3 BIN FREE R VALUE SET COUNT : 32 REMARK 3 BIN FREE R VALUE : 0.3920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2459 REMARK 3 NUCLEIC ACID ATOMS : 696 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 12 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.72000 REMARK 3 B22 (A**2) : -1.43000 REMARK 3 B33 (A**2) : 2.15000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.484 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.372 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.464 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.896 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.810 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3294 ; 0.021 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4588 ; 2.369 ; 2.229 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 297 ; 7.170 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;37.751 ;24.522 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 479 ;20.541 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;22.402 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 502 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2206 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1456 ; 0.271 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2137 ; 0.338 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 106 ; 0.186 ; 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): 53 ; 0.323 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.390 ; 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): 1535 ; 1.051 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2420 ; 1.882 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2240 ; 2.529 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2168 ; 3.832 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2IHN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-SEP-06. REMARK 100 THE DEPOSITION ID IS D_1000039581. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JAN-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : RIGAKU CONFOCAL MULTILAYER REMARK 200 OPTICS REMARK 200 OPTICS : RIGAKU CONFOCAL MULTILAYER REMARK 200 OPTICS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 92 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10803 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 38.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.810 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.74 REMARK 200 R MERGE FOR SHELL (I) : 0.32800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1TFR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18.5% (W/V) PEG 2000 MONOMETHYLETHER, REMARK 280 0.1M TRIS-HCL, 20% (W/V) GLUCOSE, PH 7.3, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 34.08000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.64500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.49500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.64500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.08000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.49500 REMARK 290 SMTRY3 4 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: C, D, 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 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 DC C 1 REMARK 465 DT D 18 REMARK 465 DA D 19 REMARK 465 DG D 20 REMARK 465 DT D 21 REMARK 465 DC D 22 REMARK 465 DA D 23 REMARK 465 DA D 24 REMARK 465 GLY A 91 REMARK 465 LYS A 92 REMARK 465 ALA A 93 REMARK 465 ARG A 94 REMARK 465 GLU A 95 REMARK 465 GLU A 96 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 DC C 5 O3' DC C 5 C3' -0.054 REMARK 500 DT C 6 C1' DT C 6 N1 0.099 REMARK 500 DT C 6 C5 DT C 6 C7 0.058 REMARK 500 DT C 8 O3' DT C 8 C3' -0.043 REMARK 500 DA C 