HEADER ENDONUCLEASE 08-NOV-96 1RNZ
TITLE RIBONUCLEASE A CRYSTALLIZED FROM 2.5M SODIUM CHLORIDE, 3.3M
TITLE 2 SODIUM FORMATE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: RIBONUCLEASE A;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: RNASE A;
COMPND 5 EC: 3.1.27.5
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, NUCLEASE, ENDONUCLEASE, GLYCOPROTEIN, SIGNAL
EXPDTA X-RAY DIFFRACTION
AUTHOR A.A.FEDOROV,D.JOSPH-MCCARTHY,E.V.FEDOROV,D.SIRAKOVA,I.GRAF,
AUTHOR 2 S.C.ALMO
REVDAT 3 24-FEB-09 1RNZ 1 VERSN
REVDAT 2 01-APR-03 1RNZ 1 JRNL
REVDAT 1 01-APR-97 1RNZ 0
JRNL AUTH A.A.FEDOROV,D.JOSEPH-MCCARTHY,E.FEDOROV,D.SIRAKOVA,
JRNL AUTH 2 I.GRAF,S.C.ALMO
JRNL TITL IONIC INTERACTIONS IN CRYSTALLINE BOVINE
JRNL TITL 2 PANCREATIC RIBONUCLEASE A.
JRNL REF BIOCHEMISTRY V. 35 15962 1996
JRNL REFN ISSN 0006-2960
JRNL PMID 8973167
JRNL DOI 10.1021/BI961533G
REMARK 1
REMARK 2
REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PROFFT, X-PLOR
REMARK 3 AUTHORS : KONNERT,HENDRICKSON,FINZEL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 82.7
REMARK 3 NUMBER OF REFLECTIONS : 10380
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 + TEST SET) : NULL
REMARK 3 R VALUE (WORKING SET) : 0.167
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 FIT/AGREEMENT OF MODEL WITH ALL DATA.
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL
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) : NULL
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 : 3
REMARK 3 SOLVENT ATOMS : 95
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.90
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) : 0.19
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA
REMARK 3 BOND LENGTH (A) : 0.011 ; 0.018
REMARK 3 ANGLE DISTANCE (A) : 0.030 ; 0.030
REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.039 ; 0.050
REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL
REMARK 3
REMARK 3 PLANE RESTRAINT (A) : 0.011 ; 0.020
REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.114 ; 0.150
REMARK 3
REMARK 3 NON-BONDED CONTACT RESTRAINTS.
REMARK 3 SINGLE TORSION (A) : 0.172 ; 0.300
REMARK 3 MULTIPLE TORSION (A) : 0.198 ; 0.300
REMARK 3 H-BOND (X...Y) (A) : 0.236 ; 0.300
REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL
REMARK 3
REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS.
REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL
REMARK 3 PLANAR (DEGREES) : 1.600 ; 2.000
REMARK 3 STAGGERED (DEGREES) : 17.000; 10.000
REMARK 3 TRANSVERSE (DEGREES) : 17.600; 10.000
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) : 2.290 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 2.480 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.950 ; 3.000
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1RNZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 1993
REMARK 200 TEMPERATURE (KELVIN) : 290
REMARK 200 PH : 5.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
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 : GRAPHITE(002)
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : AREA DETECTOR
REMARK 200 DETECTOR MANUFACTURER : SIEMENS
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11350
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900
REMARK 200 RESOLUTION RANGE LOW (A) : 27.900
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 89.0
REMARK 200 DATA REDUNDANCY : 2.190
REMARK 200 R MERGE (I) : 0.04900
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.0400
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 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: X-PLOR
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 57.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZED FROM 2.5M SODIUM
REMARK 280 CHLORIDE, 3.3M SODIUM FORMATE, PH 5.5
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z+1/3
REMARK 290 6555 -X,-X+Y,-Z+2/3
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.43267
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.71633
REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.71633
REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 43.43267
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 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 ARG A 85 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 ARG A 85 NE - CZ - NH2 ANGL. DEV. = -3.5 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 LYS A 37 -70.90 -69.93
REMARK 500 HIS A 48 64.76 -105.58
REMARK 500 GLN A 60 -138.74 -100.21
REMARK 500 ASN A 94 71.72 -102.67
REMARK 500 ALA A 122 -179.16 -172.15
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 CL A 126
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 127
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 128
DBREF 1RNZ 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 CL A 126 1
HET CL A 127 1
HET CL A 128 1
HETNAM CL CHLORIDE ION
FORMUL 2 CL 3(CL 1-)
FORMUL 5 HOH *95(H2 O)
HELIX 1 H1 THR A 3 MET A 13 1 11
HELIX 2 H2 ASN A 24 ASN A 34 1RESIDUE 34 IN 3/10 CONFIG 11
HELIX 3 H3 SER A 50 GLN A 60 1RESIDUES 56-60 IN 3/10 CONFIG 11
SHEET 1 S1A 3 LYS A 41 HIS A 48 0
SHEET 2 S1A 3 MET A 79 THR A 87 -1 N GLU A 86 O PRO A 42
SHEET 3 S1A 3 ASN A 94 LYS A 104 -1 O LYS A 104 N MET A 79
SHEET 1 S1B 3 LYS A 41 HIS A 48 0
SHEET 2 S1B 3 SER A 90 LYS A 91 -1
SHEET 3 S1B 3 ASN A 94 LYS A 104 -1 O ASN A 94 N LYS A 91
SHEET 1 S2A 4 LYS A 61 ALA A 64 0
SHEET 2 S2A 4 ASN A 71 SER A 75 -1 O CYS A 72 N VAL A 63
SHEET 3 S2A 4 HIS A 105 ASN A 113 -1 O VAL A 108 N TYR A 73
SHEET 4 S2A 4 PRO A 114 HIS A 119 -1 O VAL A 116 N GLU A 111
SHEET 1 S2B 4 LYS A 61 ALA A 64 0
SHEET 2 S2B 4 ASN A 71 SER A 75 -1 O CYS A 72 N VAL A 63
SHEET 3 S2B 4 HIS A 105 ASN A 113 -1 O VAL A 108 N TYR A 73
SHEET 4 S2B 4 ASP A 121 VAL A 124 -1 N VAL A 124 O HIS A 105
SSBOND 1 CYS A 26 CYS A 84 1555 1555 2.00
SSBOND 2 CYS A 40 CYS A 95 1555 1555 1.97
SSBOND 3 CYS A 58 CYS A 110 1555 1555 2.01
SSBOND 4 CYS A 65 CYS A 72 1555 1555 2.00
CISPEP 1 TYR A 92 PRO A 93 0 2.29
CISPEP 2 ASN A 113 PRO A 114 0 1.17
SITE 1 AC1 3 ARG A 10 ASN A 34 THR A 78
SITE 1 AC2 1 THR A 45
SITE 1 AC3 2 THR A 3 HOH A 219
CRYST1 64.562 64.562 65.149 90.00 90.00 120.00 P 32 2 1 6
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 0.015489 0.008943 0.000000 0.00000
SCALE2 0.000000 0.017885 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015349 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
