HEADER HYDROLASE 01-MAR-06 2DFH TITLE CRYSTAL STRUCTURE OF TK-RNASE HII(1-212)-C 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 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS; SOURCE 3 ORGANISM_TAXID: 69014; SOURCE 4 STRAIN: KOD1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HB101; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PJAL700K-C04 KEYWDS CHAMELEON SEQUENCE, RIBONUCLEASE HII, THERMOCOCCUS KODAKARAENSIS, KEYWDS 2 FUSION PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.KATAGIRI,K.TAKANO,H.CHON,H.MATSUMURA,Y.KOGA,S.KANAYA REVDAT 5 25-OCT-23 2DFH 1 REMARK REVDAT 4 13-JUL-11 2DFH 1 VERSN REVDAT 3 24-FEB-09 2DFH 1 VERSN REVDAT 2 10-JUL-07 2DFH 1 JRNL REMARK REVDAT 1 06-MAR-07 2DFH 0 JRNL AUTH K.TAKANO,Y.KATAGIRI,A.MUKAIYAMA,H.CHON,H.MATSUMURA,Y.KOGA, JRNL AUTH 2 S.KANAYA JRNL TITL CONFORMATIONAL CONTAGION IN A PROTEIN: STRUCTURAL PROPERTIES JRNL TITL 2 OF A CHAMELEON SEQUENCE JRNL REF PROTEINS V. 68 617 2007 JRNL REFN ISSN 0887-3585 JRNL PMID 17510955 JRNL DOI 10.1002/PROT.21451 REMARK 2 REMARK 2 RESOLUTION. 2.27 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) : 2.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.12 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1546820.800 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 9393 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) : 0.197 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 502 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 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) : 2.27 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.41 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1448 REMARK 3 BIN R VALUE (WORKING SET) : 0.2020 REMARK 3 BIN FREE R VALUE : 0.2630 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 85 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 : 1727 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 158 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.93000 REMARK 3 B22 (A**2) : 4.02000 REMARK 3 B33 (A**2) : -5.95000 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) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.17 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) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.27 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) : 21.70 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 46.58 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 2DFH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1000025356. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-04 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 : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9466 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.270 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 (%) : 98.9 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) : 2.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.1 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1IO2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 8000, 0.2M MES, 20% GLYCEROL, REMARK 280 PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 26.39900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.25950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.39100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 23.25950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.39900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.39100 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER GENERATED FROM THE REMARK 300 MONOMER IN THE ASYMMETRIC 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: 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 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 ASN A 218 CG OD1 ND2 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 ARG A 39 31.69 -79.20 REMARK 500 ASP A 40 24.99 -159.12 REMARK 500 PRO A 192 47.05 -72.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IO2 RELATED DB: PDB REMARK 900 THE WILD FORM OF THE SAME PROTEIN REMARK 900 RELATED ID: 2DFE RELATED DB: PDB REMARK 900 THE SHORTER VARIANT OF THE SAME PROTEIN REMARK 900 RELATED ID: 2DFF RELATED DB: PDB REMARK 900 THE SHORTER VARIANT OF THE SAME PROTEIN REMARK 900 RELATED ID: 2DFG RELATED DB: PDB REMARK 900 THE SHORTER VARIANT OF THE SAME PROTEIN REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE C-TERMINAL 9 RESIDUES, TQDMINKST ARE CHAMELEON REMARK 999 SEQUENCEIN. DBREF 2DFH A 1 212 UNP O74035 RNH2_PYRKO 1 212 SEQADV 2DFH THR A 213 UNP O74035 SEE REMARK 999 SEQADV 2DFH GLN A 214 UNP O74035 SEE REMARK 999 SEQADV 2DFH ASP A 215 UNP O74035 SEE REMARK 999 SEQADV 2DFH MET A 216 UNP O74035 SEE REMARK 999 SEQADV 2DFH ILE A 217 UNP O74035 SEE REMARK 999 SEQADV 2DFH ASN A 218 UNP O74035 SEE REMARK 999 SEQADV 2DFH LYS A 219 UNP O74035 SEE REMARK 999 SEQADV 2DFH SER A 220 UNP O74035 SEE REMARK 999 SEQADV 2DFH THR A 221 UNP O74035 SEE REMARK 999 SEQRES 1 A 221 MET LYS ILE ALA GLY ILE ASP GLU ALA GLY ARG GLY PRO SEQRES 2 A 221 VAL ILE GLY PRO MET VAL ILE ALA ALA VAL VAL VAL ASP SEQRES 3 A 221 GLU ASN SER LEU PRO LYS LEU GLU GLU LEU LYS VAL ARG SEQRES 4 A 221 ASP SER LYS LYS LEU THR PRO LYS ARG ARG GLU LYS LEU SEQRES 5 A 221 PHE ASN GLU ILE LEU GLY VAL LEU ASP ASP TYR VAL ILE SEQRES 6 A 221 LEU GLU LEU PRO PRO ASP VAL ILE GLY SER ARG GLU GLY SEQRES 7 A 221 THR LEU ASN GLU PHE GLU VAL GLU ASN PHE ALA LYS ALA SEQRES 8 A 221 LEU ASN SER LEU LYS VAL LYS PRO ASP VAL ILE TYR ALA SEQRES 9 A 221 ASP ALA ALA ASP VAL ASP GLU GLU ARG PHE ALA ARG GLU SEQRES 10 A 221 LEU GLY GLU ARG LEU ASN PHE GLU ALA GLU VAL VAL ALA SEQRES 11 A 221 LYS HIS LYS ALA ASP ASP ILE PHE PRO VAL VAL SER ALA SEQRES 12 A 221 ALA SER ILE LEU ALA LYS VAL THR ARG ASP ARG ALA VAL SEQRES 13 A 221 GLU LYS LEU LYS GLU GLU TYR GLY GLU ILE GLY SER GLY SEQRES 14 A 221 TYR PRO SER ASP PRO ARG THR ARG ALA PHE LEU GLU ASN SEQRES 15 A 221 TYR TYR ARG GLU HIS GLY GLU PHE PRO PRO ILE VAL ARG SEQRES 16 A 221 LYS GLY TRP LYS THR LEU LYS LYS ILE ALA GLU LYS VAL SEQRES 17 A 221 GLU SER GLU LYS THR GLN ASP MET ILE ASN LYS SER THR FORMUL 2 HOH *158(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 LEU A 60 1 16 HELIX 4 4 PRO A 69 SER A 75 1 7 HELIX 5 5 THR A 79 SER A 94 1 16 HELIX 6 6 ASP A 110 GLU A 120 1 11 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 SER A 210 1 13 SHEET 1 A 5 ASP A 62 LEU A 68 0 SHEET 2 A 5 MET A 18 ASP A 26 -1 N ALA A 22 O VAL A 64 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 TYR A 103 N ALA A 4 SHEET 5 A 5 GLU A 127 LYS A 131 1 O GLU A 127 N ILE A 102 CRYST1 52.798 78.782 46.519 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 0.018940 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012693 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021497 0.00000