10 O3' DA C 10 C3' 0.078 REMARK 500 DC C 13 O3' DC C 13 C3' -0.044 REMARK 500 DA C 14 O3' DA C 14 C3' -0.045 REMARK 500 DC C 17 O3' DC C 17 C3' -0.044 REMARK 500 DC C 18 O3' DC C 18 C3' -0.049 REMARK 500 DG D 1 C4 DG D 1 C5 -0.052 REMARK 500 DT D 5 C2 DT D 5 O2 0.085 REMARK 500 DT D 5 C5 DT D 5 C7 0.045 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 C 2 O4' - C1' - N1 ANGL. DEV. = 11.7 DEGREES REMARK 500 DT C 2 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DA C 3 O4' - C1' - N9 ANGL. DEV. = 7.8 DEGREES REMARK 500 DA C 3 C3' - O3' - P ANGL. DEV. = 10.2 DEGREES REMARK 500 DA C 4 O4' - C4' - C3' ANGL. DEV. = -5.1 DEGREES REMARK 500 DA C 4 C4' - C3' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 DA C 4 O4' - C1' - N9 ANGL. DEV. = -11.9 DEGREES REMARK 500 DA C 4 C8 - N9 - C4 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC C 5 O4' - C4' - C3' ANGL. DEV. = -4.6 DEGREES REMARK 500 DC C 5 C3' - C2' - C1' ANGL. DEV. = -6.2 DEGREES REMARK 500 DC C 5 O4' - C1' - C2' ANGL. DEV. = 3.2 DEGREES REMARK 500 DT C 6 C4' - C3' - C2' ANGL. DEV. = -7.8 DEGREES REMARK 500 DT C 6 O4' - C1' - N1 ANGL. DEV. = 7.0 DEGREES REMARK 500 DT C 6 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT C 7 O4' - C1' - N1 ANGL. DEV. = 8.1 DEGREES REMARK 500 DT C 8 O5' - C5' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 DG C 9 O4' - C1' - C2' ANGL. DEV. = 6.3 DEGREES REMARK 500 DG C 9 N3 - C4 - N9 ANGL. DEV. = -4.2 DEGREES REMARK 500 DG C 9 C3' - O3' - P ANGL. DEV. = 8.6 DEGREES REMARK 500 DA C 10 O4' - C1' - N9 ANGL. DEV. = 11.9 DEGREES REMARK 500 DA C 10 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES REMARK 500 DG C 11 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 DG C 12 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 DC C 13 O5' - C5' - C4' ANGL. DEV. = -6.6 DEGREES REMARK 500 DC C 13 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA C 14 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA C 14 C5 - C6 - N6 ANGL. DEV. = 6.0 DEGREES REMARK 500 DG C 15 C4 - C5 - N7 ANGL. DEV. = -3.5 DEGREES REMARK 500 DA C 16 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA C 16 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES REMARK 500 DC C 17 O4' - C4' - C3' ANGL. DEV. = -5.9 DEGREES REMARK 500 DC C 17 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC C 18 C6 - N1 - C2 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC C 18 C4 - C5 - C6 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC C 18 C5 - C6 - N1 ANGL. DEV. = -3.9 DEGREES REMARK 500 DC C 18 N1 - C2 - O2 ANGL. DEV. = -7.2 DEGREES REMARK 500 DC C 18 N3 - C2 - O2 ANGL. DEV. = 7.2 DEGREES REMARK 500 DC C 18 N3 - C4 - N4 ANGL. DEV. = 5.5 DEGREES REMARK 500 DC C 18 C5 - C4 - N4 ANGL. DEV. = -5.2 DEGREES REMARK 500 DG D 1 O4' - C4' - C3' ANGL. DEV. = -3.9 DEGREES REMARK 500 DG D 1 N3 - C4 - C5 ANGL. DEV. = -3.1 DEGREES REMARK 500 DG D 1 N1 - C6 - O6 ANGL. DEV. = -4.6 DEGREES REMARK 500 DG D 2 OP1 - P - OP2 ANGL. DEV. = 9.4 DEGREES REMARK 500 DG D 2 O4' - C4' - C3' ANGL. DEV. = -4.9 DEGREES REMARK 500 DG D 2 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG D 2 C6 - N1 - C2 ANGL. DEV. = -5.3 DEGREES REMARK 500 DG D 2 C5 - C6 - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 DG D 2 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 DG D 2 N9 - C4 - C5 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG D 2 N1 - C6 - O6 ANGL. DEV. = -5.