HEADER HYDROLASE/DNA 12-JUN-02 1M07 TITLE RESIDUES INVOLVED IN THE CATALYSIS AND BASE SPECIFICITY OF CYTOTOXIC TITLE 2 RIBONUCLEASE FROM BULLFROG (RANA CATESBEIANA) CAVEAT 1M07 CHIRALITY ERROR, RESIDUE 4 CHAIN C,D. SEE REMARK 400. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*CP*GP*A)-3'; COMPND 3 CHAIN: C, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RIBONUCLEASE; COMPND 7 CHAIN: A, B; COMPND 8 SYNONYM: RC-RNASE, SIALIC ACID-BINDING LECTIN, SBL-C; COMPND 9 EC: 3.1.27.5 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: RANA CATESBEIANA; SOURCE 5 ORGANISM_COMMON: BULLFROG; SOURCE 6 ORGANISM_TAXID: 8400; SOURCE 7 ORGAN: OOCYTES KEYWDS RC-RNASE-D(ACGA), RIBONUCLEASE, BULLFROG, CYTOTOXICITY, HYDROLASE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.-J.LEU,S.-S.CHERN,S.-C.WANG,Y.-Y.HSIAO,I.AMIRASLANOV,Y.-C.LIAW,Y.- AUTHOR 2 D.LIAO REVDAT 5 25-DEC-19 1M07 1 SEQADV SEQRES LINK REVDAT 4 19-NOV-14 1M07 1 REMARK VERSN REVDAT 3 24-FEB-09 1M07 1 VERSN REVDAT 2 15-MAR-05 1M07 1 JRNL REVDAT 1 21-JAN-03 1M07 0 JRNL AUTH Y.-J.LEU,S.-S.CHERN,S.-C.WANG,Y.-Y.HSIAO,I.AMIRASLANOV, JRNL AUTH 2 Y.-C.LIAW,Y.-D.LIAO JRNL TITL RESIDUES INVOLVED IN THE CATALYSIS, BASE SPECIFICITY, AND JRNL TITL 2 CYTOTOXICITY OF RIBONUCLEASE FROM RANA CATESBEIANA BASED JRNL TITL 3 UPON MUTAGENESIS AND X-RAY CRYSTALLOGRAPHY JRNL REF J.BIOL.CHEM. V. 278 7300 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12499382 JRNL DOI 10.1074/JBC.M206701200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.-J.LEU,S.-S.CHERN,S.-C.WANG,Y.-Y.HSIAO,I.R.AMIRASLANOV, REMARK 1 AUTH 2 Y.-C.LIAW,Y.-D.LIAO REMARK 1 TITL THE CRYSTAL STRUCTURE OF A CYTOTOXIC RIBONUCLEASE FROM THE REMARK 1 TITL 2 OOCYTE OF RANA CATESBEIANA REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 1 REFERENCE 2 REMARK 1 AUTH C.CHEN,K.HOM,R.F.HUANG,P.J.CHOU,Y.D.LIAO,T.HUANG REMARK 1 TITL THE SECONDARY STRUCTURE OF A PYRIMIDINE-GUANINE REMARK 1 TITL 2 SEQUENCE-SPECIFIC RIBONUCLEASE POSSESSING CYTOTOXIC ACTIVITY REMARK 1 TITL 3 FROM THE OOCYTE OF RANA CATESBEIANA REMARK 1 REF J.BIOMOL.NMR V. 8 331 1996 REMARK 1 REFN ISSN 0925-2738 REMARK 1 REFERENCE 3 REMARK 1 AUTH C.F.CHANG,C.CHEN,Y.C.CHEN,K.HOM,R.F.HUANG,T.H.HUANG REMARK 1 TITL THE SOLUTION STRUCTURE OF A CYTOTOXIC RIBONUCLEASE FROM THE REMARK 1 TITL 2 OOCYTE OF RANA CATESBEIANA (BULLFROG) REMARK 1 REF J.MOL.BIOL. V. 283 231 1998 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.1998.2082 REMARK 1 REFERENCE 4 REMARK 1 AUTH H.C.HUANG,S.C.WANG,Y.J.LEU,S.C.LU,Y.D.LIAO REMARK 1 TITL THE RANA CATESBEIANA RCR GENE ENCODING A CYTOTOXIC REMARK 1 TITL 2 RIBONUCLEASE : TISSUE DISTRIBUTION, CLONING, PURIFICATION, REMARK 1 TITL 3 CYTOTOXICITY, AND ACTIVE RESIDUES FOR RNASE ACTIVITY REMARK 1 REF J.BIOL.CHEM. V. 273 6395 1998 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.273.11.6395 REMARK 1 REFERENCE 5 REMARK 1 AUTH Y.D.LIAO,H.C.HUANG,Y.J.LEU,C.W.WEI,P.C.TANG,S.C.WANG REMARK 1 TITL PURIFICATION AND CLONING OF CYTOTOXIC RIBONUCLEASE FROM RANA REMARK 1 TITL 2 CATESBEIANA (BULLFROG) REMARK 1 REF NUCLEIC ACIDS RES. V. 28 4097 2000 REMARK 1 REFN ISSN 0305-1048 REMARK 1 DOI 10.1093/NAR/28.21.4097 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.0 REMARK 3 NUMBER