HEADER HYDROLASE 05-AUG-98 1BOL TITLE THE CRYSTAL STRUCTURE OF RIBONUCLEASE RH FROM RHIZOPUS NIVEUS AT 2.0 A TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (RIBONUCLEASE RH); COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.27.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHIZOPUS NIVEUS; SOURCE 3 ORGANISM_TAXID: 4844 KEYWDS RIBONUCLEASES, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.KURIHARA,K.T.NAKAMURA REVDAT 4 13-JUN-18 1BOL 1 REMARK REVDAT 3 24-FEB-09 1BOL 1 VERSN REVDAT 2 22-DEC-99 1BOL 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 12-AUG-98 1BOL 0 JRNL AUTH H.KURIHARA,T.NONAKA,Y.MITSUI,K.OHGI,M.IRIE,K.T.NAKAMURA JRNL TITL THE CRYSTAL STRUCTURE OF RIBONUCLEASE RH FROM RHIZOPUS JRNL TITL 2 NIVEUS AT 2.0 A RESOLUTION. JRNL REF J.MOL.BIOL. V. 255 310 1996 JRNL REFN ISSN 0022-2836 JRNL PMID 8551522 JRNL DOI 10.1006/JMBI.1996.0025 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 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) (%) : 78.2 REMARK 3 NUMBER OF REFLECTIONS : 11745 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1688 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 BOND ANGLES (DEGREES) : 3.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BOL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000008125. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 2 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) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11745 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 8.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 78.2 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.03340 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 (%): 45.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.7 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 33.85000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.15000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.25000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.15000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.85000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.25000 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 46 NE2 HIS A 46 CD2 -0.094 REMARK 500 HIS A 109 NE2 HIS A 109 CD2 -0.069 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 45 CB - CG - CD2 ANGL. DEV. = -10.8 DEGREES REMARK 500 TRP A 49 CE2 - CD2 - CG ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 67 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 TRP A 91 CD1 - CG - CD2 ANGL. DEV. = 5.0 DEGREES REMARK 500 TRP A 106 CD1 - CG - CD2 ANGL. DEV. = 7.0 DEGREES REMARK 500 TRP A 106 CG - CD1 - NE1 ANGL. DEV. = -6.5 DEGREES REMARK 500 TRP A 106 CE2 - CD2 - CG ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG A 141 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 141 NE - CZ - NH2 ANGL. DEV. = -6.8 DEGREES REMARK 500 LYS A 148 CA - CB - CG ANGL. DEV. = 15.3 DEGREES REMARK 500 TYR A 219 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES 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 SER A 2 158.03 133.79 REMARK 500 SER A 4 83.11 -45.05 REMARK 500 ASP A 64 103.33 -164.45 REMARK 500 ASP A 80 102.69 -163.96 REMARK 500 ASN A 97 88.19 -168.25 REMARK 500 ASN A 123 76.40 -158.06 REMARK 500 TYR A 144 70.58 -103.66 REMARK 500 ASP A 200 36.31 -157.57 REMARK 500 SER A 209 140.92 -178.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ACT REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: ACTIVE SITE DBREF 1BOL A 1 222 UNP P08056 RNRH_RHINI 17 238 SEQRES 1 A 222 SER SER CYS SER SER THR ALA LEU SER CYS SER ASN SER SEQRES 2 A 222 ALA ASN SER ASP THR CYS CYS SER PRO GLU TYR GLY LEU SEQRES 3 A 222 VAL VAL LEU ASN MET GLN TRP ALA PRO GLY TYR GLY PRO SEQRES 4 A 222 ASP ASN ALA PHE THR LEU HIS GLY LEU TRP PRO ASP LYS SEQRES 5 A 222 CYS SER GLY ALA TYR ALA PRO SER GLY GLY CYS ASP SER SEQRES 6 A 222 ASN ARG ALA SER SER SER ILE ALA SER VAL ILE LYS SER SEQRES 7 A 222 LYS ASP SER SER LEU TYR ASN SER MET LEU THR TYR TRP SEQRES 8 A 222 PRO SER ASN GLN GLY ASN ASN ASN VAL PHE TRP SER HIS SEQRES 9 A 222 GLU TRP SER LYS HIS GLY THR CYS VAL SER THR TYR ASP SEQRES 10 A 222 PRO ASP CYS TYR ASP ASN TYR GLU GLU GLY GLU ASP ILE SEQRES 11 A 222 VAL ASP TYR PHE GLN LYS ALA MET ASP LEU ARG SER GLN SEQRES 12 A 222 TYR ASN VAL TYR LYS ALA PHE SER SER ASN GLY ILE THR SEQRES 13 A 222 PRO GLY GLY THR TYR THR ALA THR GLU MET GLN SER ALA SEQRES 14 A 222 ILE GLU SER TYR PHE GLY ALA LYS ALA LYS ILE ASP CYS SEQRES 15 A 222 SER SER GLY THR LEU SER ASP VAL ALA LEU TYR PHE TYR SEQRES 16 A 222 VAL ARG GLY ARG ASP THR TYR VAL ILE THR ASP ALA LEU SEQRES 17 A 222 SER THR GLY SER CYS SER GLY ASP VAL GLU TYR PRO THR SEQRES 18 A 222 LYS HELIX 1 1 ILE A 72 LYS A 79 1 8 HELIX 2 2 SER A 81 TYR A 90 1 10 HELIX 3 3 ASN A 98 LYS A 108 1 11 HELIX 4 4 GLY A 110 CYS A 112 5 3 HELIX 5 5 SER A 114 TYR A 116 5 3 HELIX 6 6 PRO A 118 CYS A 120 5 3 HELIX 7 7 GLU A 128 GLN A 143 1 16 HELIX 8 8 VAL A 146 ASN A 153 1 8 HELIX 9 9 ALA A 163 PHE A 174 1 12 SHEET 1 A 4 THR A 201 THR A 205 0 SHEET 2 A 4 ASP A 189 ARG A 197 -1 N ARG A 197 O THR A 201 SHEET 3 A 4 LEU A 26 GLN A 32 -1 N MET A 31 O VAL A 190 SHEET 4 A 4 THR A 44 ASP A 51 -1 N ASP A 51 O LEU A 26 SHEET 1 B 2 GLY A 159 THR A 162 0 SHEET 2 B 2 ASP A 216 TYR A 219 -1 N TYR A 219 O GLY A 159 SHEET 1 C 2 LYS A 179 SER A 183 0 SHEET 2 C 2 THR A 186 ALA A 191 -1 N ALA A 191 O LYS A 179 SSBOND 1 CYS A 3 CYS A 20 1555 1555 2.03 SSBOND 2 CYS A 19 CYS A 120 1555 1555 2.04 SSBOND 3 CYS A 10 CYS A 53 1555 1555 2.02 SSBOND 4 CYS A 63 CYS A 112 1555 1555 2.02 SSBOND 5 CYS A 182 CYS A 213 1555 1555 1.99 SITE 1 ACT 3 HIS A 46 HIS A 109 GLU A 105 CRYST1 67.700 72.500 44.300 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 0.014771 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013793 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022573 0.00000