HEADER HYDROLASE 24-JUN-08 3DJP TITLE BOVINE SEMINAL RIBONUCLEASE- URIDINE 3' PHOSPHATE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEMINAL RIBONUCLEASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SEMINAL RNASE, S-RNASE, RIBONUCLEASE BS-1; COMPND 5 EC: 3.1.27.5 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913 KEYWDS RIBONUCLEASE, HYDROLASE, ALLOSTERIC ENZYME, ENDONUCLEASE, NUCLEASE, KEYWDS 2 SECRETED EXPDTA X-RAY DIFFRACTION AUTHOR K.DOSSI,D.D.LEONIDAS,S.E.ZOGRAPHOS,N.G.OIKONOMAKOS REVDAT 5 01-NOV-23 3DJP 1 REMARK REVDAT 4 25-OCT-17 3DJP 1 REMARK REVDAT 3 13-JUL-11 3DJP 1 VERSN REVDAT 2 20-OCT-09 3DJP 1 JRNL REVDAT 1 30-JUN-09 3DJP 0 JRNL AUTH K.DOSSI,V.G.TSIRKONE,J.M.HAYES,J.MATOUSEK,P.POUCKOVA, JRNL AUTH 2 J.SOUCEK,M.ZADINOVA,S.E.ZOGRAPHOS,D.D.LEONIDAS JRNL TITL MAPPING THE RIBONUCLEOLYTIC ACTIVE SITE OF BOVINE SEMINAL JRNL TITL 2 RIBONUCLEASE. THE BINDING OF PYRIMIDINYL PHOSPHONUCLEOTIDE JRNL TITL 3 INHIBITORS JRNL REF EUR.J.MED.CHEM. V. 44 4496 2009 JRNL REFN ISSN 0223-5234 JRNL PMID 19643512 JRNL DOI 10.1016/J.EJMECH.2009.06.039 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 30276 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1615 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2089 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE SET COUNT : 116 REMARK 3 BIN FREE R VALUE : 0.2880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1882 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 291 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 19.79 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.099 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.101 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.068 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1966 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2652 ; 1.477 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 246 ; 6.355 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 74 ;37.363 ;24.865 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 362 ;14.239 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;10.878 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1420 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 953 ; 0.194 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1356 ; 0.294 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 240 ; 0.159 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 58 ; 0.227 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 41 ; 0.167 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 18 REMARK 3 ORIGIN FOR THE GROUP (A): 9.5128 20.6646 18.4015 REMARK 3 T TENSOR REMARK 3 T11: 0.0306 T22: 0.0538 REMARK 3 T33: 0.0380 T12: 0.0045 REMARK 3 T13: 0.0030 T23: -0.0110 REMARK 3 L TENSOR REMARK 3 L11: 3.4626 L22: 3.6389 REMARK 3 L33: 4.3508 L12: 0.2000 REMARK 3 L13: -0.0464 L23: -0.8983 REMARK 3 S TENSOR REMARK 3 S11: 0.0541 S12: -0.1242 S13: 0.1372 REMARK 3 S21: 0.0541 S22: -0.0788 S23: 0.0032 