HEADER HYDROLASE 18-AUG-15 5D97 TITLE NEUTRON CRYSTAL STRUCTURE OF H2O-SOLVENT 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 ORGAN: PANCREAS KEYWDS RIBONUCLEASE A, D/H CONTRAST, HYDROLASE EXPDTA NEUTRON DIFFRACTION AUTHOR T.CHATAKE,S.FUJIWARA REVDAT 3 05-DEC-18 5D97 1 REMARK REVDAT 2 28-NOV-18 5D97 1 REMARK REVDAT 1 06-APR-16 5D97 0 JRNL AUTH T.CHATAKE,S.FUJIWARA JRNL TITL A TECHNIQUE FOR DETERMINING THE DEUTERIUM/HYDROGEN CONTRAST JRNL TITL 2 MAP IN NEUTRON MACROMOLECULAR CRYSTALLOGRAPHY JRNL REF ACTA CRYSTALLOGR D STRUCT V. 72 71 2016 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 26894536 JRNL DOI 10.1107/S2059798315021269 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 72.1 REMARK 3 NUMBER OF REFLECTIONS : 7979 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 401 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 30.7066 - 2.5959 0.89 3166 175 0.1775 0.1880 REMARK 3 2 2.5959 - 2.0605 0.71 2464 121 0.2254 0.2145 REMARK 3 3 2.0605 - 1.8001 0.56 1948 105 0.3094 0.3036 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.630 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.089 1928 REMARK 3 ANGLE : 1.000 3346 REMARK 3 CHIRALITY : 0.054 148 REMARK 3 PLANARITY : 0.006 303 REMARK 3 DIHEDRAL : 16.486 497 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5D97 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212835. REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 16-AUG-10 REMARK 230 TEMPERATURE (KELVIN) : 293.0 REMARK 230 PH : 5.80 REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR REMARK 230 BEAMLINE : 1G-A REMARK 230 WAVELENGTH OR RANGE (A) : 2.9 REMARK 230 MONOCHROMATOR : SI MONOCHROMATOR REMARK 230 OPTICS : THE BIX-3 NEUTRON DIFFRACTOMETER REMARK 230 AT JRR-3M OF JAEA REMARK 230 REMARK 230 DETECTOR TYPE : IMAGE PLATE REMARK 230 DETECTOR MANUFACTURER : MACSCIENCE REMARK 230 INTENSITY-INTEGRATION SOFTWARE : SCALEPACK REMARK 230 DATA SCALING SOFTWARE : NULL REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 7979 REMARK 230 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 230 RESOLUTION RANGE LOW (A) : 30.700 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 72.5 REMARK 230 DATA REDUNDANCY : 2.300 REMARK 230 R MERGE (I) : 0.15400 REMARK 230 R SYM (I) : NULL REMARK 230 FOR THE DATA SET : 5.6000 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 230 COMPLETENESS FOR SHELL (%) : 48.4 REMARK 230 DATA REDUNDANCY IN SHELL : 1.60 REMARK 230 R MERGE FOR SHELL (I) : 0.28100 REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 FOR SHELL : 2.900 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 230 SOFTWARE USED : CNS REMARK 230 STARTING MODEL: NULL REMARK 230 REMARK 230 REMARK: H2O-SOLVENT CRYSTAL OF RIBONUCLEASE A REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MG/ML RIBONUCLEASE A, 0.05 M SODIUM REMARK 280 ACETATE, 50% 2-PROPANOL, PH 5.8, LIQUID DIFFUSION, TEMPERATURE REMARK 280 293K 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 19.18450 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 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 ND2 ASN A 34 H2 HOH A 301 1.55 REMARK 500 ND2 ASN A 34 O HOH A 301 1.79 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 GLN A 60 -134.86 -104.20 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 IPA A 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ZZ4 RELATED DB: PDB REMARK 900 RELATED ID: 5D6U RELATED DB: PDB DBREF 5D97 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 IPA A 200 4 HETNAM IPA ISOPROPYL ALCOHOL HETSYN IPA 2-PROPANOL FORMUL 2 IPA C3 H8 O FORMUL 3 HOH *107(H2 O) HELIX 1 AA1 THR A 3 MET A 13 1 11 HELIX 2 AA2 ASN A 24 ARG A 33 1 10 HELIX 3 AA3 SER A 50 ALA A 56 1 7 HELIX 4 AA4 VAL A 57 GLN A 60 5 4 SHEET 1 AA1 3 VAL A 43 VAL A 47 0 SHEET 2 AA1 3 MET A 79 GLU A 86 -1 O CYS A 84 N ASN A 44 SHEET 3 AA1 3 TYR A 97 LYS A 104 -1 O LYS A 98 N ARG A 85 SHEET 1 AA2 4 LYS A 61 VAL A 63 0 SHEET 2 AA2 4 CYS A 72 GLN A 74 -1 O GLN A 74 N LYS A 61 SHEET 3 AA2 4 ILE A 106 GLU A 111 -1 O VAL A 108 N TYR A 73 SHEET 4 AA2 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 2.02 SSBOND 2 CYS A 40 CYS A 95 1555 1555 2.02 SSBOND 3 CYS A 58 CYS A 110 1555 1555 2.01 SSBOND 4 CYS A 65 CYS A 72 1555 1555 2.02 CISPEP 1 TYR A 92 PRO A 93 0 8.09 CISPEP 2 ASN A 113 PRO A 114 0 3.54 SITE 1 AC1 5 GLN A 11 HIS A 12 LYS A 41 HIS A 119 SITE 2 AC1 5 PHE A 120 CRYST1 30.340 38.369 53.188 90.00 105.75 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 0.032960 0.000000 0.009296 0.00000 SCALE2 0.000000 0.026063 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019535 0.00000