HEADER HYDROLASE/DNA-RNA HYBRID 24-JUL-10 3O3G TITLE T. MARITIMA RNASE H2 IN COMPLEX WITH NUCLEIC ACID SUBSTRATE AND TITLE 2 CALCIUM IONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE HII; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE HII; COMPND 5 EC: 3.1.26.4; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3'); COMPND 9 CHAIN: C; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA/RNA (5'-D(*GP*AP*CP*AP*C)-R(P*C)-D(P*TP*GP*AP*TP*TP*C)- COMPND 13 3'); COMPND 14 CHAIN: D; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: RNHB, TM_0915; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES KEYWDS RNASE H FOLD, NUCLEASE, HYDROLASE-DNA-RNA HYBRID COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.P.RYCHLIK,H.CHON,S.M.CERRITELLI,P.KLIMEK,R.J.CROUCH,M.NOWOTNY REVDAT 2 06-SEP-23 3O3G 1 REMARK LINK REVDAT 1 08-DEC-10 3O3G 0 JRNL AUTH M.P.RYCHLIK,H.CHON,S.M.CERRITELLI,P.KLIMEK,R.J.CROUCH, JRNL AUTH 2 M.NOWOTNY JRNL TITL CRYSTAL STRUCTURES OF RNASE H2 IN COMPLEX WITH NUCLEIC ACID JRNL TITL 2 REVEAL THE MECHANISM OF RNA-DNA JUNCTION RECOGNITION AND JRNL TITL 3 CLEAVAGE. JRNL REF MOL.CELL V. 40 658 2010 JRNL REFN ISSN 1097-2765 JRNL PMID 21095591 JRNL DOI 10.1016/J.MOLCEL.2010.11.001 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.1_357) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.110 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 15873 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 816 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 28.7527 - 3.8135 0.98 2702 150 0.1537 0.2168 REMARK 3 2 3.8135 - 3.0280 0.98 2633 156 0.1545 0.2276 REMARK 3 3 3.0280 - 2.6455 0.96 2571 130 0.1886 0.2704 REMARK 3 4 2.6455 - 2.4038 0.93 2458 135 0.1885 0.2569 REMARK 3 5 2.4038 - 2.2315 0.89 2372 128 0.1932 0.3074 REMARK 3 6 2.2315 - 2.1000 0.86 2321 117 0.2076 0.2870 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 53.35 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.45740 REMARK 3 B22 (A**2) : 15.47600 REMARK 3 B33 (A**2) : -9.01860 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.15430 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 2310 REMARK 3 ANGLE : 1.254 3214 REMARK 3 CHIRALITY : 0.077 365 REMARK 3 PLANARITY : 0.004 331 REMARK 3 DIHEDRAL : 18.706 913 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3O3G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000060616. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.975 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16994 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.48400 REMARK 200 R SYM FOR SHELL (I) : NULL 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: PDB ENTRY 3O3F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.3 M CACL2, 0.1 M TRIS-HCL, 20% PEG REMARK 280 3350, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 53.06100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.67350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 53.06100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.67350 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -72.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D 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 D 122 LIES ON A SPECIAL POSITION. 