HEADER HYDROLASE(ENDORIBONUCLEASE) 23-JUN-93 1RDA TITLE CRYSTAL STRUCTURES OF RIBONUCLEASE HI ACTIVE SITE MUTANTS FROM TITLE 2 ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.26.4; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562 KEYWDS HYDROLASE(ENDORIBONUCLEASE) EXPDTA X-RAY DIFFRACTION AUTHOR K.KATAYANAGI,K.MORIKAWA REVDAT 4 14-FEB-24 1RDA 1 SEQADV REVDAT 3 29-NOV-17 1RDA 1 HELIX REVDAT 2 24-FEB-09 1RDA 1 VERSN REVDAT 1 31-OCT-93 1RDA 0 JRNL AUTH K.KATAYANAGI,M.ISHIKAWA,M.OKUMURA,M.ARIYOSHI,S.KANAYA, JRNL AUTH 2 Y.KAWANO,M.SUZUKI,I.TANAKA,K.MORIKAWA JRNL TITL CRYSTAL STRUCTURES OF RIBONUCLEASE HI ACTIVE SITE MUTANTS JRNL TITL 2 FROM ESCHERICHIA COLI. JRNL REF J.BIOL.CHEM. V. 268 22092 1993 JRNL REFN ISSN 0021-9258 JRNL PMID 8408067 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.KATAYANAGI,M.MIYAGAWA,M.MATSUSHIMA,M.ISHIKAWA,S.KANAYA, REMARK 1 AUTH 2 H.NAKAMURA,M.IKEHARA,T.MATSUZAKI,K.MORIKAWA REMARK 1 TITL STRUCTURAL DETAILS OF RIBONUCLEASE H FROM ESCHERICHIA COLI REMARK 1 TITL 2 AS REFINED TO AN ATOMIC RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 223 1029 1992 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH K.KATAYANAGI,M.MIYAGAWA,M.MATSUSHIMA,M.ISHIKAWA,S.KANAYA, REMARK 1 AUTH 2 M.IKEHARA,T.MATSUZAKI,K.MORIKAWA REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF RIBONUCLEASE H FROM E. COLI REMARK 1 REF NATURE V. 347 306 1990 REMARK 1 REFN ISSN 0028-0836 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 6250 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) : 0.189 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 : 1238 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 100 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) : 0.015 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.035 ; 0.030 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.049 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.013 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.165 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.188 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.224 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : 0.243 ; 0.300 REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 2.500 ; 3.000 REMARK 3 STAGGERED (DEGREES) : 21.200; 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) : 1.073 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.747 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.826 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.765 ; 2.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1RDA 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_1000176028. 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 22.08500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 17.63500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.61500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 17.63500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.08500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.61500 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 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 O ASP A 94 CD ARG A 132 3555 2.17 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 27 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 TYR A 28 CA - CB - CG ANGL. DEV. = 17.6 DEGREES REMARK 500 ARG A 41 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 GLU A 64 CA - CB - CG ANGL. DEV. = 14.6 DEGREES REMARK 500 ILE A 66 O - C - N ANGL. DEV. = 9.6 DEGREES REMARK 500 LEU A 67 CB - CA - C ANGL. DEV. = 11.4 DEGREES REMARK 500 ASP A 70 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 75 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 106 NE - CZ - NH1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 106 NE - CZ - NH2 ANGL. DEV. = -7.5 DEGREES REMARK 500 GLU A 129 OE1 - CD - OE2 ANGL. DEV. = -7.3 DEGREES REMARK 500 ARG A 132 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 138 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 THR A 149 CA - CB - CG2 ANGL. DEV. = 9.8 DEGREES REMARK 500 GLU A 154 C - N - CA ANGL. DEV. = 16.4 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 ARG A 29 -116.20 73.67 REMARK 500 SER A 36 142.61 -174.96 REMARK 500 THR A 42 -162.17 -167.95 REMARK 500 ALA A 125 45.09 -143.14 REMARK 500 THR A 149 -70.87 -50.96 REMARK 500 GLU A 154 -126.17 -68.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 132 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1RDA A 1 155 UNP P0A7Y4 RNH_ECOLI 1 155 SEQADV 1RDA ASN A 10 UNP P0A7Y4 ASP 10 CONFLICT SEQRES 1 A 155 MET LEU LYS GLN VAL GLU ILE PHE THR ASN GLY SER CYS SEQRES 2 A 155 LEU GLY ASN PRO GLY PRO GLY GLY TYR GLY ALA ILE LEU SEQRES 3 A 155 ARG TYR ARG GLY ARG GLU LYS THR PHE SER ALA GLY TYR SEQRES 4 A 155 THR ARG THR THR ASN ASN ARG MET GLU LEU MET ALA ALA SEQRES 5 A 155 ILE VAL ALA LEU GLU ALA LEU LYS GLU HIS CYS GLU VAL SEQRES 6 A 155 ILE LEU SER THR ASP SER GLN TYR VAL ARG GLN GLY ILE SEQRES 7 A 155 THR GLN TRP ILE HIS ASN TRP LYS LYS ARG GLY TRP LYS SEQRES 8 A 155 THR ALA ASP LYS LYS PRO VAL LYS ASN VAL ASP LEU TRP SEQRES 9 A 155 GLN ARG LEU ASP ALA ALA LEU GLY GLN HIS GLN ILE LYS SEQRES 10 A 155 TRP GLU TRP VAL LYS GLY HIS ALA GLY HIS PRO GLU ASN SEQRES 11 A 155 GLU ARG CYS ASP GLU LEU ALA ARG ALA ALA ALA MET ASN SEQRES 12 A 155 PRO THR LEU GLU ASP THR GLY TYR GLN VAL GLU VAL FORMUL 2 HOH *100(H2 O) HELIX 1 A1 THR A 43 ALA A 58 1 16 HELIX 2 B1 ALA A 55 LEU A 59 5 5 HELIX 3 A2 SER A 71 THR A 79 1 9 HELIX 4 A3 TRP A 81 GLY A 89 1 9 HELIX 5 A4 ASN A 100 GLY A 112 1 13 HELIX 6 B2 ALA A 110 HIS A 114 5 5 HELIX 7 A5 HIS A 127 ALA A 141 1 15 HELIX 8 B3 ARG A 138 ASN A 143 5 6 SHEET 1 S1 5 ARG A 31 TYR A 39 0 SHEET 2 S1 5 PRO A 19 TYR A 28 -1 O TYR A 28 N ARG A 31 SHEET 3 S1 5 VAL A 5 LEU A 14 -1 N GLU A 6 O ARG A 27 SHEET 4 S1 5 CYS A 63 THR A 69 1 O GLU A 64 N VAL A 5 SHEET 5 S1 5 GLN A 115 VAL A 121 1 N GLN A 115 O CYS A 63 CISPEP 1 ASN A 16 PRO A 17 0 1.30 CRYST1 44.170 87.230 35.270 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 0.022640 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011464 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028353 0.00000