HEADER HYDROLASE 14-MAY-08 3D4A TITLE CRYSTAL STRUCTURE OF RIBONUCLEASE SA2 WITH 3'-GMP OBTAINED BY LIGAND TITLE 2 DIFFUSION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: RIBONUCLEASE SA2; COMPND 5 EC: 3.1.4.8; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES AUREOFACIENS; SOURCE 3 ORGANISM_TAXID: 1894; SOURCE 4 STRAIN: R8/12; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: NOVABLUE; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PEH200 KEYWDS RIBONUCLEASE, MONONUCLEOTIDE, PROTEIN-MONONUCLEOTIDE COMPLEX, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.BAUEROVA-HLINKOVA,J.SEVCIK REVDAT 5 06-NOV-24 3D4A 1 REMARK REVDAT 4 01-NOV-23 3D4A 1 REMARK REVDAT 3 13-JUL-11 3D4A 1 VERSN REVDAT 2 04-AUG-09 3D4A 1 JRNL REVDAT 1 26-MAY-09 3D4A 0 JRNL AUTH V.BAUEROVA-HLINKOVA,R.DVORSKY,D.PERECKO,F.POVAZANEC,J.SEVCIK JRNL TITL STRUCTURE OF RNASE SA2 COMPLEXES WITH MONONUCLEOTIDES - NEW JRNL TITL 2 ASPECTS OF CATALYTIC REACTION AND SUBSTRATE RECOGNITION JRNL REF FEBS J. V. 276 4156 2009 JRNL REFN ISSN 1742-464X JRNL PMID 19558492 JRNL DOI 10.1111/J.1742-4658.2009.07125.X REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.3 REMARK 3 NUMBER OF REFLECTIONS : 15801 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) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 869 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 790 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 61.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 49 REMARK 3 BIN FREE R VALUE : 0.3320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2232 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 133 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 43.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.46000 REMARK 3 B22 (A**2) : 3.82000 REMARK 3 B33 (A**2) : -2.57000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.54000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.322 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.241 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.178 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2340 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3186 ; 1.520 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 274 ; 6.926 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 123 ;30.583 ;22.602 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 349 ;19.548 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;21.128 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 320 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1867 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1049 ; 0.208 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1557 ; 0.302 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 146 ; 0.186 ; 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): 52 ; 0.304 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.280 ; 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): 1407 ; 0.618 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2245 ; 1.041 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1061 ; 1.538 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 941 ; 2.327 ; 4.500 