PDB Short entry for 1BEL HEADER HYDROLASE 21-DEC-95 1BEL TITLE HYDROLASE PHOSPHORIC DIESTER, RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE A; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.27.5; COMPND 5 OTHER_DETAILS: PH 4.5 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 ORGAN: PANCREAS KEYWDS HYDROLASE (PHOSPHORIC DIESTER, RNA), NUCLEASE, ENDONUCLEASE, KEYWDS 2 GLYCOPROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.H.DUNG,J.A.BELL REVDAT 4 02-AUG-23 1BEL 1 REMARK REVDAT 3 24-FEB-09 1BEL 1 VERSN REVDAT 2 27-JUL-99 1BEL 1 JRNL REMARK REVDAT 1 14-OCT-96 1BEL 0 JRNL AUTH M.H.DUNG,J.A.BELL JRNL TITL STRUCTURE OF CRYSTAL FORM IX OF BOVINE PANCREATIC JRNL TITL 2 RIBONUCLEASE A. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 53 419 1997 JRNL REFN ISSN 0907-4449 JRNL PMID 15299907 JRNL DOI 10.1107/S0907444997000929 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.0 REMARK 3 NUMBER OF REFLECTIONS : 12318 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : NULL 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 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1500 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 12318 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 951 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 82 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 16.100 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.010 ; 1.000 ; 983 REMARK 3 BOND ANGLES (DEGREES) : 1.925 ; 1.500 ; 1321 REMARK 3 TORSION ANGLES (DEGREES) : NULL ; 0.000 ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; 0.000 ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.010 ; 1.500 ; 28 REMARK 3 GENERAL PLANES (A) : 0.016 ; 4.000 ; 140 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; 0.000 ; NULL REMARK 3 NON-BONDED CONTACTS (A) : 0.008 ; 20.000; 4 REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : BABINET REMARK 3 KSOL : 0.57 REMARK 3 BSOL : 117.0 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : TNT PROTGEO REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FINAL B VALUES CALCULATED BY GRADIENT REMARK 3 METHOD REMARK 4 REMARK 4 1BEL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171663. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-AUG-92 REMARK 200 TEMPERATURE (KELVIN) : 292.0 REMARK 200 PH : 4.50 REMARK 200 NUMBER OF CRYSTALS USED : 4 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BIOTEX REMARK 200 DATA SCALING SOFTWARE : BIOTEX REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12318 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.0 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.3600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.0 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 : 4.220 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MERLOT REMARK 200 STARTING MODEL: PDB ENTRY 3RN3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 60% METHANOL, PH 4.50 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 22.95000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.45000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.40000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.45000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.95000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.40000 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 GLU A 86 CD GLU A 86 OE1 0.073 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 ASP A 14 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 14 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP A 53 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ASP A 53 CB - CG - OD2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ASP A 83 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 83 CB - CG - OD2 ANGL. DEV. = -8.9 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 ASP A 38 -45.68 72.89 REMARK 500 GLN A 60 -138.32 -90.67 REMARK 500 ASN A 71 35.27 -96.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MOH A 170 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MOH A 171 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MOH A 172 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MOH A 173 DBREF 1BEL A 1 124 UNP P61823 RNAS1_BOVIN 27 150 SEQRES 1 A 124 LYS GLU THR ALA ALA ALA LYS PHE GLU ARG GLN HIS MET SEQRES 2 A 124 ASP SER SER THR SER ALA ALA SER SER SER ASN TYR CYS SEQRES 3 A 124 ASN GLN MET MET LYS SER ARG ASN LEU THR LYS ASP ARG SEQRES 4 A 124 CYS LYS PRO VAL ASN THR PHE VAL HIS GLU SER LEU ALA SEQRES 5 A 124 ASP VAL GLN ALA VAL CYS SER GLN LYS ASN VAL ALA CYS SEQRES 6 A 124 LYS ASN GLY GLN THR ASN CYS TYR GLN SER TYR SER THR SEQRES 7 A 124 MET SER ILE THR ASP CYS ARG GLU THR GLY SER SER LYS SEQRES 8 A 124 TYR PRO ASN CYS ALA TYR LYS THR THR GLN ALA ASN LYS SEQRES 9 A 124 HIS ILE ILE VAL ALA CYS GLU GLY ASN PRO TYR VAL PRO SEQRES 10 A 124 VAL HIS PHE ASP ALA SER VAL HET SO4 A 150 5 HET SO4 A 151 5 HET MOH A 170 2 HET MOH A 171 2 HET MOH A 172 2 HET MOH A 173 2 HETNAM SO4 SULFATE ION HETNAM MOH METHANOL FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 MOH 4(C H4 O) FORMUL 8 HOH *82(H2 O) HELIX 1 1 ALA A 4 HIS A 12 1 9 HELIX 2 2 TYR A 25 SER A 32 1 8 HELIX 3 3 LEU A 51 SER A 59 1 9 SHEET 1 A 3 VAL A 43 VAL A 47 0 SHEET 2 A 3 MET A 79 GLU A 86 -1 N CYS A 84 O ASN A 44 SHEET 3 A 3 TYR A 97 LYS A 104 -1 N LYS A 104 O MET A 79 SHEET 1 B 4 LYS A 61 VAL A 63 0 SHEET 2 B 4 CYS A 72 GLN A 74 -1 N GLN A 74 O LYS A 61 SHEET 3 B 4 ILE A 106 ALA A 109 -1 N VAL A 108 O TYR A 73 SHEET 4 B 4 HIS A 119 SER A 123 -1 N ALA A 122 O ILE A 107 SSBOND 1 CYS A 26 CYS A 84 1555 1555 2.03 SSBOND 2 CYS A 40 CYS A 95 1555 1555 2.04 SSBOND 3 CYS A 58 CYS A 110 1555 1555 2.03 SSBOND 4 CYS A 65 CYS A 72 1555 1555 2.02 CISPEP 1 TYR A 92 PRO A 93 0 5.48 CISPEP 2 ASN A 113 PRO A 114 0 1.29 SITE 1 AC1 7 SER A 22 SER A 23 ASN A 34 LYS A 37 SITE 2 AC1 7 SER A 50 MOH A 171 HOH A 254 SITE 1 AC2 7 GLN A 11 HIS A 12 LYS A 41 HIS A 119 SITE 2 AC2 7 PHE A 120 HOH A 252 HOH A 273 SITE 1 AC3 4 ALA A 6 GLN A 60 TYR A 76 SER A 77 SITE 1 AC4 5 LYS A 37 LEU A 51 ALA A 52 SO4 A 150 SITE 2 AC4 5 HOH A 266 SITE 1 AC5 5 ARG A 10 GLN A 11 ASN A 34 LEU A 35 SITE 2 AC5 5 HOH A 203 SITE 1 AC6 3 TYR A 73 GLU A 86 SER A 90 CRYST1 45.900 44.800 52.900 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 0.021786 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022321 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018904 0.00000