REMARK 3 S31: 0.0594 S32: 0.1773 S33: 0.0247 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 19 A 58 REMARK 3 ORIGIN FOR THE GROUP (A): 26.3255 29.9690 5.8279 REMARK 3 T TENSOR REMARK 3 T11: 0.0510 T22: 0.0249 REMARK 3 T33: 0.0557 T12: 0.0245 REMARK 3 T13: -0.0274 T23: -0.0224 REMARK 3 L TENSOR REMARK 3 L11: 4.1949 L22: 1.3718 REMARK 3 L33: 1.2672 L12: 1.3262 REMARK 3 L13: -0.6131 L23: -0.4598 REMARK 3 S TENSOR REMARK 3 S11: 0.0734 S12: -0.2138 S13: -0.0139 REMARK 3 S21: 0.0467 S22: -0.0605 S23: 0.1470 REMARK 3 S31: -0.0779 S32: -0.0702 S33: -0.0129 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 59 A 68 REMARK 3 ORIGIN FOR THE GROUP (A): 42.6860 42.8321 1.5084 REMARK 3 T TENSOR REMARK 3 T11: 0.0994 T22: -0.0076 REMARK 3 T33: -0.0171 T12: -0.0649 REMARK 3 T13: 0.0341 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 3.4908 L22: 13.3609 REMARK 3 L33: 14.1360 L12: -5.6855 REMARK 3 L13: -6.1415 L23: 11.4162 REMARK 3 S TENSOR REMARK 3 S11: 0.2102 S12: -0.0109 S13: -0.0124 REMARK 3 S21: -0.9571 S22: 0.1924 S23: -0.3382 REMARK 3 S31: -1.0615 S32: 0.4402 S33: -0.4025 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 69 A 85 REMARK 3 ORIGIN FOR THE GROUP (A): 35.4497 37.0811 -0.9122 REMARK 3 T TENSOR REMARK 3 T11: 0.1150 T22: 0.0185 REMARK 3 T33: 0.0292 T12: 0.0232 REMARK 3 T13: -0.0350 T23: 0.0210 REMARK 3 L TENSOR REMARK 3 L11: 3.5453 L22: 2.0446 REMARK 3 L33: 1.2667 L12: 1.3765 REMARK 3 L13: 0.3362 L23: 0.6918 REMARK 3 S TENSOR REMARK 3 S11: 0.0951 S12: 0.2794 S13: 0.0516 REMARK 3 S21: -0.2049 S22: -0.0024 S23: 0.0480 REMARK 3 S31: -0.1252 S32: 0.0844 S33: -0.0928 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 86 A 99 REMARK 3 ORIGIN FOR THE GROUP (A): 15.2799 36.9080 11.1569 REMARK 3 T TENSOR REMARK 3 T11: -0.0667 T22: 0.0672 REMARK 3 T33: 0.2923 T12: 0.0772 REMARK 3 T13: 0.0229 T23: -0.2275 REMARK 3 L TENSOR REMARK 3 L11: 5.2514 L22: 2.9795 REMARK 3 L33: 19.4883 L12: 2.7135 REMARK 3 L13: 0.0295 L23: 2.4150 REMARK 3 S TENSOR REMARK 3 S11: 0.0931 S12: -0.9166 S13: 1.2606 REMARK 3 S21: 0.0166 S22: -0.5261 S23: 1.1640 REMARK 3 S31: -0.8828 S32: -1.1900 S33: 0.4331 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 100 A 124 REMARK 3 ORIGIN FOR THE GROUP (A): 36.7266 35.9489 1.6980 REMARK 3 T TENSOR REMARK 3 T11: 0.0720 T22: 0.0148 REMARK 3 T33: 0.0283 T12: -0.0096 REMARK 3 T13: -0.0350 T23: 0.0186 REMARK 3 L TENSOR REMARK 3 L11: 4.3163 L22: 1.7504 REMARK 3 L33: 2.3205 L12: -1.2090 REMARK 3 L13: 2.3134 L23: -0.7696 REMARK 3 S TENSOR REMARK 3 S11: -0.0212 S12: 0.1149 S13: 0.0408 REMARK 3 S21: -0.1285 S22: 0.0044 S23: 0.0274 REMARK 3 S31: -0.1157 S32: 0.0761 S33: 0.0168 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 23 REMARK 3 ORIGIN FOR THE GROUP (A): 30.7513 26.7327 6.6778 REMARK 3 T TENSOR REMARK 3 T11: 0.0482 T22: 0.0309 REMARK 3 T33: 0.0826 T12: 0.0094 REMARK 3 T13: -0.0112 T23: 0.0290 REMARK 3 L TENSOR REMARK 3 L11: 4.8229 L22: 2.5670 REMARK 3 L33: 1.5420 