HEADER HYDROLASE 09-JUL-09 3I7W
TITLE HIGH PRESSURE STRUCTURE OF WILD-TYPE RNASE A (0.67 GPA)
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;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS;
SOURCE 3 ORGANISM_COMMON: BOVINE;
SOURCE 4 ORGANISM_TAXID: 9913;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBRX
KEYWDS RIBONUCLEASE A, RNASE A, HIGH PRESSURE, DISULFIDE BOND, ENDONUCLEASE,
KEYWDS 2 GLYCATION, GLYCOPROTEIN, HYDROLASE, NUCLEASE, SECRETED
EXPDTA X-RAY DIFFRACTION
AUTHOR K.LEWINSKI,K.KURPIEWSKA,K.DZIUBEK,A.KATRUSIAK,J.FONT,M.RIBO,
AUTHOR 2 M.VILANOVA
REVDAT 6 01-NOV-23 3I7W 1 REMARK
REVDAT 5 01-NOV-17 3I7W 1 REMARK
REVDAT 4 09-AUG-17 3I7W 1 JRNL
REVDAT 3 26-APR-17 3I7W 1 JRNL
REVDAT 2 19-JAN-11 3I7W 1 REMARK
REVDAT 1 04-AUG-09 3I7W 0
JRNL AUTH K.KURPIEWSKA,K.DZIUBEK,A.KATRUSIAK,J.FONT,M.RIBO,M.VILANOVA,
JRNL AUTH 2 K.LEWINSKI
JRNL TITL STRUCTURAL INVESTIGATION OF RIBONUCLEASE A CONFORMATIONAL
JRNL TITL 2 PREFERENCES USING HIGH PRESSURE PROTEIN CRYSTALLOGRAPHY
JRNL REF CHEM.PHYS. V. 468 53 2016
JRNL REFN ISSN 0301-0104
JRNL DOI 10.1016/J.CHEMPHYS.2016.01.010
REMARK 2
REMARK 2 RESOLUTION. 2.35 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 : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1091275.170
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.4
REMARK 3 NUMBER OF REFLECTIONS : 6332
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) : 0.252
REMARK 3 FREE R VALUE : 0.295
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800
REMARK 3 FREE R VALUE TEST SET COUNT : 310
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.017
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) : 2.35
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 59.00
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 629
REMARK 3 BIN R VALUE (WORKING SET) : 0.3960
REMARK 3 BIN FREE R VALUE : 0.5600
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.30
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 42
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.086
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 : 2
REMARK 3 SOLVENT ATOMS : 47
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 30.50
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.41
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -5.50600
REMARK 3 B22 (A**2) : -0.07800
REMARK 3 B33 (A**2) : 5.58400
REMARK 3 B12 (A**2) : 6.97900
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.36
REMARK 3 ESD FROM SIGMAA (A) : 0.47
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) : 0.40
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.65
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.007
REMARK 3 BOND ANGLES (DEGREES) : 1.180
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.60
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.700
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 1.736 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.971 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 2.403 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.545 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.41
REMARK 3 BSOL : 19.79
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 : PROTEIN_REP.PARAM
REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM
REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM
REMARK 3 PARAMETER FILE 4 : ION.PARAM
REMARK 3 PARAMETER FILE 5 : NULL
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP
REMARK 3 TOPOLOGY FILE 3 : WATER.TOP
REMARK 3 TOPOLOGY FILE 4 : ION.TOP
REMARK 3 TOPOLOGY FILE 5 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 3I7W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-JUL-09.
REMARK 100 THE DEPOSITION ID IS D_1000054075.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 24-JAN-08
REMARK 200 TEMPERATURE (KELVIN) : 298.0
REMARK 200 PH : 6.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : SEALED TUBE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS FR590
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.7107
REMARK 200 MONOCHROMATOR : GRAPHITE
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : NONIUS KAPPA CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6408
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4
REMARK 200 DATA REDUNDANCY : 1.800
REMARK 200 R MERGE (I) : 0.13500
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.48
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5
REMARK 200 DATA REDUNDANCY IN SHELL : 1.80
REMARK 200 R MERGE FOR SHELL (I) : 0.39700
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: CNS
REMARK 200 STARTING MODEL: 1FS3
REMARK 200
REMARK 200 REMARK: PRESSURE: 0.67 GPA
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 54.31
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, SODIUM CHLORIDE,
REMARK 280 SODIUM ACETATE, PH 6.0, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 298K
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 42.20000
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 21.10000
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 21.10000
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 42.20000
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: 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 ALA A 20 103.75 -57.74
REMARK 500 SER A 22 -168.60 68.54
REMARK 500 HIS A 48 73.21 -101.92
REMARK 500 GLN A 60 -130.19 -106.19
REMARK 500 SER A 89 51.40 -105.50
REMARK 500 ALA A 122 -175.16 -177.48
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 125
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 126
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3DH5 RELATED DB: PDB
REMARK 900 RELATED ID: 3I7X RELATED DB: PDB
REMARK 900 RELATED ID: 3I7Y RELATED DB: PDB
DBREF 3I7W 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 125 1
HET CL A 126 1
HETNAM CL CHLORIDE ION
FORMUL 2 CL 2(CL 1-)
FORMUL 4 HOH *47(H2 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 VAL A 57 1 8
HELIX 4 4 CYS A 58 GLN A 60 5 3
SHEET 1 A 5 VAL A 43 VAL A 47 0
SHEET 2 A 5 MET A 79 GLU A 86 -1 O CYS A 84 N ASN A 44
SHEET 3 A 5 TYR A 97 GLU A 111 -1 O ALA A 102 N ILE A 81
SHEET 4 A 5 CYS A 72 GLN A 74 -1 N TYR A 73 O VAL A 108
SHEET 5 A 5 LYS A 61 VAL A 63 -1 N LYS A 61 O GLN A 74
SHEET 1 B 4 VAL A 43 VAL A 47 0
SHEET 2 B 4 MET A 79 GLU A 86 -1 O CYS A 84 N ASN A 44
SHEET 3 B 4 TYR A 97 GLU A 111 -1 O ALA A 102 N ILE A 81
SHEET 4 B 4 VAL A 116 VAL A 124 -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 2.02
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 0.29
CISPEP 2 ASN A 113 PRO A 114 0 -0.16
SITE 1 AC1 3 ARG A 10 ASN A 34 THR A 78
SITE 1 AC2 3 HIS A 12 ASN A 44 THR A 45
CRYST1 63.552 63.552 63.300 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 0.015735 0.009085 0.000000 0.00000
SCALE2 0.000000 0.018169 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015798 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
