HEADER HYDROLASE 01-MAR-06 2DFE TITLE CRYSTAL STRUCTURE OF TK-RNASE HII(1-200)-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-C01 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 4 13-JUL-11 2DFE 1 VERSN REVDAT 3 24-FEB-09 2DFE 1 VERSN REVDAT 2 10-JUL-07 2DFE 1 JRNL REVDAT 1 06-MAR-07 2DFE 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. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1313909.480 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 7709 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) : 0.227 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 383 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.015 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1232 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 1.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 18 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.073 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1649 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.74000 REMARK 3 B22 (A**2) : -1.09000 REMARK 3 B33 (A**2) : -0.65000 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) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.24 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) : 0.40 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.34 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.74 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 : 0.39 REMARK 3 BSOL : 40.75 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 2DFE 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 RCSB ID CODE IS RCSB025353. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-05 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 : SPRING-8 REMARK 200 BEAMLINE : BL41XU 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 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8628 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 (%) : 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) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 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 (%): 38.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTAL SCREEN I SOLUTION NO. 6 (0.1M REMARK 280 TRIS-HCL PH 8.5, 0.2M MGCL2, 30% PEG 4000), 100% GLYCEROL IN A 9: REMARK 280 1 RATIO, 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 30.78500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.29000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.99500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.29000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.78500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.99500 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 LYS A 196 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 LEU A 80 32.08 -76.14 REMARK 500 LYS A 133 66.78 35.67 REMARK 500 GLU A 165 92.86 -65.16 REMARK 500 HIS A 187 -13.82 -156.22 REMARK 500 TRP A 198 -38.32 165.31 REMARK 500 GLN A 202 43.44 38.54 REMARK 500 MET A 204 47.59 -75.82 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: 2DFF RELATED DB: PDB REMARK 900 THE LONGER VARIANT OF THE SAME PROTEIN REMARK 900 RELATED ID: 2DFG RELATED DB: PDB REMARK 900 THE LONGER VARIANT OF THE SAME PROTEIN REMARK 900 RELATED ID: 2DFH RELATED DB: PDB REMARK 900 THE LONGER VARIANT OF THE SAME PROTEIN REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE C-TERMINAL 9 RESIDUES, TQDMINKST ARE CHAMELEON REMARK 999 SEQUENCEIN. DBREF 2DFE A 1 200 UNP O74035 RNH2_PYRKO 1 200 SEQADV 2DFE THR A 201 UNP O74035 SEE REMARK 999 SEQADV 2DFE GLN A 202 UNP O74035 SEE REMARK 999 SEQADV 2DFE ASP A 203 UNP O74035 SEE REMARK 999 SEQADV 2DFE MET A 204 UNP O74035 SEE REMARK 999 SEQADV 2DFE ILE A 205 UNP O74035 SEE REMARK 999 SEQADV 2DFE ASN A 206 UNP O74035 SEE REMARK 999 SEQADV 2DFE LYS A 207 UNP O74035 SEE REMARK 999 SEQADV 2DFE SER A 208 UNP O74035 SEE REMARK 999 SEQADV 2DFE THR A 209 UNP O74035 SEE REMARK 999 SEQRES 1 A 209 MET LYS ILE ALA GLY ILE ASP GLU ALA GLY ARG GLY PRO SEQRES 2 A 209 VAL ILE GLY PRO MET VAL ILE ALA ALA VAL VAL VAL ASP SEQRES 3 A 209 GLU ASN SER LEU PRO LYS LEU GLU GLU LEU LYS VAL ARG SEQRES 4 A 209 ASP SER LYS LYS LEU THR PRO LYS ARG ARG GLU LYS LEU SEQRES 5 A 209 PHE ASN GLU ILE LEU GLY VAL LEU ASP ASP TYR VAL ILE SEQRES 6 A 209 LEU GLU LEU PRO PRO ASP VAL ILE GLY SER ARG GLU GLY SEQRES 7 A 209 THR LEU ASN GLU PHE GLU VAL GLU ASN PHE ALA LYS ALA SEQRES 8 A 209 LEU ASN SER LEU LYS VAL LYS PRO ASP VAL ILE TYR ALA SEQRES 9 A 209 ASP ALA ALA ASP VAL ASP GLU GLU ARG PHE ALA ARG GLU SEQRES 10 A 209 LEU GLY GLU ARG LEU ASN PHE GLU ALA GLU VAL VAL ALA SEQRES 11 A 209 LYS HIS LYS ALA ASP ASP ILE PHE PRO VAL VAL SER ALA SEQRES 12 A 209 ALA SER ILE LEU ALA LYS VAL THR ARG ASP ARG ALA VAL SEQRES 13 A 209 GLU LYS LEU LYS GLU GLU TYR GLY GLU ILE GLY SER GLY SEQRES 14 A 209 TYR PRO SER ASP PRO ARG THR ARG ALA PHE LEU GLU ASN SEQRES 15 A 209 TYR TYR ARG GLU HIS GLY GLU PHE PRO PRO ILE VAL ARG SEQRES 16 A 209 LYS GLY TRP LYS THR THR GLN ASP MET ILE ASN LYS SER SEQRES 17 A 209 THR FORMUL 2 HOH *110(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 ILE A 73 5 5 HELIX 5 5 LEU A 80 SER A 94 1 15 HELIX 6 6 ASP A 110 ARG A 121 1 12 HELIX 7 7 PHE A 138 GLY A 164 1 27 HELIX 8 8 ASP A 173 GLU A 186 1 14 HELIX 9 9 ARG A 195 THR A 200 1 6 SHEET 1 A 5 ASP A 62 LEU A 68 0 SHEET 2 A 5 MET A 18 ASP A 26 -1 N MET A 18 O 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 TYR A 103 N ALA A 4 SHEET 5 A 5 GLU A 127 LYS A 131 1 O VAL A 129 N ALA A 104 CRYST1 61.570 67.990 44.580 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 0.016242 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014708 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022432 0.00000 MASTER 260 0 0 9 5 0 0 6 0 0 0 17 END