HEADER HYDROLASE 31-JUL-05 2D0A TITLE CRYSTAL STRUCTURE OF BST-RNASE HIII COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE HIII; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE HIII; COMPND 5 EC: 3.1.26.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: MIC2067(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET25B KEYWDS RIBONUCLEASE H, RNA/DNA HYBRID, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.CHON,H.MATSUMURA,Y.KOGA,K.TAKANO,S.KANAYA REVDAT 3 13-MAR-24 2D0A 1 REMARK REVDAT 2 24-FEB-09 2D0A 1 VERSN REVDAT 1 18-JUL-06 2D0A 0 JRNL AUTH H.CHON,H.MATSUMURA,Y.KOGA,K.TAKANO,S.KANAYA JRNL TITL CRYSTAL STRUCTURE AND STRUCTURE-BASED MUTATIONAL ANALYSES OF JRNL TITL 2 RNASE HIII FROM BACILLUS STEAROTHERMOPHILUS: A NEW TYPE 2 JRNL TITL 3 RNASE H WITH TBP-LIKE SUBSTRATE-BINDING DOMAIN AT THE N JRNL TITL 4 TERMINUS JRNL REF J.MOL.BIOL. V. 356 165 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16343535 JRNL DOI 10.1016/J.JMB.2005.11.017 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1354273.510 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.4 REMARK 3 NUMBER OF REFLECTIONS : 15124 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) : 0.207 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 745 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2217 REMARK 3 BIN R VALUE (WORKING SET) : 0.2530 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 115 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.028 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2363 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 219 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.64000 REMARK 3 B22 (A**2) : 6.50000 REMARK 3 B33 (A**2) : -5.86000 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) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : 0.23 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) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.30 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.700 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.990 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.740 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.480 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.330 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 39.54 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 2D0A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000024827. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-04 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0066 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER DIP-6040 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15163 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 33.71050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.58150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.71050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.58150 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 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 MET A 1 REMARK 465 LYS A 310 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 468 O HOH A 507 2.11 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 HIS A 19 -82.38 -55.05 REMARK 500 PHE A 204 4.41 -69.34 REMARK 500 ALA A 268 37.85 -145.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2D0B RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH MG2+ REMARK 900 RELATED ID: 2D0C RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH MN2+ DBREF 2D0A A 1 310 UNP Q6L6Q4 Q6L6Q4_BACST 1 310 SEQRES 1 A 310 MET SER ASN TYR VAL ILE GLN ALA ASP GLN GLN LEU LEU SEQRES 2 A 310 ASP ALA LEU ARG ALA HIS TYR GLU GLY ALA LEU SER ASP SEQRES 3 A 310 ARG LEU PRO ALA GLY ALA LEU PHE ALA VAL LYS ARG PRO SEQRES 4 A 310 ASP VAL VAL ILE THR ALA TYR ARG SER GLY LYS VAL LEU SEQRES 5 A 310 PHE GLN GLY LYS ALA ALA GLU GLN GLU ALA ALA LYS TRP SEQRES 6 A 310 ILE SER GLY ALA SER ALA SER ASN GLU THR ALA ASP HIS SEQRES 7 A 310 GLN PRO SER ALA LEU ALA ALA HIS GLN LEU GLY SER LEU SEQRES 8 A 310 SER ALA ILE GLY SER ASP GLU VAL GLY THR GLY ASP TYR SEQRES 9 A 310 PHE GLY PRO ILE VAL VAL ALA ALA ALA TYR VAL ASP ARG SEQRES 10 A 310 PRO HIS ILE ALA LYS ILE ALA ALA LEU GLY VAL LYS ASP SEQRES 11 A 310 SER LYS GLN LEU ASN ASP GLU ALA ILE LYS ARG ILE ALA SEQRES 12 A 310 PRO ALA ILE MET GLU THR VAL PRO HIS ALA VAL THR VAL SEQRES 13 A 310 LEU ASP ASN PRO GLN TYR ASN ARG TRP GLN ARG SER GLY SEQRES 14 A 310 MET PRO GLN THR LYS MET LYS ALA LEU LEU HIS ASN ARG SEQRES 15 A 310 THR LEU VAL LYS LEU VAL ASP ALA ILE ALA PRO ALA GLU SEQRES 16 A 310 PRO GLU ALA ILE ILE ILE ASP GLU PHE LEU LYS ARG ASP SEQRES 17 A 310 SER TYR PHE ARG TYR LEU SER ASP GLU ASP ARG ILE ILE SEQRES 18 A 310 ARG GLU ARG VAL HIS CYS LEU PRO LYS ALA GLU SER VAL SEQRES 19 A 310 HIS VAL SER VAL ALA ALA ALA SER ILE ILE ALA ARG TYR SEQRES 20 A 310 VAL PHE LEU GLU GLU MET GLU GLN LEU SER ARG ALA VAL SEQRES 21 A 310 GLY LEU LEU LEU PRO LYS GLY ALA GLY ALA ILE VAL ASP SEQRES 22 A 310 GLU ALA ALA ALA ARG ILE ILE ARG ALA ARG GLY GLU GLU SEQRES 23 A 310 MET LEU GLU THR CYS ALA LYS LEU HIS PHE ALA ASN THR SEQRES 24 A 310 LYS LYS ALA LEU ALA ILE ALA LYS ARG ARG LYS FORMUL 2 HOH *219(H2 O) HELIX 1 1 ASP A 9 TYR A 20 1 12 HELIX 2 2 ALA A 57 LYS A 64 1 8 HELIX 3 3 GLN A 79 SER A 81 5 3 HELIX 4 4 ALA A 82 GLY A 89 1 8 HELIX 5 5 ASP A 116 PRO A 118 5 3 HELIX 6 6 HIS A 119 LEU A 126 1 8 HELIX 7 7 ASN A 135 GLU A 148 1 14 HELIX 8 8 ASP A 158 ARG A 167 1 10 HELIX 9 9 PRO A 171 ALA A 192 1 22 HELIX 10 10 LYS A 206 LEU A 214 1 9 HELIX 11 11 LYS A 230 VAL A 234 5 5 HELIX 12 12 HIS A 235 GLY A 261 1 27 HELIX 13 13 GLY A 269 GLY A 284 1 16 HELIX 14 14 MET A 287 ALA A 292 1 6 HELIX 15 15 ALA A 297 ARG A 309 1 13 SHEET 1 A 5 ALA A 32 ARG A 38 0 SHEET 2 A 5 VAL A 41 TYR A 46 -1 O ALA A 45 N LEU A 33 SHEET 3 A 5 LYS A 50 GLN A 54 -1 O GLN A 54 N VAL A 42 SHEET 4 A 5 ASN A 3 GLN A 7 -1 N ILE A 6 O VAL A 51 SHEET 5 A 5 SER A 70 SER A 72 -1 O SER A 72 N ASN A 3 SHEET 1 B 5 HIS A 152 LEU A 157 0 SHEET 2 B 5 ILE A 108 VAL A 115 -1 N ILE A 108 O LEU A 157 SHEET 3 B 5 ALA A 93 VAL A 99 -1 N GLY A 95 O ALA A 113 SHEET 4 B 5 ALA A 198 ASP A 202 1 O ILE A 200 N ILE A 94 SHEET 5 B 5 VAL A 225 LEU A 228 1 O HIS A 226 N ILE A 199 CISPEP 1 ALA A 192 PRO A 193 0 0.22 CRYST1 67.421 109.163 48.602 90.00 90.00 90.00 P 21 21 2 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 0.014832 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009161 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020575 0.00000