L12: 1.9742 REMARK 3 L13: -0.2110 L23: 0.1163 REMARK 3 S TENSOR REMARK 3 S11: -0.0182 S12: -0.1112 S13: -0.2223 REMARK 3 S21: 0.0301 S22: -0.0522 S23: 0.0235 REMARK 3 S31: -0.0638 S32: -0.0604 S33: 0.0704 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 24 B 31 REMARK 3 ORIGIN FOR THE GROUP (A): 18.6962 19.2112 7.7921 REMARK 3 T TENSOR REMARK 3 T11: 0.0361 T22: 0.0178 REMARK 3 T33: 0.0357 T12: 0.0225 REMARK 3 T13: 0.0665 T23: 0.0075 REMARK 3 L TENSOR REMARK 3 L11: 3.2372 L22: 4.8094 REMARK 3 L33: 3.6668 L12: 3.4551 REMARK 3 L13: 0.5092 L23: -0.9245 REMARK 3 S TENSOR REMARK 3 S11: -0.1663 S12: -0.0821 S13: 0.0095 REMARK 3 S21: -0.3191 S22: 0.0554 S23: -0.2244 REMARK 3 S31: 0.1679 S32: 0.1390 S33: 0.1108 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 32 B 65 REMARK 3 ORIGIN FOR THE GROUP (A): 7.2020 15.2527 15.8632 REMARK 3 T TENSOR REMARK 3 T11: 0.0647 T22: 0.0681 REMARK 3 T33: 0.0280 T12: 0.0179 REMARK 3 T13: -0.0084 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: 2.0150 L22: 2.1059 REMARK 3 L33: 2.2540 L12: 0.1948 REMARK 3 L13: -0.3930 L23: -1.1377 REMARK 3 S TENSOR REMARK 3 S11: -0.0126 S12: -0.2376 S13: -0.0780 REMARK 3 S21: -0.0828 S22: -0.0084 S23: -0.0420 REMARK 3 S31: 0.1810 S32: 0.0204 S33: 0.0210 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 66 B 82 REMARK 3 ORIGIN FOR THE GROUP (A): 0.0171 10.0891 15.6357 REMARK 3 T TENSOR REMARK 3 T11: 0.0808 T22: 0.0644 REMARK 3 T33: 0.0136 T12: -0.0381 REMARK 3 T13: -0.0311 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 0.9962 L22: 2.9026 REMARK 3 L33: 3.6881 L12: 0.7137 REMARK 3 L13: 0.0012 L23: -2.7103 REMARK 3 S TENSOR REMARK 3 S11: -0.0428 S12: -0.1086 S13: 0.0095 REMARK 3 S21: -0.2614 S22: 0.2405 S23: 0.1677 REMARK 3 S31: 0.2944 S32: -0.3816 S33: -0.1977 REMARK 3 REMARK 3 TLS GROUP : 11 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 83 B 100 REMARK 3 ORIGIN FOR THE GROUP (A): 21.8600 10.4713 8.0304 REMARK 3 T TENSOR REMARK 3 T11: 0.1077 T22: 0.0274 REMARK 3 T33: 0.1073 T12: 0.1416 REMARK 3 T13: 0.1594 T23: 0.0874 REMARK 3 L TENSOR REMARK 3 L11: 6.4270 L22: 2.8912 REMARK 3 L33: 6.6112 L12: 0.8414 REMARK 3 L13: 2.7353 L23: -0.6849 REMARK 3 S TENSOR REMARK 3 S11: -0.0437 S12: 0.0570 S13: -0.5601 REMARK 3 S21: -0.4327 S22: -0.2787 S23: -0.7046 REMARK 3 S31: 0.7394 S32: 0.8738 S33: 0.3224 REMARK 3 REMARK 3 TLS GROUP : 12 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 101 B 124 REMARK 3 ORIGIN FOR THE GROUP (A): 2.1676 12.5496 16.5417 REMARK 3 T TENSOR REMARK 3 T11: 0.0591 T22: 0.0541 REMARK 3 T33: 0.0139 T12: -0.0170 REMARK 3 T13: -0.0012 T23: -0.0094 REMARK 3 L TENSOR REMARK 3 L11: 0.8173 L22: 2.0020 REMARK 3 L33: 4.4927 L12: -0.2990 REMARK 3 L13: 0.0596 L23: -0.0636 REMARK 3 S TENSOR REMARK 3 S11: 0.0113 S12: 0.0154 S13: 0.0196 REMARK 3 S21: -0.0546 S22: 0.1266 S23: -0.0256 REMARK 3 S31: 0.3326 S32: -0.0509 S33: -0.1379 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3DJP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000048122. