HEADER HYDROLASE 25-JUL-01 1IQQ TITLE CRYSTAL STRUCTURE OF JAPANESE PEAR S3-RNASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: S3-RNASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RIBONUCLEASE S-3; COMPND 5 EC: 3.1.27.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYRUS PYRIFOLIA; SOURCE 3 ORGANISM_TAXID: 3767 KEYWDS PYRUS PYRIFOLIA, JAPANESE PEAR, S-RNASE, SELF-INCOMPATIBILITY, T2 KEYWDS 2 FAMILY RIBONUCLEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.MATSUURA,H.SAKAI,S.NORIOKA REVDAT 8 30-OCT-24 1IQQ 1 REMARK REVDAT 7 27-DEC-23 1IQQ 1 HETSYN LINK REVDAT 6 29-JUL-20 1IQQ 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE ATOM REVDAT 5 13-JUL-11 1IQQ 1 VERSN REVDAT 4 24-FEB-09 1IQQ 1 VERSN REVDAT 3 14-JAN-03 1IQQ 1 REMARK REVDAT 2 19-DEC-01 1IQQ 1 JRNL REVDAT 1 07-NOV-01 1IQQ 0 JRNL AUTH T.MATSUURA,H.SAKAI,M.UNNO,K.IDA,M.SATO,F.SAKIYAMA,S.NORIOKA JRNL TITL CRYSTAL STRUCTURE AT 1.5-A RESOLUTION OF PYRUS PYRIFOLIA JRNL TITL 2 PISTIL RIBONUCLEASE RESPONSIBLE FOR GAMETOPHYTIC JRNL TITL 3 SELF-INCOMPATIBILITY. JRNL REF J.BIOL.CHEM. V. 276 45261 2001 JRNL REFN ISSN 0021-9258 JRNL PMID 11577107 JRNL DOI 10.1074/JBC.M107617200 REMARK 2 REMARK 2 RESOLUTION. 1.50 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 727947.440 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 33368 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) : 0.172 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1653 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5078 REMARK 3 BIN R VALUE (WORKING SET) : 0.1730 REMARK 3 BIN FREE R VALUE : 0.2040 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 257 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1643 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 59 REMARK 3 SOLVENT ATOMS : 266 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.98000 REMARK 3 B22 (A**2) : 1.78000 REMARK 3 B33 (A**2) : -0.80000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.31000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.14 REMARK 3 ESD FROM SIGMAA (A) : -0.0 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) : 0.17 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.05 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.022 REMARK 3 BOND ANGLES (DEGREES) : 2.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.540 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) : 1.920 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.520 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.260 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.280 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 48.41 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 : CARBOHYDRATE_REP.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 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IQQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUL-01. REMARK 100 THE DEPOSITION ID IS D_1000005190. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL40B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : FIXED-EXIT DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : BENDING MAGNET REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33441 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 21.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 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) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.6 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: MIR REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG6000, MES, SODIUM ACETATE, PH 7.