HEADER HYDROLASE 07-AUG-98 1BOX TITLE N39S MUTANT OF RNASE SA FROM STREPTOMYCES AUREOFACIENS COMPND MOL_ID: 1; COMPND 2 MOLECULE: GUANYL-SPECIFIC RIBONUCLEASE SA; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.27.3; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES AUREOFACIENS; SOURCE 3 ORGANISM_TAXID: 1894; SOURCE 4 STRAIN: BMK; SOURCE 5 GENE: U39467; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: NOVABLUE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PEH100; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PUC19 KEYWDS HYDROLASE, RIBONUCLEASE, MUTANT EXPDTA X-RAY DIFFRACTION AUTHOR E.J.HEBERT,A.GILETTO,J.SEVCIK,L.URBANIKOVA,K.S.WILSON,Z.DAUTER, AUTHOR 2 C.N.PACE REVDAT 7 20-NOV-24 1BOX 1 REMARK REVDAT 6 09-AUG-23 1BOX 1 REMARK REVDAT 5 24-FEB-09 1BOX 1 VERSN REVDAT 4 21-MAR-01 1BOX 1 COMPND SOURCE REMARK REVDAT 3 12-JAN-00 1BOX 1 HEADER TITLE REVDAT 2 29-DEC-99 1BOX 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 29-DEC-99 1BOX 0 JRNL AUTH E.J.HEBERT,A.GILETTO,J.SEVCIK,L.URBANIKOVA,K.S.WILSON, JRNL AUTH 2 Z.DAUTER,C.N.PACE JRNL TITL CONTRIBUTION OF A CONSERVED ASPARAGINE TO THE CONFORMATIONAL JRNL TITL 2 STABILITY OF RIBONUCLEASES SA, BA, AND T1. JRNL REF BIOCHEMISTRY V. 37 16192 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9819211 JRNL DOI 10.1021/BI9815243 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 12724 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 + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.000 REMARK 3 FREE R VALUE TEST SET COUNT : 895 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 728 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 95 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.20 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.084 REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.023 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.040 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.042 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.035 ; 0.040 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.220 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.171 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.285 ; 0.300 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) : 0.000 ; 15.000 REMARK 3 PLANAR (DEGREES) : 6.100 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 16.600; 15.000 REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.885 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.967 ; 5.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.426 ; 6.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.930 ; 8.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BOX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUN-99. REMARK 100 THE DEPOSITION ID IS D_1000008014. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-97 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 8.0 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 : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MSC "LONG" MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12724 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 14.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 57.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.47100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1RGG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP VAPOUR EQUILIBRATION REMARK 280 DROP: 10 MG/ML OF PROTEIN 0.1 M TRIS-HCL BUFFER AT PH 8.0 12,5 % REMARK 280 PEG 6000 RESERVOIR: 25 % PEG 6000 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 20.74500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.82500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.32500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 25.82500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.74500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.32500 REMARK 290 SMTRY3 4 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 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 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 ASP A 1 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 40 CD NE CZ NH1 NH2 REMARK 470 GLU A 41 CD OE1 OE2 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 OH TYR A 49 O HOH A 136 2.02 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 ASP A 25 CA - CB - CG ANGL. DEV. = -15.5 DEGREES REMARK 500 TYR A 30 CB - CG - CD1 ANGL. DEV. = -3.9 DEGREES REMARK 500 TYR A 49 CB - CG - CD2 ANGL. DEV. = -8.8 DEGREES REMARK 500 TYR A 49 CB - CG - CD1 ANGL. DEV. = 9.8 DEGREES REMARK 500 TYR A 52 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES REMARK 500 TYR A 52 CG - CD2 - CE2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 63 NH1 - CZ - NH2 ANGL. DEV. = -8.9 DEGREES REMARK 500 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 17.5 DEGREES REMARK 500 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -8.7 DEGREES REMARK 500 ARG A 65 CG - CD - NE ANGL. DEV. = 14.9 DEGREES REMARK 500 ARG A 65 CD - NE - CZ ANGL. DEV. = 51.7 DEGREES REMARK 500 ARG A 65 NE - CZ - NH1 ANGL. DEV. = 18.9 DEGREES REMARK 500 ARG A 65 NE - CZ - NH2 ANGL. DEV. = -13.3 DEGREES REMARK 500 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 68 NE - CZ - NH2 ANGL. DEV. = -10.4 DEGREES REMARK 500 ARG A 69 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 69 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 GLU A 78 OE1 - CD - OE2 ANGL. DEV. = 7.6 DEGREES REMARK 500 ASP A 84 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 TYR A 86 CB - CG - CD1 ANGL. DEV. = 4.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 1BOX A 1 96 UNP P05798 RNSA_STRAU 1 96 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 SER 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 VAL 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 FORMUL 2 HOH *95(H2 O) HELIX 1 1 LEU A 8 ALA A 10 5 3 HELIX 2 2 PRO A 13 ALA A 23 1 11 SHEET 1 A 2 THR A 5 CYS A 7 0 SHEET 2 A 2 LEU A 91 ASP A 93 1 N LEU A 91 O VAL A 6 SHEET 1 B 3 HIS A 53 THR A 56 0 SHEET 2 B 3 ARG A 69 THR A 72 -1 N THR A 72 O HIS A 53 SHEET 3 B 3 ASP A 79 THR A 82 -1 N THR A 82 O ARG A 69 SSBOND 1 CYS A 7 CYS A 96 1555 1555 2.00 CISPEP 1 GLY A 26 PRO A 27 0 5.61 CRYST1 41.490 46.650 51.650 90.00 90.00 90.00 P 21 21 21 4 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 0.024102 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021436 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019361 0.00000