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 5 A 19 REMARK 3 ORIGIN FOR THE GROUP (A): 68.0254 5.8840 -27.7112 REMARK 3 T TENSOR REMARK 3 T11: 0.0642 T22: 0.0571 REMARK 3 T33: -0.0381 T12: -0.1353 REMARK 3 T13: 0.0237 T23: -0.0055 REMARK 3 L TENSOR REMARK 3 L11: 3.4822 L22: 8.7593 REMARK 3 L33: 4.6643 L12: -1.6176 REMARK 3 L13: -0.0193 L23: 1.0642 REMARK 3 S TENSOR REMARK 3 S11: 0.0687 S12: 0.0011 S13: 0.2850 REMARK 3 S21: -0.0062 S22: -0.1204 S23: 0.1755 REMARK 3 S31: -0.6898 S32: 0.4855 S33: 0.0517 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 20 A 61 REMARK 3 ORIGIN FOR THE GROUP (A): 61.7789 -4.6101 -18.2193 REMARK 3 T TENSOR REMARK 3 T11: 0.0231 T22: 0.0672 REMARK 3 T33: -0.0040 T12: -0.0193 REMARK 3 T13: 0.0031 T23: 0.0038 REMARK 3 L TENSOR REMARK 3 L11: 2.6412 L22: 1.8382 REMARK 3 L33: 2.3333 L12: -0.0023 REMARK 3 L13: -0.3765 L23: 0.3677 REMARK 3 S TENSOR REMARK 3 S11: 0.0859 S12: -0.2551 S13: -0.0319 REMARK 3 S21: 0.1799 S22: -0.1007 S23: -0.0197 REMARK 3 S31: 0.0131 S32: 0.2324 S33: 0.0147 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 62 A 67 REMARK 3 ORIGIN FOR THE GROUP (A): 79.1009 -7.3720 -19.0699 REMARK 3 T TENSOR REMARK 3 T11: 0.2990 T22: 0.3640 REMARK 3 T33: 0.7940 T12: 0.0284 REMARK 3 T13: -0.1822 T23: 0.2223 REMARK 3 L TENSOR REMARK 3 L11: 1.1078 L22: 21.6434 REMARK 3 L33: 41.5159 L12: 4.8496 REMARK 3 L13: 0.7424 L23: 7.3712 REMARK 3 S TENSOR REMARK 3 S11: 2.4659 S12: 1.4040 S13: 1.9866 REMARK 3 S21: 0.7683 S22: -0.6541 S23: -3.8134 REMARK 3 S31: 0.5927 S32: 4.8435 S33: -1.8117 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 68 A 97 REMARK 3 ORIGIN FOR THE GROUP (A): 63.7492 3.3203 -20.5736 REMARK 3 T TENSOR REMARK 3 T11: 0.0418 T22: 0.1294 REMARK 3 T33: -0.0108 T12: -0.0657 REMARK 3 T13: 0.0105 T23: -0.0008 REMARK 3 L TENSOR REMARK 3 L11: 2.4955 L22: 2.0750 REMARK 3 L33: 2.1890 L12: 1.0691 REMARK 3 L13: -0.2913 L23: 0.0671 REMARK 3 S TENSOR REMARK 3 S11: 0.1457 S12: -0.0698 S13: 0.2486 REMARK 3 S21: -0.0215 S22: -0.1564 S23: -0.0566 REMARK 3 S31: -0.3983 S32: 0.2444 S33: 0.0107 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 : B 1 B 25 REMARK 3 ORIGIN FOR THE GROUP (A): 65.8225 -25.5388 12.9650 REMARK 3 T TENSOR REMARK 3 T11: -0.0044 T22: -0.0401 REMARK 3 T33: 0.0362 T12: 0.1102 REMARK 3 T13: 0.0079 T23: -0.0401 REMARK 3 L TENSOR REMARK 3 L11: 5.0550 L22: 0.6239 REMARK 3 L33: 6.0020 L12: -1.5501 REMARK 3 L13: 1.8775 L23: -1.4635 REMARK 3 S TENSOR REMARK 3 S11: -0.0159 S12: 0.6878 S13: -0.2423 REMARK 3 S21: -0.0689 S22: 0.0456 S23: 0.0685 REMARK 3 S31: 0.6554 S32: 0.0153 S33: -0.0297 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 : B 26 B 49 REMARK 3 ORIGIN FOR THE GROUP (A): 61.3631 -20.8848 25.0703 REMARK 3 T TENSOR REMARK 3 T11: -0.0656 T22: 0.0185 REMARK 3 T33: 0.0268 T12: 0.0678 REMARK 3 T13: 0.0339 T23: 0.0561 REMARK 3 L TENSOR REMARK 3 L11: 7.8747 L22: 5.1486 REMARK 3 L33: 5.7262 L12: -0.9993 REMARK 3 L13: 2.3132 L23: -1.1446 REMARK 3 S TENSOR REMARK 3 S11: -0.0107 S12: -0.2315 S13: -0.4829 REMARK 3 S21: 0.3513 S22: 0.2355 S23: 0.5522 REMARK 3 S31: 0.1450 S32: -0.3887 S33: -0.2248 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 50 B 82 REMARK 3 