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 26.29500 REMARK 290 SMTRY3 2 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, 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 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 GLU A 163 CB GLU A 163 CG -0.130 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 56 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 133 NE - CZ - NH2 ANGL. DEV. = -4.0 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 TRP A 68 53.43 -140.70 REMARK 500 ASP A 73 102.55 -167.42 REMARK 500 ILE A 111 -70.39 -96.65 REMARK 500 ALA A 146 46.46 -140.98 REMARK 500 REMARK 500 REMARK: NULL DBREF 1IQQ A 1 200 UNP O80323 RNS3_PYRPY 23 222 SEQRES 1 A 200 TYR ASP TYR PHE GLN PHE THR GLN GLN TYR GLN LEU ALA SEQRES 2 A 200 VAL CYS ASN SER ASN ARG THR LEU CYS LYS ASP PRO PRO SEQRES 3 A 200 ASP LYS LEU PHE THR VAL HIS GLY LEU TRP PRO SER ASN SEQRES 4 A 200 MET VAL GLY PRO ASP PRO SER LYS CYS PRO ILE LYS ASN SEQRES 5 A 200 ILE ARG LYS ARG GLU LYS LEU LEU GLU HIS GLN LEU GLU SEQRES 6 A 200 ILE ILE TRP PRO ASN VAL PHE ASP ARG THR LYS ASN ASN SEQRES 7 A 200 LEU PHE TRP ASP LYS GLU TRP MET LYS HIS GLY SER CYS SEQRES 8 A 200 GLY TYR PRO THR ILE ASP ASN GLU ASN HIS TYR PHE GLU SEQRES 9 A 200 THR VAL ILE LYS MET TYR ILE SER LYS LYS GLN ASN VAL SEQRES 10 A 200 SER ARG ILE LEU SER LYS ALA LYS ILE GLU PRO ASP GLY SEQRES 11 A 200 LYS LYS ARG ALA LEU LEU ASP ILE GLU ASN ALA ILE ARG SEQRES 12 A 200 ASN GLY ALA ASP ASN LYS LYS PRO LYS LEU LYS CYS GLN SEQRES 13 A 200 LYS LYS GLY THR THR THR GLU LEU VAL GLU ILE THR LEU SEQRES 14 A 200 CYS SER ASP LYS SER GLY GLU HIS PHE ILE ASP CYS PRO SEQRES 15 A 200 HIS PRO PHE GLU PRO ILE SER PRO HIS TYR CYS PRO THR SEQRES 16 A 200 ASN ASN ILE LYS TYR MODRES 1IQQ ASN A 116 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET XYP B 4 9 HET MAN B 5 11 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM XYP BETA-D-XYLOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN XYP BETA-D-XYLOSE; D-XYLOSE; XYLOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 2 BMA C6 H12 O6 FORMUL 2 XYP C5 H10 O5 FORMUL 2 MAN C6 H12 O6 FORMUL 3 HOH *266(H2 O) HELIX 1 H1 GLN A 11 VAL A 14 1 4 HELIX 2 H2 LYS A 58 ILE A 67 1 10 HELIX 3 H3 ARG A 74 LYS A 76 5 3 HELIX 4 H4 ASN A 77 LYS A 87 1 11 HELIX 5 H4 GLY A 89 CYS A 91 5 3 HELIX 6 H5 GLU A 99 TYR A 110 1 12 HELIX 7 H6 VAL A 117 LYS A 123 1 7 HELIX 8 H7 LEU A 135 ARG A 143 1 9 SHEET 1 S1 1 TYR A 3 TYR A 10 0 SHEET 1 S2 1 PHE A 30 SER A 38 0 SHEET 1 S3 1 LYS A 132 ARG A 133 0 SHEET 1 S4 1 LYS A 152 LYS A 158 0 SHEET 1 S5 1 THR A 161 SER A 171 0 SHEET 1 S6 1 PHE A 178 ILE A 179 0 SHEET 1 S7 1 ILE A 198 LYS A 199 0 SSBOND 1 CYS A 15 CYS A 22 1555 1555 2.03 SSBOND 2 CYS A 48 CYS A 91 1555 1555 2.08 SSBOND 3 CYS A 155 CYS A 193 1555 1555 2.05 SSBOND 4 CYS A 170 CYS A 181 1555 1555 2.09 LINK ND2 ASN A 116 C1 NAG B 1 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.37 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.39 LINK O2 BMA B 3 C1 XYP B 4 1555 1555 1.38 LINK O3 BMA B 3 C1 MAN B 5 1555 1555 1.41 CISPEP 1 TYR A 93 PRO A 94 0 -0.32 CRYST1 45.650 52.590 47.570 90.00 106.45 90.00 P 1 21 1 2 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 0.021908 0.000000 0.006469 0.00000 SCALE2 0.000000 0.019014 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021918 0.00000