OF REFLECTIONS : 17518 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) : 0.189 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1369 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1880 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE : 0.2714 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 163 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1736 REMARK 3 NUCLEIC ACID ATOMS : 160 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 323 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 15.03000 REMARK 3 B22 (A**2) : -7.76000 REMARK 3 B33 (A**2) : -7.27000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.85000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.20 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) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 BOND ANGLES (DEGREES) : 2.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 4.300 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.270 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.840 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.090 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.140 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : CNS BULK SOLVENT MODEL USED REMARK 3 KSOL : 0.44 REMARK 3 BSOL : 68.85 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : PCA.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : PCA.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1M07 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUL-02. REMARK 100 THE DEPOSITION ID IS D_1000016434. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-00 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.05 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : KOHZU DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ADSC REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18075 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 19.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 200 DATA REDUNDANCY : 6.810 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : 0.07300 REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.18000 REMARK 200 R SYM FOR SHELL (I) : 0.18000 REMARK 200 FOR SHELL : 6.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1KM8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M POTASSIUM SODIUM TARTRATE REMARK 280 TETRAHYDRATE, 24 % PEG 8000, 0.05 M SODIUM CITRATE, PH 5.6, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 26.78300 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, 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 400 REMARK 400 COMPOUND REMARK 400 THE ATOMS (C6, N9, C4, C4', C5', C2', N7, C8, N1) OF REMARK 400 RESIDUE 4 CHAIN C,D WAS FIXED IN THE REFINEMENT. 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 NH1 ARG A 36 O HOH A 774 2.08 REMARK 500 O HOH A 970 O HOH A 1097 2.09 REMARK 500 O HOH B 1145 O HOH B 1396 2.11 REMARK 500 O HOH C 1081 O HOH C 1360 2.12 REMARK 500 O HOH A 1036 O HOH A 1164 2.13 REMARK 500 REMARK 500 REMARK: NULL 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 HOH A 721 O HOH B 918 2656 2.16 REMARK 500 O HOH C 769 O HOH A 704 2646 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DA C 4 C5' DA C 4 C4' 0.082 REMARK 500 