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 GLU A 5 CG CD OE1 OE2 REMARK 470 GLU A 41 CG CD OE1 OE2 REMARK 470 ARG A 56 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 202 CG CD OE1 OE2 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 4 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 DC C 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG C 7 O4' - C1' - N9 ANGL. DEV. = 11.1 DEGREES REMARK 500 DG C 10 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT C 11 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA D 2 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC D 3 C3' - C2' - C1' ANGL. DEV. = -6.2 DEGREES REMARK 500 DC D 3 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 DA D 4 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC D 5 O4' - C4' - C3' ANGL. DEV. = -3.8 DEGREES REMARK 500 DC D 5 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES REMARK 500 DT D 7 N3 - C4 - O4 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT D 7 C5 - C4 - O4 ANGL. DEV. = -4.4 DEGREES REMARK 500 DT D 11 O4' - C1' - N1 ANGL. DEV. = 2.8 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 ASP A 45 -132.32 169.56 REMARK 500 SER A 46 -54.48 -156.59 REMARK 500 ASN A 81 158.05 80.47 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 A 1 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 18 OD1 REMARK 620 2 GLU A 19 O 93.4 REMARK 620 3 HOH A 229 O 83.1 175.9 REMARK 620 4 HOH A 230 O 88.7 84.0 93.8 REMARK 620 5 C D 6 OP1 105.0 102.6 80.5 164.2 REMARK 620 6 DT D 7 OP2 162.2 92.6 90.2 75.2 90.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 224 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 18 OD2 REMARK 620 2 GLU A 19 OE2 85.9 REMARK 620 3 ASP A 107 OD2 62.2 147.5 REMARK 620 4 HOH A 238 O 127.8 66.3 127.9 REMARK 620 5 DC D 5 O3' 133.9 113.5 94.5 98.1 REMARK 620 6 C D 6 OP1 80.0 105.1 76.8 147.8 55.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 225 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 124 OD2 REMARK 620 2 ASP A 124 OD1 41.4 REMARK 620 3 HOH A 266 O 59.0 86.6 REMARK 620 4 C D 6 OP2 78.8 119.8 60.5 REMARK 620 5 HOH D 182 O 75.3 81.3 121.2 76.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 13 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 233 O REMARK 620 2 HOH A 235 O 118.4 REMARK 620 3 HOH A 239 O 82.5 76.2 REMARK 620 4 HOH A 312 O 59.7 78.0 114.3 REMARK 620 5 HOH C 234 O 156.3 83.5 95.0 139.9 REMARK 620 6 HOH D 129 O 92.9 120.6 162.2 77.3 82.3 REMARK 620 7 HOH D 236 O 80.7 151.9 87.0 129.9 75.6 75.2 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 224 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 225 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 226 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA C 13 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ETJ RELATED DB: PDB REMARK 900 APO STRUCTURE OF T. MARITIMA RNASE H2 REMARK 900 RELATED ID: 3O3F RELATED DB: PDB REMARK 900 T. MARITIMA RNASE H2 D107N IN COMPLEX WITH NUCLEIC ACID SUBSTRATE REMARK 900 AND MAGNESIUM IONS REMARK 900 RELATED ID: 3O3H RELATED DB: PDB DBREF 3O3G A 2 223 UNP Q9X017 RNH2_THEMA 2 223 DBREF 3O3G C 1 12 PDB 3O3G 3O3G 1 12 DBREF 3O3G D 1 12 PDB 3O3G 3O3G 1 12 SEQRES 1 A 222 GLY ILE ASP GLU LEU TYR LYS LYS GLU PHE GLY ILE VAL SEQRES 2 A 222 ALA GLY VAL ASP GLU ALA GLY ARG GLY CYS LEU ALA GLY SEQRES 3 A 222 PRO VAL VAL ALA ALA ALA VAL VAL LEU GLU LYS GLU ILE SEQRES 4 A 222 GLU GLY ILE ASN ASP SER LYS GLN LEU SER PRO ALA LYS SEQRES 5 A 222 ARG GLU ARG LEU LEU ASP GLU ILE MET