ORIGIN FOR THE GROUP (A): 62.7189 -22.8070 20.9308 REMARK 3 T TENSOR REMARK 3 T11: -0.0138 T22: 0.1064 REMARK 3 T33: 0.0618 T12: 0.0666 REMARK 3 T13: 0.0104 T23: 0.0090 REMARK 3 L TENSOR REMARK 3 L11: 2.7917 L22: 3.7553 REMARK 3 L33: 5.3265 L12: -1.8163 REMARK 3 L13: 0.3570 L23: 0.0819 REMARK 3 S TENSOR REMARK 3 S11: 0.0373 S12: 0.2924 S13: -0.5184 REMARK 3 S21: 0.2007 S22: -0.1470 S23: 0.5090 REMARK 3 S31: 0.7455 S32: -0.0421 S33: 0.1097 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 83 B 97 REMARK 3 ORIGIN FOR THE GROUP (A): 69.0251 -26.4320 17.5610 REMARK 3 T TENSOR REMARK 3 T11: -0.0628 T22: -0.0483 REMARK 3 T33: 0.1525 T12: 0.1828 REMARK 3 T13: 0.0173 T23: -0.0210 REMARK 3 L TENSOR REMARK 3 L11: 6.7565 L22: 2.0343 REMARK 3 L33: 21.6018 L12: 1.7472 REMARK 3 L13: -1.8533 L23: -5.1207 REMARK 3 S TENSOR REMARK 3 S11: 0.4779 S12: 0.1795 S13: -0.4197 REMARK 3 S21: -0.1564 S22: -0.2320 S23: 0.2828 REMARK 3 S31: 0.3323 S32: 0.5868 S33: -0.2459 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 : C 5 C 37 REMARK 3 ORIGIN FOR THE GROUP (A): 64.3181 -5.1274 11.4941 REMARK 3 T TENSOR REMARK 3 T11: -0.0159 T22: 0.1445 REMARK 3 T33: -0.0600 T12: 0.0321 REMARK 3 T13: 0.0014 T23: 0.0655 REMARK 3 L TENSOR REMARK 3 L11: 7.2661 L22: 1.7610 REMARK 3 L33: 2.6377 L12: -0.6202 REMARK 3 L13: 0.0395 L23: 0.3693 REMARK 3 S TENSOR REMARK 3 S11: 0.0915 S12: 0.4020 S13: 0.0470 REMARK 3 S21: 0.0333 S22: -0.1866 S23: -0.1414 REMARK 3 S31: -0.3675 S32: 0.1774 S33: 0.0951 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 : C 38 C 62 REMARK 3 ORIGIN FOR THE GROUP (A): 59.9154 -9.2867 -0.1144 REMARK 3 T TENSOR REMARK 3 T11: -0.0145 T22: 0.3005 REMARK 3 T33: -0.0539 T12: 0.1142 REMARK 3 T13: -0.0040 T23: 0.0123 REMARK 3 L TENSOR REMARK 3 L11: 3.0398 L22: 2.4161 REMARK 3 L33: 4.5533 L12: -1.3813 REMARK 3 L13: -1.6910 L23: 0.0709 REMARK 3 S TENSOR REMARK 3 S11: 0.1872 S12: 0.6865 S13: -0.1218 REMARK 3 S21: -0.1608 S22: -0.2661 S23: 0.0552 REMARK 3 S31: -0.3115 S32: -0.5653 S33: 0.0789 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 : C 67 C 84 REMARK 3 ORIGIN FOR THE GROUP (A): 64.2110 -6.8802 5.0201 REMARK 3 T TENSOR REMARK 3 T11: 0.0123 T22: 0.2765 REMARK 3 T33: -0.0563 T12: 0.0446 REMARK 3 T13: 0.0117 T23: 0.0576 REMARK 3 L TENSOR REMARK 3 L11: 6.0330 L22: 9.1277 REMARK 3 L33: 6.4182 L12: 2.1122 REMARK 3 L13: -2.9938 L23: -4.3852 REMARK 3 S TENSOR REMARK 3 S11: 0.6438 S12: 0.5704 S13: 0.3194 REMARK 3 S21: 0.2934 S22: -0.4852 S23: 0.2111 REMARK 3 S31: -0.6852 S32: 0.1712 S33: -0.1586 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 : C 85 C 97 REMARK 3 ORIGIN FOR THE GROUP (A): 70.0593 -8.7779 3.4965 REMARK 3 T TENSOR REMARK 3 T11: -0.1693 T22: 0.2140 REMARK 3 T33: -0.0256 T12: 0.0531 REMARK 3 T13: -0.0098 T23: 0.1161 REMARK 3 L TENSOR REMARK 3 L11: 16.0837 L22: 3.4086 REMARK 3 L33: 26.3462 L12: -6.6068 REMARK 3 L13: 13.0876 L23: -2.0740 REMARK 3 S TENSOR REMARK 3 S11: 0.7331 S12: 1.1679 S13: -0.3097 REMARK 3 S21: -0.1247 S22: -0.8617 S23: -0.0044 REMARK 3 S31: -0.3101 S32: 0.7680 S33: 0.1286 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 3D4A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000047573. