HEADER HYDROLASE(PHOSPHORIC DIESTER,RNA) 11-JUL-94 2RLN TITLE THERMODYNAMIC AND STRUCTURAL CONSEQUENCES OF CHANGING A SULPHUR ATOM TITLE 2 TO A METHYLENE GROUP IN THE M13NLE MUTATION IN RIBONUCLEASE S COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE; COMPND 3 CHAIN: S; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RIBONUCLEASE S (S-PROTEIN); COMPND 7 CHAIN: E; COMPND 8 EC: 3.1.27.5; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 MOL_ID: 2; SOURCE 3 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 4 ORGANISM_COMMON: CATTLE; SOURCE 5 ORGANISM_TAXID: 9913; SOURCE 6 ORGAN: PANCREAS KEYWDS HYDROLASE(PHOSPHORIC DIESTER, RNA) EXPDTA X-RAY DIFFRACTION AUTHOR G.RATNAPARKHI,R.VARADARAJAN REVDAT 5 09-OCT-24 2RLN 1 REMARK LINK REVDAT 4 29-NOV-17 2RLN 1 HELIX REVDAT 3 24-FEB-09 2RLN 1 VERSN REVDAT 2 01-APR-03 2RLN 1 JRNL REVDAT 1 01-NOV-94 2RLN 0 JRNL AUTH J.THOMSON,G.S.RATNAPARKHI,R.VARADARAJAN,J.M.STURTEVANT, JRNL AUTH 2 F.M.RICHARDS JRNL TITL THERMODYNAMIC AND STRUCTURAL CONSEQUENCES OF CHANGING A JRNL TITL 2 SULFUR ATOM TO A METHYLENE GROUP IN THE M13NLE MUTATION IN JRNL TITL 3 RIBONUCLEASE-S. JRNL REF BIOCHEMISTRY V. 33 8587 1994 JRNL REFN ISSN 0006-2960 JRNL PMID 8031793 JRNL DOI 10.1021/BI00194A025 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.VARADARAJAN,F.M.RICHARDS REMARK 1 TITL CRYSTALLOGRAPHIC STRUCTURES OF RIBONUCLEASE S VARIANTS WITH REMARK 1 TITL 2 NONPOLAR SUBSTITUTIONS AT POSITION 13: PACKING AND CAVITIES REMARK 1 REF BIOCHEMISTRY V. 31 12315 1992 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH E.E.KIM,R.VARADARAJAN,H.W.WYCKOFF,F.M.RICHARDS REMARK 1 TITL REFINEMENT OF THE CRYSTAL STRUCTURE OF RIBONUCLEASE S. REMARK 1 TITL 2 COMPARISON WITH AND BETWEEN THE VARIOUS RIBONUCLEASE A REMARK 1 TITL 3 STRUCTURES REMARK 1 REF BIOCHEMISTRY V. 31 12304 1992 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 8851 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 SET) : 0.174 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 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 923 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 54 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 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RLN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178565. 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 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 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 (%): 40.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 32.45000 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 64.90000 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 64.90000 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 32.45000 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: 1720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: S, E 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 400 REMARK 400 COMPOUND REMARK 400 THIS RNASE S (M13NLE) MUTANT IS ONE OF A SERIES OF REMARK 400 MUTANTS OF RNASE S AT POSITION 13. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER E 16 REMARK 465 THR E 17 REMARK 465 SER E 18 REMARK 465 ALA E 19 REMARK 465 ALA E 20 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 SER E 22 -144.99 -124.98 REMARK 500 HIS E 48 61.77 -101.99 REMARK 500 GLN E 60 -135.36 -98.63 REMARK 500 ALA E 122 -178.87 -179.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ACT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 E 125 DBREF 2RLN E 16 124 UNP P00656 RNP_BOVIN 42 150 DBREF 2RLN S 1 16 PDB 2RLN 2RLN 1 16 SEQRES 1 S 16 LYS GLU THR ALA ALA ALA LYS PHE GLU ARG GLN HIS NLE SEQRES 2 S 16 ASP SER NH2 SEQRES 1 E 109 SER THR SER ALA ALA SER SER SER ASN TYR CYS ASN GLN SEQRES 2 E 109 MET MET LYS SER ARG ASN LEU THR LYS ASP ARG CYS LYS SEQRES 3 E 109 PRO VAL ASN THR PHE VAL HIS GLU SER LEU ALA ASP VAL SEQRES 4 E 109 GLN ALA VAL CYS SER GLN LYS ASN VAL ALA CYS LYS ASN SEQRES 5 E 109 GLY GLN THR ASN CYS TYR GLN SER TYR SER THR MET SER SEQRES 6 E 109 ILE THR ASP CYS ARG GLU THR GLY SER SER LYS TYR PRO SEQRES 7 E 109 ASN CYS ALA TYR LYS THR THR GLN ALA ASN LYS HIS ILE SEQRES 8 E 109 ILE VAL ALA CYS GLU GLY ASN PRO TYR VAL PRO VAL HIS SEQRES 9 E 109 PHE ASP ALA SER VAL MODRES 2RLN NLE S 13 LEU NORLEUCINE HET NLE S 13 8 HET NH2 S 16 1 HET SO4 E 125 5 HETNAM NLE NORLEUCINE HETNAM NH2 AMINO GROUP HETNAM SO4 SULFATE ION FORMUL 1 NLE C6 H13 N O2 FORMUL 1 NH2 H2 N FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *54(H2 O) HELIX 1 H1 THR S 3 NLE S 13 1 11 HELIX 2 H2 ASN E 24 ASN E 34 134 IN 3/10 CONFORMATION 11 HELIX 3 H3 SER E 50 GLN E 60 156 - 60 IN 3/10 CONFORMATION 11 SHEET 1 S1 3 LYS E 41 HIS E 48 0 SHEET 2 S1 3 MET E 79 THR E 87 -1 SHEET 3 S1 3 ALA E 96 LYS E 104 -1 SHEET 1 S2 4 LYS E 61 ALA E 64 0 SHEET 2 S2 4 ASN E 71 SER E 75 -1 SHEET 3 S2 4 HIS E 105 GLU E 111 -1 SHEET 4 S2 4 VAL E 116 VAL E 124 -1 SSBOND 1 CYS E 26 CYS E 84 1555 1555 2.03 SSBOND 2 CYS E 40 CYS E 95 1555 1555 2.03 SSBOND 3 CYS E 58 CYS E 110 1555 1555 2.03 SSBOND 4 CYS E 65 CYS E 72 1555 1555 2.04 LINK C HIS S 12 N NLE S 13 1555 1555 1.32 LINK C NLE S 13 N ASP S 14 1555 1555 1.33 LINK C SER S 15 N NH2 S 16 1555 1555 1.32 CISPEP 1 TYR E 92 PRO E 93 0 -0.01 CISPEP 2 ASN E 113 PRO E 114 0 0.21 SITE 1 ACT 9 HIS S 12 LYS E 41 VAL E 43 ASN E 44 SITE 2 ACT 9 THR E 45 HIS E 119 PHE E 120 ASP E 121 SITE 3 ACT 9 SER E 123 SITE 1 AC1 4 HIS E 119 PHE E 120 HOH E 215 HIS S 12 CRYST1 44.740 44.740 97.350 90.00 90.00 120.00 P 31 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 0.022351 0.012905 0.000000 0.00000 SCALE2 0.000000 0.025809 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010272 0.00000