HEADER HYDROLASE 15-APR-03 1UCL TITLE MUTANTS OF RNASE SA COMPND MOL_ID: 1; COMPND 2 MOLECULE: GUANYL-SPECIFIC RIBONUCLEASE SA; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RNASE SA; COMPND 5 EC: 3.1.27.3; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES AUREOFACIENS; SOURCE 3 ORGANISM_TAXID: 1894; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PEH100 KEYWDS PROTEIN STABILITY, HYDROGEN BOND, BURIAL POLAR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.TAKANO,J.M.SCHOLTZ,J.C.SACCHETTINI,C.N.PACE REVDAT 4 27-DEC-23 1UCL 1 REMARK REVDAT 3 10-NOV-21 1UCL 1 REMARK SEQADV REVDAT 2 24-FEB-09 1UCL 1 VERSN REVDAT 1 09-SEP-03 1UCL 0 JRNL AUTH K.TAKANO,J.M.SCHOLTZ,J.C.SACCHETTINI,C.N.PACE JRNL TITL THE CONTRIBUTION OF POLAR GROUP BURIAL TO PROTEIN STABILITY JRNL TITL 2 IS STRONGLY CONTEXT-DEPENDENT JRNL REF J.BIOL.CHEM. V. 278 31790 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12799387 JRNL DOI 10.1074/JBC.M304177200 REMARK 2 REMARK 2 RESOLUTION. 1.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 295717.640 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 17252 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) : 0.176 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1708 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 1.82 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.93 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2299 REMARK 3 BIN R VALUE (WORKING SET) : 0.2160 REMARK 3 BIN FREE R VALUE : 0.2490 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 225 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1492 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 274 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 5.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.11000 REMARK 3 B22 (A**2) : 1.85000 REMARK 3 B33 (A**2) : 0.25000 REMARK 3 B12 (A**2) : 0.00000 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) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.10 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) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.690 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) : 1.300 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.970 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.630 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.030 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.44 REMARK 3 BSOL : 63.62 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UCL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-APR-03. REMARK 100 THE DEPOSITION ID IS D_1000005678. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 8.4 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17301 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM SULFATE, 0.1M HEPES-NA REMARK 280 PH 7.5, 2%(V/V) PEG400, PH 8.4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 32.13050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 19.17200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.82900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 19.17200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.13050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.82900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RGG RELATED DB: PDB REMARK 900 WILD-TYPE RNASE SA REMARK 900 RELATED ID: 1UCI RELATED DB: PDB REMARK 900 RNASE SA, V2T MUTANT REMARK 900 RELATED ID: 1UCJ RELATED DB: PDB REMARK 900 RNASE SA, V36T MUTANT REMARK 900 RELATED ID: 1UCK RELATED DB: PDB REMARK 900 RNASE SA, V43T MUTANT DBREF 1UCL A 1 96 UNP P05798 RNSA_STRAU 1 96 DBREF 1UCL B 1 96 UNP P05798 RNSA_STRAU 1 96 SEQADV 1UCL THR A 57 UNP P05798 VAL 57 ENGINEERED MUTATION SEQADV 1UCL THR B 57 UNP P05798 VAL 57 ENGINEERED MUTATION SEQRES 1 A 96 ASP VAL SER GLY THR VAL CYS LEU SER ALA LEU PRO PRO SEQRES 2 A 96 GLU ALA THR ASP THR LEU ASN LEU ILE ALA SER ASP GLY SEQRES 3 A 96 PRO PHE PRO TYR SER GLN ASP GLY VAL VAL PHE GLN ASN SEQRES 4 A 96 ARG GLU SER VAL LEU PRO THR GLN SER TYR GLY TYR TYR SEQRES 5 A 96 HIS GLU TYR THR THR ILE THR PRO GLY ALA ARG THR ARG SEQRES 6 A 96 GLY THR ARG ARG ILE ILE THR GLY GLU ALA THR GLN GLU SEQRES 7 A 96 ASP TYR TYR THR GLY ASP HIS TYR ALA THR PHE SER LEU SEQRES 8 A 96 ILE ASP GLN THR CYS SEQRES 1 B 96 ASP VAL SER GLY THR VAL CYS LEU SER ALA LEU PRO PRO SEQRES 2 B 96 GLU ALA THR ASP THR LEU ASN LEU ILE ALA SER ASP GLY SEQRES 3 B 96 PRO PHE PRO TYR SER GLN ASP GLY VAL VAL PHE GLN ASN SEQRES 4 B 96 ARG GLU SER VAL LEU PRO THR GLN SER TYR GLY TYR TYR SEQRES 5 B 96 HIS GLU TYR THR THR ILE THR PRO GLY ALA ARG THR ARG SEQRES 6 B 96 GLY THR ARG ARG ILE ILE THR GLY GLU ALA THR GLN GLU SEQRES 7 B 96 ASP TYR TYR THR GLY ASP HIS TYR ALA THR PHE SER LEU SEQRES 8 B 96 ILE ASP GLN THR CYS HET SO4 A1001 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *274(H2 O) HELIX 1 1 SER A 9 LEU A 11 5 3 HELIX 2 2 PRO A 12 SER A 24 1 13 HELIX 3 3 SER B 9 LEU B 11 5 3 HELIX 4 4 PRO B 12 ASP B 25 1 14 SHEET 1 A 5 THR A 5 CYS A 7 0 SHEET 2 A 5 SER A 90 ASP A 93 1 O ASP A 93 N VAL A 6 SHEET 3 A 5 ASP A 79 THR A 82 -1 N TYR A 81 O SER A 90 SHEET 4 A 5 ARG A 69 GLY A 73 -1 N ILE A 71 O TYR A 80 SHEET 5 A 5 TYR A 52 THR A 56 -1 N HIS A 53 O THR A 72 SHEET 1 B 6 THR B 5 CYS B 7 0 SHEET 2 B 6 SER B 90 ASP B 93 1 O ASP B 93 N VAL B 6 SHEET 3 B 6 ASP B 79 THR B 82 -1 N TYR B 81 O SER B 90 SHEET 4 B 6 ARG B 69 THR B 72 -1 N ILE B 71 O TYR B 80 SHEET 5 B 6 HIS B 53 THR B 56 -1 N HIS B 53 O THR B 72 SHEET 6 B 6 VAL B 35 VAL B 36 -1 N VAL B 35 O GLU B 54 SSBOND 1 CYS A 7 CYS A 96 1555 1555 2.03 SSBOND 2 CYS B 7 CYS B 96 1555 1555 2.03 CISPEP 1 GLY A 26 PRO A 27 0 0.02 CISPEP 2 GLY B 26 PRO B 27 0 -0.07 SITE 1 AC1 7 ALA A 62 ARG A 63 THR A 64 HOH A1053 SITE 2 AC1 7 HOH A1091 PRO B 12 ARG B 68 CRYST1 64.261 77.658 38.344 90.00 90.00 90.00 P 21 21 21 8 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 0.015562 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012877 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026080 0.00000