HEADER HYDROLASE 21-APR-09 3A1R TITLE NEUTRON CRYSTAL STRUCTURE ANALYSIS OF BOVINE PANCREATIC RIBONUCLEASE A COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE PANCREATIC; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE 1, RNASE A; COMPND 5 EC: 3.1.27.5 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 OTHER_DETAILS: PANCREAS KEYWDS BOVINE PANCREATIC RIBONUCLEASE A, NEUTRON STRUCTURE, ENDONUCLEASE, KEYWDS 2 GLYCATION, GLYCOPROTEIN, HYDROLASE, SECRETED, DISULFIDE BOND, KEYWDS 3 NUCLEASE EXPDTA NEUTRON DIFFRACTION AUTHOR D.YAGI,I.TANAKA,N.NIIMURA REVDAT 7 06-NOV-24 3A1R 1 REMARK REVDAT 6 01-NOV-23 3A1R 1 REMARK REVDAT 5 18-JUL-18 3A1R 1 REMARK REVDAT 4 13-JUN-18 3A1R 1 REMARK REVDAT 3 07-MAR-18 3A1R 1 REMARK REVDAT 2 13-JUL-11 3A1R 1 VERSN REVDAT 1 01-SEP-09 3A1R 0 JRNL AUTH D.YAGI,T.YAMADA,K.KURIHARA,Y.OHNISHI,M.YAMASHITA,T.TAMADA, JRNL AUTH 2 I.TANAKA,R.KUROKI,N.NIIMURA JRNL TITL A NEUTRON CRYSTALLOGRAPHIC ANALYSIS OF PHOSPHATE-FREE JRNL TITL 2 RIBONUCLEASE A AT 1.7 A RESOLUTION JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 65 892 2009 JRNL REFN ISSN 0907-4449 JRNL PMID 19690366 JRNL DOI 10.1107/S0907444909018885 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 666500.050 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 63.9 REMARK 3 NUMBER OF REFLECTIONS : 15029 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) : 0.195 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 750 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 23.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 870 REMARK 3 BIN R VALUE (WORKING SET) : 0.3330 REMARK 3 BIN FREE R VALUE : 0.3680 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 50 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.052 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 : 0 REMARK 3 SOLVENT ATOMS : 92 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.19000 REMARK 3 B22 (A**2) : -0.25000 REMARK 3 B33 (A**2) : -0.94000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.32000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.14 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) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.260 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ANISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.320 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.820 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.850 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.910 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.06 REMARK 3 BSOL : 13.00 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 : PRO3.PARAM REMARK 3 PARAMETER FILE 2 : SOL.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PRO2.TOP REMARK 3 TOPOLOGY FILE 2 : SOL.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3A1R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000028702. REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 22-AUG-05 REMARK 230 TEMPERATURE (KELVIN) : 298.0 REMARK 230 PH : 6.20 REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR REMARK 230 BEAMLINE : 1G-B REMARK 230 WAVELENGTH OR RANGE (A) : 2.6 REMARK 230 MONOCHROMATOR : ELLASTICALLY BENT SILICON REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : IMAGE PLATE REMARK 230 DETECTOR MANUFACTURER : MACSCIENCE REMARK 230 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 230 DATA SCALING SOFTWARE : SCALEPACK REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 15039 REMARK 230 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 230 RESOLUTION RANGE LOW (A) : 80.000 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 64.0 REMARK 230 DATA REDUNDANCY : 2.100 REMARK 230 R MERGE (I) : 0.08600 REMARK 230 R SYM (I) : NULL REMARK 230 FOR THE DATA SET : 8.4000 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 230 COMPLETENESS FOR SHELL (%) : 19.5 REMARK 230 DATA REDUNDANCY IN SHELL : NULL REMARK 230 R MERGE FOR SHELL (I) : 0.21000 REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 FOR SHELL : 3.070 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : CNS REMARK 230 STARTING MODEL: PDB ENTRY 1KF4 REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% TERT-BUTYL ALCOHOL, TEMPERATURE REMARK 280 298K, THEN THE CRYSTAL WAS SOAKED IN HEAVY WATER SOLUTION, PH6.2, REMARK 280 FOR TWO MONTHS, BATCH REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 19.27900 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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: 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 GLN A 60 -129.20 -107.72 REMARK 500 REMARK 500 REMARK: NULL DBREF 3A1R 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 FORMUL 2 DOD *92(D2 O) HELIX 1 1 THR A 3 MET A 13 1 11 HELIX 2 2 ASN A 24 ARG A 33 1 10 HELIX 3 3 SER A 50 ALA A 56 1 7 HELIX 4 4 VAL A 57 GLN A 60 5 4 SHEET 1 A 3 VAL A 43 VAL A 47 0 SHEET 2 A 3 MET A 79 GLU A 86 -1 O CYS A 84 N ASN A 44 SHEET 3 A 3 TYR A 97 LYS A 104 -1 O THR A 100 N ASP A 83 SHEET 1 B 4 LYS A 61 VAL A 63 0 SHEET 2 B 4 CYS A 72 GLN A 74 -1 O GLN A 74 N LYS A 61 SHEET 3 B 4 ILE A 106 GLU A 111 -1 O VAL A 108 N TYR A 73 SHEET 4 B 4 VAL A 116 SER A 123 -1 O VAL A 118 N ALA A 109 SSBOND 1 CYS A 26 CYS A 84 1555 1555 2.03 SSBOND 2 CYS A 40 CYS A 95 1555 1555 2.03 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 0.04 CISPEP 2 ASN A 113 PRO A 114 0 0.08 CRYST1 30.380 38.558 53.398 90.00 105.78 90.00 P 1 21 1 2 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 0.032916 0.000000 0.009302 0.00000 SCALE2 0.000000 0.025935 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019461 0.00000