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8088 REMARK 200 MONOCHROMATOR : CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31892 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 27.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04100 REMARK 200 FOR THE DATA SET : 19.0000 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 (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.38900 REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 1R5D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG4000, 0.1M SODIUM ACETATE, 0.1M REMARK 280 TRIS/HCL, PH8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K 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 24.09600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.33150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.60900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.33150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.09600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.60900 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.7 KCAL/MOL 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: 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 O HOH B 260 O HOH B 261 2.12 REMARK 500 O2P UA3 A 125 O HOH A 229 2.14 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 GLY A 88 C GLY A 88 O 0.112 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 GLN A 60 -140.42 -102.01 REMARK 500 ASN A 94 75.62 -100.18 REMARK 500 GLN B 60 -143.19 -104.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER B 15 GLY B 16 42.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UA3 A 125 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UA3 B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DJO RELATED DB: PDB REMARK 900 BS-RNASE URIDINE 2' PHOSPHATE COMPLEX REMARK 900 RELATED ID: 3DJQ RELATED DB: PDB REMARK 900 BS-RNASE URIDINE 5' DIPHOSPHATE COMPLEX REMARK 900 RELATED ID: 3DJV RELATED DB: PDB REMARK 900 BS-RNASE CYTIDINE 3' PHOSPHATE COMPLEX REMARK 900 RELATED ID: 3DJX RELATED DB: PDB REMARK 900 BS-RNASE CYTIDINE 5' PHOSPHATE COMPLEX DBREF 3DJP A 1 124 UNP P00669 RNS_BOVIN 27 150 DBREF 3DJP B 1 124 UNP P00669 RNS_BOVIN 27 150 SEQRES 1 A 124 LYS GLU SER ALA ALA ALA LYS PHE GLU ARG GLN HIS MET SEQRES 2 A 124 ASP SER GLY ASN SER PRO SER SER SER SER ASN TYR CYS SEQRES 3 A 124 ASN LEU MET MET CYS CYS ARG LYS MET THR GLN GLY LYS SEQRES 4 A 124 CYS LYS PRO VAL ASN THR PHE VAL HIS GLU SER LEU ALA SEQRES 5 A 124 ASP VAL LYS ALA VAL CYS SER GLN LYS LYS VAL THR CYS SEQRES 6 A 124 LYS ASN GLY GLN THR ASN CYS TYR GLN SER LYS SER THR SEQRES 7 A 124 MET ARG ILE THR ASP CYS ARG GLU THR GLY SER SER LYS SEQRES 8 A 124 TYR PRO ASN CYS ALA TYR LYS THR THR GLN VAL GLU LYS SEQRES 9 A 124 HIS ILE ILE VAL ALA CYS GLY GLY LYS PRO SER VAL PRO SEQRES 10 A 124 VAL HIS PHE ASP ALA SER VAL SEQRES 1 B 124 LYS GLU SER ALA ALA ALA LYS PHE GLU ARG GLN HIS MET SEQRES 2 B 124 ASP