HEADER HYDROLASE 27-OCT-17 6ETL
TITLE ATOMIC RESOLUTION STRUCTURE OF RNASE A (DATA COLLECTION 2)
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
KEYWDS RAMAN MICROSPECTROSCOPY, RIBONUCLEASE, ATOMIC RESOLUTION, RADIATION
KEYWDS 2 DAMAGE, PHOTODAMAGE, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR M.CATERINO,A.VERGARA,A.MERLINO
REVDAT 1 21-FEB-18 6ETL 0
JRNL AUTH A.VERGARA,M.CATERINO,A.MERLINO
JRNL TITL RAMAN-MARKERS OF X-RAY RADIATION DAMAGE OF PROTEINS.
JRNL REF INT. J. BIOL. MACROMOL. V. 111 1194 2018
JRNL REFN ISSN 1879-0003
JRNL PMID 29374529
JRNL DOI 10.1016/J.IJBIOMAC.2018.01.135
REMARK 2
REMARK 2 RESOLUTION. 0.85 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : SHELXL
REMARK 3 AUTHORS : G.M.SHELDRICK
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.85
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9
REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF).
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.103
REMARK 3 FREE R VALUE (NO CUTOFF) : 0.122
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 4106
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL
REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 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 : 12
REMARK 3 SOLVENT ATOMS : 233
REMARK 3
REMARK 3 MODEL REFINEMENT.
REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL
REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL
REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL
REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL
REMARK 3 NUMBER OF RESTRAINTS : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.
REMARK 3 BOND LENGTHS (A) : NULL
REMARK 3 ANGLE DISTANCES (A) : NULL
REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL
REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL
REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL
REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL
REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL
REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL
REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL
REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED: NULL
REMARK 3
REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL
REMARK 3 SPECIAL CASE: NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 6ETL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-OCT-17.
REMARK 100 THE DEPOSITION ID IS D_1200007159.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 26-SEP-11
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.3
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SLS
REMARK 200 BEAMLINE : X10SA
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.7749
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 95598
REMARK 200 RESOLUTION RANGE HIGH (A) : 0.850
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8
REMARK 200 DATA REDUNDANCY : 3.300
REMARK 200 R MERGE (I) : 0.04700
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 38.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.85
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.88
REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9
REMARK 200 DATA REDUNDANCY IN SHELL : 3.20
REMARK 200 R MERGE FOR SHELL (I) : 0.35300
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 39.68
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: FREE-INTERFACE DIFFUSION OF A 10 UL OF
REMARK 280 30 MG ML-1 PROTEIN SOLUTION, 20 MM SODIUM CITRATE AT PH 5.3
REMARK 280 AGAIST 10 UL ISOPROPANOL 99.9% ISOPROPANOL., LIQUID DIFFUSION,
REMARK 280 TEMPERATURE 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 18.98550
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 TOTAL BURIED SURFACE AREA: 470 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 7090 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 7.0 KCAL/MOL
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
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 HG SER A 77 O HOH A 373 2645 1.51
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 LYS A 7 CD - CE - NZ ANGL. DEV. = 15.2 DEGREES
REMARK 500 ASP A 38 CB - CG - OD2 ANGL. DEV. = -7.7 DEGREES
REMARK 500 CYS A 72 N - CA - CB ANGL. DEV. = -12.1 DEGREES
REMARK 500 CYS A 72 CA - CB - SG ANGL. DEV. = -11.3 DEGREES
REMARK 500 ARG A 85 NE - CZ - NH2 ANGL. DEV. = 3.4 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 GLN A 60 -137.80 -104.65
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 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue IPA A 202
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue IPA A 203
DBREF 6ETL 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 201 8
HET IPA A 202 4
HET IPA A 203 4
HETNAM IPA ISOPROPYL ALCOHOL
HETSYN IPA 2-PROPANOL
FORMUL 2 IPA 3(C3 H8 O)
FORMUL 5 HOH *233(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 THR A 82 N PHE A 46
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 2.06
SSBOND 2 CYS A 40 CYS A 95 1555 1555 2.10
SSBOND 3 CYS A 58 CYS A 110 1555 1555 2.04
SSBOND 4 CYS A 65 CYS A 72 1555 1555 2.05
CISPEP 1 TYR A 92 PRO A 93 0 3.13
CISPEP 2 ASN A 113 PRO A 114 0 7.20
SITE 1 AC1 8 ARG A 33 LYS A 61 VAL A 63 GLN A 74
SITE 2 AC1 8 IPA A 203 HOH A 353 HOH A 407 HOH A 433
SITE 1 AC2 2 ASN A 103 HOH A 420
SITE 1 AC3 9 ASP A 14 SER A 16 MET A 29 ARG A 33
SITE 2 AC3 9 GLN A 74 IPA A 201 HOH A 381 HOH A 403
SITE 3 AC3 9 HOH A 530
CRYST1 29.125 37.971 52.541 90.00 105.83 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 0.034335 0.000000 0.009735 0.00000
SCALE2 0.000000 0.026336 0.000000 0.00000
SCALE3 0.000000 0.000000 0.019783 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
