HEADER HYDROLASE 28-DEC-00 1IO2 TITLE CRYSTAL STRUCTURE OF TYPE 2 RIBONUCLEASE H FROM HYPERTHERMOPHILIC TITLE 2 ARCHAEON, THERMOCOCCUS KODAKARAENSIS KOD1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE HII; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-213; COMPND 5 EC: 3.1.26.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS; SOURCE 3 ORGANISM_TAXID: 69014; SOURCE 4 STRAIN: KOD1; SOURCE 5 GENE: RNHB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HB101; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PJAL700K KEYWDS ENDONUCLEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.MUROYA,D.TSUCHIYA,M.ISHIKAWA,M.HARUKI,M.MORIKAWA REVDAT 5 27-DEC-23 1IO2 1 REMARK REVDAT 4 13-JUL-11 1IO2 1 VERSN REVDAT 3 24-FEB-09 1IO2 1 VERSN REVDAT 2 21-JAN-03 1IO2 1 REMARK REVDAT 1 18-APR-01 1IO2 0 JRNL AUTH A.MUROYA,D.TSUCHIYA,M.ISHIKAWA,M.HARUKI,M.MORIKAWA,S.KANAYA, JRNL AUTH 2 K.MORIKAWA JRNL TITL CATALYTIC CENTER OF AN ARCHAEAL TYPE 2 RIBONUCLEASE H AS JRNL TITL 2 REVEALED BY X-RAY CRYSTALLOGRAPHIC AND MUTATIONAL ANALYSES. JRNL REF PROTEIN SCI. V. 10 707 2001 JRNL REFN ISSN 0961-8368 JRNL PMID 11274461 JRNL DOI 10.1110/PS.48001 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 84.5 REMARK 3 NUMBER OF REFLECTIONS : 14723 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 SET) : 0.223 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1011 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.03 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 68.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 546 REMARK 3 BIN R VALUE (WORKING SET) : 0.2180 REMARK 3 BIN FREE R VALUE : 0.2750 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 46 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1652 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 216 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.15000 REMARK 3 B22 (A**2) : -0.13960 REMARK 3 B33 (A**2) : 1.24600 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.13 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.160 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.697 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.320 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.597 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 0.297 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 0.502 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.44 REMARK 3 BSOL : 66.40 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IO2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-JAN-01. REMARK 100 THE DEPOSITION ID IS D_1000005109. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : MONOCHROMETER REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15205 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.25400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, PH 6.50, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293.0K 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 21.77000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.16000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.49500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.16000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.77000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.49500 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 34 CG CD OE1 OE2 REMARK 470 LYS A 37 CG CD CE NZ REMARK 470 ARG A 39 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 40 CG OD1 OD2 REMARK 470 LYS A 43 CG CD CE NZ REMARK 470 LYS A 158 CG CD CE NZ REMARK 470 LYS A 196 CG CD CE NZ REMARK 470 LYS A 202 CG CD CE NZ REMARK 470 LYS A 213 CG CD CE NZ 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 40 51.86 -106.19 REMARK 500 PRO A 192 43.50 -76.88 REMARK 500 LYS A 196 -33.47 -38.18 REMARK 500 LYS A 212 129.66 -22.76 REMARK 500 REMARK 500 REMARK: NULL DBREF 1IO2 A 1 213 UNP O74035 RNH2_PYRKO 1 213 SEQRES 1 A 213 MET LYS ILE ALA GLY ILE ASP GLU ALA GLY ARG GLY PRO SEQRES 2 A 213 VAL ILE GLY PRO MET VAL ILE ALA ALA VAL VAL VAL ASP SEQRES 3 A 213 GLU ASN SER LEU PRO LYS LEU GLU GLU LEU LYS VAL ARG SEQRES 4 A 213 ASP SER LYS LYS LEU THR PRO LYS ARG ARG GLU LYS LEU SEQRES 5 A 213 PHE ASN GLU ILE LEU GLY VAL LEU ASP ASP TYR VAL ILE SEQRES 6 A 213 LEU GLU LEU PRO PRO ASP VAL ILE GLY SER ARG GLU GLY SEQRES 7 A 213 THR LEU ASN GLU PHE GLU VAL GLU ASN PHE ALA LYS ALA SEQRES 8 A 213 LEU ASN SER LEU LYS VAL LYS PRO ASP VAL ILE TYR ALA SEQRES 9 A 213 ASP ALA ALA ASP VAL ASP GLU GLU ARG PHE ALA ARG GLU SEQRES 10 A 213 LEU GLY GLU ARG LEU ASN PHE GLU ALA GLU VAL VAL ALA SEQRES 11 A 213 LYS HIS LYS ALA ASP ASP ILE PHE PRO VAL VAL SER ALA SEQRES 12 A 213 ALA SER ILE LEU ALA LYS VAL THR ARG ASP ARG ALA VAL SEQRES 13 A 213 GLU LYS LEU LYS GLU GLU TYR GLY GLU ILE GLY SER GLY SEQRES 14 A 213 TYR PRO SER ASP PRO ARG THR ARG ALA PHE LEU GLU ASN SEQRES 15 A 213 TYR TYR ARG GLU HIS GLY GLU PHE PRO PRO ILE VAL ARG SEQRES 16 A 213 LYS GLY TRP LYS THR LEU LYS LYS ILE ALA GLU LYS VAL SEQRES 17 A 213 GLU SER GLU LYS LYS FORMUL 2 HOH *216(H2 O) HELIX 1 1 SER A 29 LEU A 36 1 8 HELIX 2 2 LYS A 37 SER A 41 5 5 HELIX 3 3 THR A 45 GLY A 58 1 14 HELIX 4 4 PRO A 69 SER A 75 1 7 HELIX 5 5 THR A 79 LEU A 95 1 17 HELIX 6 6 ASP A 110 ARG A 121 1 12 HELIX 7 7 LYS A 133 PHE A 138 1 6 HELIX 8 8 PHE A 138 GLY A 164 1 27 HELIX 9 9 ASP A 173 GLY A 188 1 16 HELIX 10 10 TRP A 198 LYS A 212 1 15 SHEET 1 A 5 ASP A 62 LEU A 68 0 SHEET 2 A 5 MET A 18 ASP A 26 -1 O MET A 18 N LEU A 68 SHEET 3 A 5 LYS A 2 ALA A 9 -1 N ILE A 3 O VAL A 25 SHEET 4 A 5 VAL A 101 ASP A 105 1 O VAL A 101 N ALA A 4 SHEET 5 A 5 GLU A 127 LYS A 131 1 O GLU A 127 N ILE A 102 CRYST1 43.540 72.990 78.320 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 0.022967 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013701 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012768 0.00000