HEADER HYDROLASE 11-APR-05 1X1P TITLE CRYSTAL STRUCTURE OF TK-RNASE HII(1-197)-A(28-42) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE HII; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-197; COMPND 5 SYNONYM: RNASE HII, TK-RNASE HII; COMPND 6 EC: 3.1.26.4; COMPND 7 ENGINEERED: 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 KEYWDS RIBONUCLEASE HII, AMYLOID PEPTIDE, THERMOCOCCUS KODAKARAENSIS, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.TAKANO,S.ENDO,A.MUKAIYAMA,H.CHON,H.MATSUMURA,Y.KOGA,S.KANAYA REVDAT 4 13-MAR-24 1X1P 1 SEQADV REVDAT 3 13-JUL-11 1X1P 1 VERSN REVDAT 2 24-FEB-09 1X1P 1 VERSN REVDAT 1 17-JAN-06 1X1P 0 JRNL AUTH K.TAKANO,S.ENDO,A.MUKAIYAMA,H.CHON,H.MATSUMURA,Y.KOGA, JRNL AUTH 2 S.KANAYA JRNL TITL STRUCTURE OF AMYLOID BETA FRAGMENTS IN AQUEOUS ENVIRONMENTS JRNL REF FEBS J. V. 273 150 2006 JRNL REFN ISSN 1742-464X JRNL PMID 16367755 JRNL DOI 10.1111/J.1742-4658.2005.05051.X REMARK 2 REMARK 2 RESOLUTION. 2.80 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1073481.450 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 7859 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) : 0.245 REMARK 3 FREE R VALUE : 0.300 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 419 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1219 REMARK 3 BIN R VALUE (WORKING SET) : 0.3640 REMARK 3 BIN FREE R VALUE : 0.4200 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 48 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.061 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1624 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 48 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 74.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 66.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 26.55000 REMARK 3 B22 (A**2) : -17.99000 REMARK 3 B33 (A**2) : -8.56000 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) : 0.42 REMARK 3 ESD FROM SIGMAA (A) : 0.44 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) : 0.51 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.49 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810 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 : 0.34 REMARK 3 BSOL : 44.40 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 1X1P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-APR-05. REMARK 100 THE DEPOSITION ID IS D_1000024267. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 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) : 0.9 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 : 8435 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 95.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.4 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 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200MM MES, 11% PEG8000, 20% GLYCEROL, REMARK 280 PH 7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 35.09700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.62900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.09700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.62900 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 LYS A 37 CG CD CE NZ REMARK 470 ARG A 39 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 43 CG CD CE NZ REMARK 470 LYS A 196 CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 VAL A 206 O 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 44 148.97 -38.79 REMARK 500 PRO A 70 -178.28 -64.19 REMARK 500 ARG A 76 49.70 26.49 REMARK 500 ASN A 81 20.30 -73.43 REMARK 500 ALA A 107 79.26 -104.53 REMARK 500 ASP A 108 23.82 40.34 REMARK 500 HIS A 187 -10.05 -147.19 REMARK 500 VAL A 206 74.26 33.18 REMARK 500 REMARK 500 REMARK: NULL DBREF 1X1P A 1 197 UNP O74035 RNH2_PYRKO 1 197 SEQADV 1X1P ALA A 198 UNP O74035 CLONING ARTIFACT SEQADV 1X1P GLY A 199 UNP O74035 CLONING ARTIFACT SEQADV 1X1P ALA A 200 UNP O74035 CLONING ARTIFACT SEQADV 1X1P ILE A 201 UNP O74035 CLONING ARTIFACT SEQADV 1X1P ILE A 202 UNP O74035 CLONING ARTIFACT SEQADV 1X1P GLY A 203 UNP O74035 CLONING ARTIFACT SEQADV 1X1P LEU A 204 UNP O74035 CLONING ARTIFACT SEQADV 1X1P ALA A 205 UNP O74035 CLONING ARTIFACT SEQADV 1X1P VAL A 206 UNP O74035 CLONING ARTIFACT SEQADV 1X1P GLY A 207 UNP O74035 CLONING ARTIFACT SEQADV 1X1P GLY A 208 UNP O74035 CLONING ARTIFACT SEQADV 1X1P VAL A 209 UNP O74035 CLONING ARTIFACT SEQADV 1X1P VAL A 210 UNP O74035 CLONING ARTIFACT SEQADV 1X1P ILE A 211 UNP O74035 CLONING ARTIFACT SEQADV 1X1P ALA A 212 UNP O74035 CLONING ARTIFACT SEQRES 1 A 212 MET LYS ILE ALA GLY ILE ASP GLU ALA GLY ARG GLY PRO SEQRES 2 A 212 VAL ILE GLY PRO MET VAL ILE ALA ALA VAL VAL VAL ASP SEQRES 3 A 212 GLU ASN SER LEU PRO LYS LEU GLU GLU LEU LYS VAL ARG SEQRES 4 A 212 ASP SER LYS LYS LEU THR PRO LYS ARG ARG GLU LYS LEU SEQRES 5 A 212 PHE ASN GLU ILE LEU GLY VAL LEU ASP ASP TYR VAL ILE SEQRES 6 A 212 LEU GLU LEU PRO PRO ASP VAL ILE GLY SER ARG GLU GLY SEQRES 7 A 212 THR LEU ASN GLU PHE GLU VAL GLU ASN PHE ALA LYS ALA SEQRES 8 A 212 LEU ASN SER LEU LYS VAL LYS PRO ASP VAL ILE TYR ALA SEQRES 9 A 212 ASP ALA ALA ASP VAL ASP GLU GLU ARG PHE ALA ARG GLU SEQRES 10 A 212 LEU GLY GLU ARG LEU ASN PHE GLU ALA GLU VAL VAL ALA SEQRES 11 A 212 LYS HIS LYS ALA ASP ASP ILE PHE PRO VAL VAL SER ALA SEQRES 12 A 212 ALA SER ILE LEU ALA LYS VAL THR ARG ASP ARG ALA VAL SEQRES 13 A 212 GLU LYS LEU LYS GLU GLU TYR GLY GLU ILE GLY SER GLY SEQRES 14 A 212 TYR PRO SER ASP PRO ARG THR ARG ALA PHE LEU GLU ASN SEQRES 15 A 212 TYR TYR ARG GLU HIS GLY GLU PHE PRO PRO ILE VAL ARG SEQRES 16 A 212 LYS GLY ALA GLY ALA ILE ILE GLY LEU ALA VAL GLY GLY SEQRES 17 A 212 VAL VAL ILE ALA FORMUL 2 HOH *48(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 PHE A 83 ASN A 93 1 11 HELIX 5 5 ASP A 110 LEU A 122 1 13 HELIX 6 6 PHE A 138 GLY A 164 1 27 HELIX 7 7 ASP A 173 GLU A 186 1 14 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 ALA A 106 1 O TYR A 103 N ALA A 4 SHEET 5 A 5 GLU A 127 HIS A 132 1 O GLU A 127 N ILE A 102 SHEET 1 B 2 LEU A 204 ALA A 205 0 SHEET 2 B 2 GLY A 208 VAL A 209 -1 O GLY A 208 N ALA A 205 CRYST1 70.194 101.258 42.498 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 0.014246 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009876 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023531 0.00000