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 82 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 ASP A 2 66.22 -166.91 REMARK 500 ASP A 8 82.76 11.67 REMARK 500 GLU A 9 -98.70 -102.89 REMARK 500 ASP A 19 81.29 -69.46 REMARK 500 GLN A 22 -81.34 -85.95 REMARK 500 PRO A 33 166.86 -39.84 REMARK 500 LYS A 35 86.30 -10.00 REMARK 500 THR A 60 30.14 -80.61 REMARK 500 ASN A 89 106.01 51.61 REMARK 500 THR A 98 -18.35 169.05 REMARK 500 LYS A 128 -18.96 123.24 REMARK 500 SER A 153 143.26 173.53 REMARK 500 ASP A 157 -18.18 -49.29 REMARK 500 SER A 182 95.76 59.65 REMARK 500 ASP A 210 31.55 -86.50 REMARK 500 ASP A 235 88.92 -174.54 REMARK 500 VAL A 241 -60.74 -102.82 REMARK 500 ILE A 258 -50.60 -129.07 REMARK 500 SER A 277 34.62 -96.07 REMARK 500 ARG A 283 65.91 -64.66 REMARK 500 LYS A 297 0.24 -45.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TFR RELATED DB: PDB REMARK 900 WILD TYPE RNASE H FROM BACTERIOPHAGE T4 IN THE PRESENCE OF TWO REMARK 900 HYDRATED MAGNESIUM IONS IN THE ACTIVE SITE DBREF 2IHN A 1 305 UNP P13319 RNH_BPT4 1 305 DBREF 2IHN C 1 18 PDB 2IHN 2IHN 1 18 DBREF 2IHN D 1 24 PDB 2IHN 2IHN 1 24 SEQADV 2IHN ASN A 132 UNP P13319 ASP 132 ENGINEERED MUTATION SEQRES 1 C 18 DC DT DA DA DC DT DT DT DG DA DG DG DC SEQRES 2 C 18 DA DG DA DC DC SEQRES 1 D 24 DG DG DT DC DT DG DC DC DT DC DA DA DG SEQRES 2 D 24 DA DC DG DG DT DA DG DT DC DA DA SEQRES 1 A 305 MET ASP LEU GLU MET MET LEU ASP GLU ASP TYR LYS GLU SEQRES 2 A 305 GLY ILE CYS LEU ILE ASP PHE SER GLN ILE ALA LEU SER SEQRES 3 A 305 THR ALA LEU VAL ASN PHE PRO ASP LYS GLU LYS ILE ASN SEQRES 4 A 305 LEU SER MET VAL ARG HIS LEU ILE LEU ASN SER ILE LYS SEQRES 5 A 305 PHE ASN VAL LYS LYS ALA LYS THR LEU GLY TYR THR LYS SEQRES 6 A 305 ILE VAL LEU CYS ILE ASP ASN ALA LYS SER GLY TYR TRP SEQRES 7 A 305 ARG ARG ASP PHE ALA TYR TYR TYR LYS LYS ASN ARG GLY SEQRES 8 A 305 LYS ALA ARG GLU GLU SER THR TRP ASP TRP GLU GLY TYR SEQRES 9 A 305 PHE GLU SER SER HIS LYS VAL ILE ASP GLU LEU LYS ALA SEQRES 10 A 305 TYR MET PRO TYR ILE VAL MET ASP ILE ASP LYS TYR GLU SEQRES 11 A 305 ALA ASN ASP HIS ILE ALA VAL LEU VAL LYS LYS PHE SER SEQRES 12 A 305 LEU GLU GLY HIS LYS ILE LEU ILE ILE SER SER ASP GLY SEQRES 13 A 305 ASP PHE THR GLN LEU HIS LYS TYR PRO ASN VAL LYS GLN SEQRES 14 A 305 TRP SER PRO MET HIS LYS LYS TRP VAL LYS ILE LYS SER SEQRES 15 A 305 GLY SER ALA GLU ILE ASP CYS MET THR LYS ILE LEU LYS SEQRES 16 A 305 GLY ASP LYS LYS ASP ASN VAL ALA SER VAL LYS VAL ARG SEQRES 17 A 305 SER ASP PHE TRP PHE THR ARG VAL GLU GLY GLU ARG THR SEQRES 18 A 305 PRO SER MET LYS THR SER ILE VAL GLU ALA ILE ALA ASN SEQRES 19 A 305 ASP ARG GLU GLN ALA LYS VAL LEU LEU THR GLU SER GLU SEQRES 20 A 305 TYR ASN ARG TYR LYS GLU ASN LEU VAL LEU ILE ASP PHE SEQRES 21 A 305 ASP TYR ILE PRO ASP ASN ILE ALA SER ASN ILE VAL ASN SEQRES 22 A 305 TYR TYR ASN SER TYR LYS LEU PRO PRO ARG GLY LYS ILE SEQRES 23 A 305 TYR SER TYR PHE VAL LYS ALA GLY LEU SER LYS LEU THR SEQRES 24 A 305 ASN SER ILE ASN GLU PHE FORMUL 4 HOH *12(H2 O) HELIX 1 1 PHE A 20 PHE A 32 1 13 HELIX 2 2 ASN A 39 THR A 60 1 22 HELIX 3 3 TYR A 77 ALA A 83 1 7 HELIX 4 4 ASP A 100 MET A 119 1 20 HELIX 5 5 GLU A 130 GLY A 146 1 17 HELIX 6 6 ASP A 155 TYR A 164 5 10 HELIX 7 7 SER A 184 GLY A 196 1 13 HELIX 8 8 LYS A 225 ASP A 235 1 11 HELIX 9 9 GLN A 238 LEU A 243 1 6 HELIX 10 10 THR A 244 ASP A 259 1 16 HELIX 11 11 PRO A 264 SER A 277 1 14 HELIX 12 12 ILE A 286 GLY A 294 1 9 HELIX 13 13 SER A 296 SER A 301 5 6 SHEET 1 A 5 ILE A 122 MET A 124 0 SHEET 2 A 5 TYR A 63 CYS A 69 1 N LEU A 68 O ILE A 122 SHEET 3 A 5 GLY A 14 ASP A 19 1 N CYS A 16 O VAL A 67 SHEET 4 A 5 LYS A 148 ILE A 152 1 O ILE A 152 N LEU A 17 SHEET 5 A 5 VAL A 167 TRP A 170 1 O TRP A 170 N ILE A 151 CRYST1 68.160 84.990 89.290 90.00 90.00 90.00 P 21 21 21 4 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 0.014671 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011766 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011199 0.00000