PDB Short entry for 1SSC HEADER ENDONUCLEASE 05-OCT-94 1SSC TITLE THE 1.6 ANGSTROMS STRUCTURE OF A SEMISYNTHETIC RIBONUCLEASE TITLE 2 CRYSTALLIZED FROM AQUEOUS ETHANOL. COMPARISON WITH TITLE 3 CRYSTALS FROM SALT SOLUTIONS AND WITH RNASE A FROM AQUEOUS TITLE 4 ALCOHOL SOLUTIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RIBONUCLEASE A; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 7 ORGANISM_COMMON: CATTLE; SOURCE 8 ORGANISM_TAXID: 9913 KEYWDS ENDONUCLEASE EXPDTA X-RAY DIFFRACTION AUTHOR V.S.J.DE MEL,M.S.DOSCHER,P.D.MARTIN,F.RODIER,B.F.P.EDWARDS REVDAT 2 24-FEB-09 1SSC 1 VERSN REVDAT 1 26-JAN-95 1SSC 0 JRNL AUTH S.J.DE MEL,M.S.DOSCHER,P.D.MARTIN,F.RODIER, JRNL AUTH 2 B.F.EDWARDS JRNL TITL 1.6 A STRUCTURE OF SEMISYNTHETIC RIBONUCLEASE JRNL TITL 2 CRYSTALLIZED FROM AQUEOUS ETHANOL. COMPARISON WITH JRNL TITL 3 CRYSTALS FROM SALT SOLUTIONS AND WITH RIBONUCLEASE JRNL TITL 4 A FROM AQUEOUS ALCOHOL SOLUTIONS. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 51 1003 1995 JRNL REFN ISSN 0907-4449 JRNL PMID 15299768 JRNL DOI 10.1107/S0907444995004574 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH V.S.J.DE MEL,P.D.MARTIN,M.S.DOSCHER,B.F.P.EDWARDS REMARK 1 TITL STRUCTURAL CHANGES THAT ACCOMPANY THE REDUCED REMARK 1 TITL 2 CATALYTIC EFFICIENCY OF TWO SEMISYNTHETIC REMARK 1 TITL 3 RIBONUCLEASE ANALOGS REMARK 1 REF J.BIOL.CHEM. V. 267 247 1992 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 2 REMARK 1 AUTH P.D.MARTIN,M.S.DOSCHER,B.F.P.EDWARDS REMARK 1 TITL THE REFINED CRYSTAL STRUCTURE OF FULLY ACTIVE REMARK 1 TITL 2 SEMISYNTHETIC RIBONUCLEASE AT 1.8-A RESOLUTION. REMARK 1 REF J.BIOL.CHEM. V. 262 15930 1987 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ, X-PLOR, FRODO REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : NULL 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 : 943 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 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) : 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL 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) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL 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) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE CLOSE CONTACT BETWEEN THE ASP REMARK 3 83 OD2 AND ARG 85 NH2 IS DUE TO WEAK DENSITY AND DISORDER REMARK 3 ASSOCIATED WITH THE ARG 85 RESIDUE. REMARK 4 REMARK 4 1SSC 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 : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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 (%): 44.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 19.17000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 OD2 ASP A 83 NH2 ARG A 85 2.05 REMARK 500 O HOH A 137 O HOH A 191 2.12 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 ARG A 10 NH1 - CZ - NH2 ANGL. DEV. = -9.1 DEGREES REMARK 500 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 10 NE - CZ - NH2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 39 CD - NE - CZ ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG A 39 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 THR A 70 N - CA - CB ANGL. DEV. = -15.3 DEGREES REMARK 500 ASP A 83 CB - CG - OD2 ANGL. DEV. = -7.9 DEGREES REMARK 500 ARG A 85 NE - CZ - NH1 ANGL. DEV. = 7.3 DEGREES REMARK 500 ARG A 85 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 GLU A 86 OE1 - CD - OE2 ANGL. DEV. = 7.3 DEGREES REMARK 500 GLY A 112 CA - C - O ANGL. DEV. = -13.1 DEGREES REMARK 500 VAL B 118 N - CA - CB ANGL. DEV. = -15.3 DEGREES REMARK 500 ASP B 121 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 VAL B 124 CB - CA - C ANGL. DEV. = 13.7 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 HIS A 48 59.38 -100.21 REMARK 500 GLN A 60 -135.66 -97.40 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 PO4 A 125 DBREF 1SSC A 1 112 UNP P61823 RNAS1_BOVIN 27 138 DBREF 1SSC B 114 124 UNP P61823 RNAS1_BOVIN 140 150 SEQRES 1 A 112 LYS GLU THR ALA ALA ALA LYS PHE GLU ARG GLN HIS MET SEQRES 2 A 112 ASP SER SER THR SER ALA ALA SER SER SER ASN TYR CYS SEQRES 3 A 112 ASN GLN MET MET LYS SER ARG ASN LEU THR LYS ASP ARG SEQRES 4 A 112 CYS LYS PRO VAL ASN THR PHE VAL HIS GLU SER LEU ALA SEQRES 5 A 112 ASP VAL GLN ALA VAL CYS SER GLN LYS ASN VAL ALA CYS SEQRES 6 A 112 LYS ASN GLY GLN THR ASN CYS TYR GLN SER TYR SER THR SEQRES 7 A 112 MET SER ILE THR ASP CYS ARG GLU THR GLY SER SER LYS SEQRES 8 A 112 TYR PRO ASN CYS ALA TYR LYS THR THR GLN ALA ASN LYS SEQRES 9 A 112 HIS ILE ILE VAL ALA CYS GLU GLY SEQRES 1 B 11 PRO TYR VAL PRO VAL HIS PHE ASP ALA SER VAL HET PO4 A 125 5 HETNAM PO4 PHOSPHATE ION FORMUL 3 PO4 O4 P 3- FORMUL 4 HOH *95(H2 O) HELIX 1 H1 THR A 3 MET A 13 1 11 HELIX 2 H2 ASN A 24 ASN A 34 1 11 HELIX 3 H3 SER A 50 GLN A 60 1 11 SHEET 1 S1 3 PRO A 42 HIS A 48 0 SHEET 2 S1 3 ASN A 71 TYR A 92 -1 N THR A 82 O PHE A 46 SHEET 3 S1 3 ASN A 94 CYS A 110 -1 N ALA A 102 O ILE A 81 SSBOND 1 CYS A 26 CYS A 84 1555 1555 2.06 SSBOND 2 CYS A 40 CYS A 95 1555 1555 1.97 SSBOND 3 CYS A 58 CYS A 110 1555 1555 1.97 SSBOND 4 CYS A 65 CYS A 72 1555 1555 2.01 CISPEP 1 TYR A 92 PRO A 93 0 1.68 SITE 1 AC1 7 GLN A 11 HIS A 12 LYS A 41 HOH A 141 SITE 2 AC1 7 HOH A 200 HIS B 119 PHE B 120 CRYST1 30.360 38.340 53.550 90.00 106.35 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 0.032938 0.000000 0.009663 0.00000 SCALE2 0.000000 0.026082 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019461 0.00000