SER GLY ASN SER PRO SER SER SER SER ASN TYR CYS SEQRES 3 B 124 ASN LEU MET MET CYS CYS ARG LYS MET THR GLN GLY LYS SEQRES 4 B 124 CYS LYS PRO VAL ASN THR PHE VAL HIS GLU SER LEU ALA SEQRES 5 B 124 ASP VAL LYS ALA VAL CYS SER GLN LYS LYS VAL THR CYS SEQRES 6 B 124 LYS ASN GLY GLN THR ASN CYS TYR GLN SER LYS SER THR SEQRES 7 B 124 MET ARG ILE THR ASP CYS ARG GLU THR GLY SER SER LYS SEQRES 8 B 124 TYR PRO ASN CYS ALA TYR LYS THR THR GLN VAL GLU LYS SEQRES 9 B 124 HIS ILE ILE VAL ALA CYS GLY GLY LYS PRO SER VAL PRO SEQRES 10 B 124 VAL HIS PHE ASP ALA SER VAL HET UA3 A 125 21 HET UA3 B 201 21 HETNAM UA3 URACIL ARABINOSE-3'-PHOSPHATE HETSYN UA3 1-(3-O-PHOSPHONO-BETA-L-ARABINOFURANOSYL)PYRIMIDINE-2, HETSYN 2 UA3 4(1H,3H)-DIONE FORMUL 3 UA3 2(C9 H13 N2 O9 P) FORMUL 5 HOH *291(H2 O) HELIX 1 1 SER A 3 MET A 13 1 11 HELIX 2 2 SER A 21 SER A 23 5 3 HELIX 3 3 ASN A 24 ARG A 33 1 10 HELIX 4 4 SER A 50 VAL A 57 1 8 HELIX 5 5 CYS A 58 GLN A 60 5 3 HELIX 6 6 SER B 3 MET B 13 1 11 HELIX 7 7 ASN B 24 ARG B 33 1 10 HELIX 8 8 SER B 50 VAL B 57 1 8 HELIX 9 9 CYS B 58 GLN B 60 5 3 SHEET 1 A 5 VAL A 43 VAL A 47 0 SHEET 2 A 5 MET A 79 GLU A 86 -1 O THR A 82 N PHE A 46 SHEET 3 A 5 TYR A 97 GLY A 111 -1 O LYS A 98 N ARG A 85 SHEET 4 A 5 CYS A 72 GLN A 74 -1 N TYR A 73 O VAL A 108 SHEET 5 A 5 LYS A 61 VAL A 63 -1 N LYS A 61 O GLN A 74 SHEET 1 B 4 VAL A 43 VAL A 47 0 SHEET 2 B 4 MET A 79 GLU A 86 -1 O THR A 82 N PHE A 46 SHEET 3 B 4 TYR A 97 GLY A 111 -1 O LYS A 98 N ARG A 85 SHEET 4 B 4 VAL A 116 VAL A 124 -1 O VAL A 118 N ALA A 109 SHEET 1 C 5 VAL B 43 VAL B 47 0 SHEET 2 C 5 MET B 79 GLU B 86 -1 O THR B 82 N PHE B 46 SHEET 3 C 5 TYR B 97 GLY B 111 -1 O LYS B 98 N ARG B 85 SHEET 4 C 5 CYS B 72 GLN B 74 -1 N TYR B 73 O VAL B 108 SHEET 5 C 5 LYS B 61 VAL B 63 -1 N LYS B 61 O GLN B 74 SHEET 1 D 4 VAL B 43 VAL B 47 0 SHEET 2 D 4 MET B 79 GLU B 86 -1 O THR B 82 N PHE B 46 SHEET 3 D 4 TYR B 97 GLY B 111 -1 O LYS B 98 N ARG B 85 SHEET 4 D 4 VAL B 116 VAL B 124 -1 O VAL B 118 N ALA B 109 SSBOND 1 CYS A 26 CYS A 84 1555 1555 2.03 SSBOND 2 CYS A 31 CYS B 32 1555 1555 2.04 SSBOND 3 CYS A 32 CYS B 31 1555 1555 2.04 SSBOND 4 CYS A 40 CYS A 95 1555 1555 2.04 SSBOND 5 CYS A 58 CYS A 110 1555 1555 2.03 SSBOND 6 CYS A 65 CYS A 72 1555 1555 2.03 SSBOND 7 CYS B 26 CYS B 84 1555 1555 2.03 SSBOND 8 CYS B 40 CYS B 95 1555 1555 2.04 SSBOND 9 CYS B 58 CYS B 110 1555 1555 2.02 SSBOND 10 CYS B 65 CYS B 72 1555 1555 2.01 CISPEP 1 TYR A 92 PRO A 93 0 1.20 CISPEP 2 LYS A 113 PRO A 114 0 -3.30 CISPEP 3 TYR B 92 PRO B 93 0 5.62 CISPEP 4 LYS B 113 PRO B 114 0 6.57 SITE 1 AC1 7 LYS A 41 ASN A 44 THR A 45 HIS A 119 SITE 2 AC1 7 PHE A 120 GLN B 11 HIS B 12 SITE 1 AC2 6 HIS A 12 LYS B 41 ASN B 44 THR B 45 SITE 2 AC2 6 HIS B 119 PHE B 120 CRYST1 48.192 59.218 82.663 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 0.020750 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016887 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012097 0.00000