GLU LYS ALA ALA SEQRES 6 A 222 VAL GLY ILE GLY ILE ALA SER PRO GLU GLU ILE ASP LEU SEQRES 7 A 222 TYR ASN ILE PHE ASN ALA THR LYS LEU ALA MET ASN ARG SEQRES 8 A 222 ALA LEU GLU ASN LEU SER VAL LYS PRO SER PHE VAL LEU SEQRES 9 A 222 VAL ASP GLY LYS GLY ILE GLU LEU SER VAL PRO GLY THR SEQRES 10 A 222 CYS LEU VAL LYS GLY ASP GLN LYS SER LYS LEU ILE GLY SEQRES 11 A 222 ALA ALA SER ILE VAL ALA LYS VAL PHE ARG ASP ARG LEU SEQRES 12 A 222 MET SER GLU PHE HIS ARG MET TYR PRO GLN PHE SER PHE SEQRES 13 A 222 HIS LYS HIS LYS GLY TYR ALA THR LYS GLU HIS LEU ASN SEQRES 14 A 222 GLU ILE ARG LYS ASN GLY VAL LEU PRO ILE HIS ARG LEU SEQRES 15 A 222 SER PHE GLU PRO VAL LEU GLU LEU LEU THR ASP ASP LEU SEQRES 16 A 222 LEU ARG GLU PHE PHE GLU LYS GLY LEU ILE SER GLU ASN SEQRES 17 A 222 ARG PHE GLU ARG ILE LEU ASN LEU LEU GLY ALA ARG LYS SEQRES 18 A 222 SER SEQRES 1 C 12 DG DA DA DT DC DA DG DG DT DG DT DC SEQRES 1 D 12 DG DA DC DA DC C DT DG DA DT DT DC HET CA A 1 1 HET CA A 224 1 HET CA A 225 1 HET CA A 226 1 HET CA C 13 1 HETNAM CA CALCIUM ION FORMUL 4 CA 5(CA 2+) FORMUL 9 HOH *244(H2 O) HELIX 1 1 GLY A 2 GLY A 12 1 11 HELIX 2 2 SER A 50 LYS A 64 1 15 HELIX 3 3 SER A 73 ASN A 96 1 24 HELIX 4 4 LYS A 122 LYS A 126 5 5 HELIX 5 5 SER A 127 TYR A 152 1 26 HELIX 6 6 SER A 156 LYS A 161 1 6 HELIX 7 7 THR A 165 GLY A 176 1 12 HELIX 8 8 PHE A 185 GLU A 190 1 6 HELIX 9 9 THR A 193 LYS A 203 1 11 HELIX 10 10 SER A 207 ARG A 221 1 15 SHEET 1 A 5 ALA A 65 ALA A 72 0 SHEET 2 A 5 VAL A 29 LEU A 36 -1 N ALA A 33 O GLY A 68 SHEET 3 A 5 VAL A 14 ALA A 20 -1 N ALA A 20 O VAL A 30 SHEET 4 A 5 PHE A 103 ASP A 107 1 O LEU A 105 N ALA A 15 SHEET 5 A 5 GLY A 117 LEU A 120 1 O THR A 118 N VAL A 106 LINK CA CA A 1 OD1 ASP A 18 1555 1555 2.44 LINK CA CA A 1 O GLU A 19 1555 1555 2.48 LINK CA CA A 1 O HOH A 229 1555 1555 2.59 LINK CA CA A 1 O HOH A 230 1555 1555 2.61 LINK CA CA A 1 OP1 C D 6 1555 1555 2.38 LINK CA CA A 1 OP2 DT D 7 1555 1555 2.47 LINK OD2 ASP A 18 CA CA A 224 1555 1555 2.49 LINK OE2 GLU A 19 CA CA A 224 1555 1555 2.45 LINK OD2 ASP A 107 CA CA A 224 1555 1555 2.57 LINK OD2 ASP A 124 CA CA A 225 1555 1555 3.07 LINK OD1 ASP A 124 CA CA A 225 1555 1555 3.19 LINK CA CA A 224 O HOH A 238 1555 1555 3.18 LINK CA CA A 224 O3' DC D 5 1555 1555 2.73 LINK CA CA A 224 OP1 C D 6 1555 1555 2.57 LINK CA CA A 225 O HOH A 266 1555 1555 2.78 LINK CA CA A 225 OP2 C D 6 1555 1555 3.00 LINK CA CA A 225 O HOH D 182 1555 1555 2.67 LINK O HOH A 233 CA CA C 13 1555 1555 2.67 LINK O HOH A 235 CA CA C 13 1555 1555 2.62 LINK O HOH A 239 CA CA C 13 1555 1555 2.60 LINK O HOH A 312 CA CA C 13 1555 1555 3.07 LINK CA CA C 13 O HOH C 234 1555 1555 2.74 LINK CA CA C 13 O HOH D 129 1555 1555 2.73 LINK CA CA C 13 O HOH D 236 1555 1555 2.83 CISPEP 1 ARG A 221 LYS A 222 0 -6.32 CISPEP 2 ARG A 221 LYS A 222 0 -6.82 SITE 1 AC1 6 ASP A 18 GLU A 19 HOH A 229 HOH A 230 SITE 2 AC1 6 C D 6 DT D 7 SITE 1 AC2 5 ASP A 18 GLU A 19 ASP A 107 DC D 5 SITE 2 AC2 5 C D 6 SITE 1 AC3 4 ASP A 124 HOH A 266 C D 6 HOH D 182 SITE 1 AC4 3 ASN A 91 ASN A 216 HOH A 299 SITE 1 AC5 7 HOH A 233 HOH A 235 HOH A 239 HOH A 312 SITE 2 AC5 7 HOH C 234 HOH D 129 HOH D 236 CRYST1 106.122 47.347 79.012 90.00 132.81 90.00 C 1 2 1 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 0.009423 0.000000 0.008729 0.00000 SCALE2 0.000000 0.021121 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017252 0.00000