DA C 4 C4' DA C 4 C3' 0.120 REMARK 500 DA C 4 C4' DA C 4 C3' 0.152 REMARK 500 DA C 4 O4' DA C 4 C1' 0.085 REMARK 500 DA C 4 O4' DA C 4 C4' 0.112 REMARK 500 DA C 4 O4' DA C 4 C4' 0.139 REMARK 500 DA C 4 C1' DA C 4 N9 0.103 REMARK 500 DA C 4 C2 DA C 4 N3 0.068 REMARK 500 DA C 4 C6 DA C 4 N6 0.158 REMARK 500 DA D 4 C5' DA D 4 C4' 0.085 REMARK 500 DA D 4 C4' DA D 4 C3' 0.129 REMARK 500 DA D 4 C4' DA D 4 C3' 0.145 REMARK 500 DA D 4 O4' DA D 4 C1' 0.158 REMARK 500 DA D 4 O4' DA D 4 C4' 0.125 REMARK 500 DA D 4 O4' DA D 4 C4' 0.180 REMARK 500 DA D 4 C1' DA D 4 N9 0.101 REMARK 500 DA D 4 C1' DA D 4 N9 0.179 REMARK 500 DA D 4 C2 DA D 4 N3 0.069 REMARK 500 DA D 4 C6 DA D 4 N6 0.150 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 DA C 4 O4' - C4' - C3' ANGL. DEV. = -11.3 DEGREES REMARK 500 DA C 4 O4' - C4' - C3' ANGL. DEV. = -11.0 DEGREES REMARK 500 DA C 4 C5' - C4' - C3' ANGL. DEV. = 7.6 DEGREES REMARK 500 DA C 4 C4' - C3' - C2' ANGL. DEV. = 6.0 DEGREES REMARK 500 DA C 4 N9 - C1' - C2' ANGL. DEV. = 16.3 DEGREES REMARK 500 DA C 4 N9 - C1' - C2' ANGL. DEV. = 24.4 DEGREES REMARK 500 DA C 4 O4' - C1' - N9 ANGL. DEV. = 7.8 DEGREES REMARK 500 DA C 4 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 DA C 4 C2 - N3 - C4 ANGL. DEV. = -4.8 DEGREES REMARK 500 DA C 4 C8 - N9 - C1' ANGL. DEV. = 37.5 DEGREES REMARK 500 DA C 4 C8 - N9 - C1' ANGL. DEV. = 26.0 DEGREES REMARK 500 DA C 4 C4 - N9 - C1' ANGL. DEV. = -38.3 DEGREES REMARK 500 DA C 4 C4 - N9 - C1' ANGL. DEV. = -26.9 DEGREES REMARK 500 DA D 4 O4' - C4' - C3' ANGL. DEV. = -12.7 DEGREES REMARK 500 DA D 4 O4' - C4' - C3' ANGL. DEV. = -7.3 DEGREES REMARK 500 DA D 4 C5' - C4' - C3' ANGL. DEV. = -12.6 DEGREES REMARK 500 DA D 4 C1' - O4' - C4' ANGL. DEV. = 6.6 DEGREES REMARK 500 DA D 4 C1' - O4' - C4' ANGL. DEV. = 6.1 DEGREES REMARK 500 DA D 4 C4' - C3' - C2' ANGL. DEV. = 6.0 DEGREES REMARK 500 DA D 4 C4' - C3' - C2' ANGL. DEV. = 6.8 DEGREES REMARK 500 DA D 4 C3' - C2' - C1' ANGL. DEV. = 7.8 DEGREES REMARK 500 DA D 4 O4' - C1' - C2' ANGL. DEV. = -10.8 DEGREES REMARK 500 DA D 4 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 DA D 4 N9 - C1' - C2' ANGL. DEV. = 21.1 DEGREES REMARK 500 DA D 4 O4' - C1' - N9 ANGL. DEV. = 17.7 DEGREES REMARK 500 DA D 4 C2 - N3 - C4 ANGL. DEV. = -4.2 DEGREES REMARK 500 DA D 4 C8 - N9 - C1' ANGL. DEV. = 35.4 DEGREES REMARK 500 DA D 4 C8 - N9 - C1' ANGL. DEV. = 24.1 DEGREES REMARK 500 DA D 4 C4 - N9 - C1' ANGL. DEV. = -35.1 DEGREES REMARK 500 DA D 4 C4 - N9 - C1' ANGL. DEV. = -33.9 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 ASN A 57 83.49 -163.51 REMARK 500 ASN B 57 91.85 -166.04 REMARK 500 MET B 58 148.98 -171.74 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 DA C 4 0.12 SIDE CHAIN REMARK 500 DA D 4 0.20 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 PCA A 1 15.46 REMARK 500 PCA B 1 16.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KM8 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH D(ACGA) DBREF 1M07 A 1 111 UNP P11916 RNASO_RANCA 1 111 DBREF 1M07 B 1 111 UNP P11916 RNASO_RANCA 1 111 DBREF 1M07 C 1 4 PDB 1M07 1M07 1 4 DBREF 1M07 D 1 4 PDB 1M07 1M07 1 4 SEQRES 1 C 4 DA DC DG DA SEQRES 1 D 4 DA DC DG DA SEQRES 1 A 111 PCA ASN TRP ALA THR PHE GLN GLN LYS HIS ILE ILE ASN SEQRES 2 A 111 THR PRO ILE ILE ASN CYS ASN THR ILE MET ASP ASN ASN SEQRES 3 A 111 ILE TYR ILE VAL GLY GLY GLN CYS LYS ARG VAL ASN THR SEQRES 4 A 111 PHE ILE ILE SER SER ALA THR THR VAL LYS ALA ILE CYS SEQRES 5 A 111 THR GLY VAL ILE ASN MET ASN VAL LEU SER THR THR ARG SEQRES 6 A 111 PHE GLN LEU ASN THR CYS THR ARG THR SER ILE THR PRO SEQRES 7 A 111 ARG PRO CYS PRO TYR SER SER ARG THR GLU THR ASN TYR SEQRES 8 A 111 ILE CYS VAL LYS CYS GLU ASN GLN TYR PRO VAL HIS PHE SEQRES 9 A 111 ALA GLY ILE GLY ARG CYS PRO SEQRES 1 B 111 PCA ASN TRP ALA THR PHE GLN GLN LYS HIS ILE ILE ASN SEQRES 2 B 111 THR PRO ILE ILE ASN CYS ASN THR ILE MET ASP ASN ASN SEQRES 3 B 111 ILE TYR ILE VAL GLY GLY GLN CYS LYS ARG VAL ASN THR SEQRES 4 B 111 PHE ILE ILE SER SER ALA THR THR VAL LYS ALA ILE CYS SEQRES 5 B 111 THR GLY VAL ILE ASN MET ASN VAL LEU SER THR THR ARG SEQRES 6 B 111 PHE GLN LEU ASN THR CYS THR ARG THR SER ILE THR PRO SEQRES 7 B 111 ARG PRO CYS PRO TYR SER SER ARG THR GLU THR ASN TYR SEQRES 8 B 111 ILE CYS VAL LYS CYS GLU ASN GLN TYR PRO VAL HIS PHE SEQRES 9 B 111 ALA GLY ILE GLY ARG CYS PRO MODRES 1M07 PCA A 1 GLN PYROGLUTAMIC ACID MODRES 1M07 PCA B 1 GLN PYROGLUTAMIC ACID HET PCA A 1 8 HET PCA B 1 8 HETNAM PCA PYROGLUTAMIC ACID FORMUL 3 PCA 2(C5 H7 N O3) FORMUL 5 HOH *323(H2 O) HELIX 1 1 ASN A 2 HIS A 10 1 9 HELIX 2 2 ASN A 18 MET A 23 1 6 HELIX 3 3 ASN A 25 ILE A 27 5 3 HELIX 4 4 SER A 44 ALA A 50 1 7 HELIX 5 5 ILE A 51 THR A 53 5 3 HELIX 6 6 ASN B 2 HIS B 10 1 9 HELIX 7 7 ASN B 18 MET B 23 1 6 HELIX 8 8 ASN B 25 ILE B 27 5 3 HELIX 9 9 SER B 44 ALA B 50 1 7 HELIX 10 10 ILE B 51 THR B 53 5 3 SHEET 1 A 4 ILE A 11 ILE A 12 0 SHEET 2 A 4 VAL A 37 ILE A 42 1 O ILE A 41 N ILE A 12 SHEET 3 A 4 PHE A 66 ARG A 73 -1 O ASN A 69 N PHE A 40 SHEET 4 A 4 TYR A 83 ASN A 90 -1 O ARG A 86 N THR A 70 SHEET 1 B 2 ILE A 29 VAL A 30 0 SHEET 2 B 2 GLN A 33 CYS A 34 -1 O GLN A 33 N VAL A 30 SHEET 1 C 3 ASN A 57 LEU A 61 0 SHEET 2 C 3 ILE A 92 GLU A 97 -1 O VAL A 94 N VAL A 60 SHEET 3 C 3 TYR A 100 ILE A 107 -1 O GLY A 106 N CYS A 93 SHEET 1 D 4 ILE B 11 ILE B 12 0 SHEET 2 D 4 VAL B 37 ILE B 42 1 O ILE B 41 N ILE B 12 SHEET 3 D 4 PHE B 66 ARG B 73 -1 O CYS B 71 N ASN B 38 SHEET 4 D 4 TYR B 83 ASN B 90 -1 O ARG B 86 N THR B 70 SHEET 1 E 2 ILE B 29 VAL B 30 0 SHEET 2 E 2 GLN B 33 CYS B 34 -1 O GLN B 33 N VAL B 30 SHEET 1 F 3 ASN B 57 LEU B 61 0 SHEET 2 F 3 ILE B 92 GLU B 97 -1 O VAL B 94 N VAL B 60 SHEET 3 F 3 TYR B 100 ILE B 107 -1 O GLY B 106 N CYS B 93 SSBOND 1 CYS A 19 CYS A 71 1555 1555 2.02 SSBOND 2 CYS A 34 CYS A 81 1555 1555 2.03 SSBOND 3 CYS A 52 CYS A 96 1555 1555 2.03 SSBOND 4 CYS A 93 CYS A 110 1555 1555 2.05 SSBOND 5 CYS B 19 CYS B 71 1555 1555 2.04 SSBOND 6 CYS B 34 CYS B 81 1555 1555 2.03 SSBOND 7 CYS B 52 CYS B 96 1555 1555 2.03 SSBOND 8 CYS B 93 CYS B 110 1555 1555 2.04 LINK C PCA A 1 N ASN A 2 1555 1555 1.46 LINK C PCA B 1 N ASN B 2 1555 1555 1.47 CISPEP 1 ARG A 79 PRO A 80 0 -0.07 CISPEP 2 ARG B 79 PRO B 80 0 -0.11 CRYST1 28.629 53.566 72.203 90.00 98.31 90.00 P 1 21 1 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 0.034930 0.000000 0.005101 0.00000 SCALE2 0.000000 0.018669 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013997 0.00000