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 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 : X31 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16671 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.4 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 59.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.16200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1PY3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PHOSPHATE BUFFER, PH REMARK 280 7.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 50.76050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.95650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.76050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.95650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 105 LIES ON A SPECIAL POSITION. 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 ALA A 1 REMARK 465 ASP A 2 REMARK 465 SER B 64 REMARK 465 ASN B 65 REMARK 465 ALA C 1 REMARK 465 ASP C 2 REMARK 465 PRO C 3 REMARK 465 ALA C 4 REMARK 465 GLY C 63 REMARK 465 SER C 64 REMARK 465 ASN C 65 REMARK 465 ASP C 66 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 43 OE1 OE2 REMARK 480 ASN B 33 OD1 ND2 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 A 126 O HOH A 163 2.16 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 GLU A 43 CD GLU A 43 OE1 0.390 REMARK 500 GLU A 43 CD GLU A 43 OE2 0.433 REMARK 500 ARG C 96 CZ ARG C 96 NH1 0.181 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 GLU A 43 OE1 - CD - OE2 ANGL. DEV. = -40.8 DEGREES REMARK 500 ARG C 96 NE - CZ - NH2 ANGL. DEV. = -6.2 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 SER A 64 -153.70 -103.47 REMARK 500 ASP A 85 46.72 -140.92 REMARK 500 ARG B 67 -73.53 -124.90 REMARK 500 ASP C 85 37.69 -140.69 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 GLU A 43 0.20 SIDE CHAIN 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 SO4 A 98 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 98 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3GP B 99 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2SAR RELATED DB: PDB REMARK 900 STRUCTURE OF RIBONUCLEASE SA WITH 3'-GMP REMARK 900 RELATED ID: 1GMP RELATED DB: PDB REMARK 900 STRUCTURE OF RIBONUCLEASE SA WITH 2'-GMP REMARK 900 RELATED ID: 1RSN RELATED DB: PDB REMARK 900 STRUCTURE OF RIBONUCLEASE SA WITH EXO-2',3'-CYCLOPHOSPHOROTIOATE REMARK 900 RELATED ID: 1PY3 RELATED DB: PDB REMARK 900 STRUCTURE OF RIBONUCLEASE SA2 WITHOUT LIGAND REMARK 900 RELATED ID: 1PYL RELATED DB: PDB REMARK 900 STRUCTURE OF RIBONUCLEASE SA2 WITHOUT LIGAND REMARK 900 RELATED ID: 3D5G RELATED DB: PDB REMARK 900 RELATED ID: 3D5I RELATED DB: PDB DBREF 3D4A A 1 97 UNP Q53752 Q53752_STRAU 67 163 DBREF 3D4A B 1 97 UNP Q53752 Q53752_STRAU 67 163 DBREF 3D4A C 1 97 UNP Q53752 Q53752_STRAU 67 163 SEQRES 1 A 97 ALA ASP PRO ALA LEU ALA ASP VAL CYS ARG THR LYS LEU SEQRES 2 A 97 PRO SER GLN ALA GLN ASP THR LEU ALA LEU ILE ALA LYS SEQRES 3 A 97 ASN GLY PRO TYR PRO TYR ASN ARG ASP GLY VAL VAL PHE SEQRES 4 A 97 GLU ASN ARG GLU SER ARG LEU PRO LYS LYS GLY ASN GLY SEQRES 5 A 97 TYR TYR HIS GLU PHE THR VAL VAL THR PRO GLY SER ASN SEQRES 6 A 97 ASP ARG GLY THR ARG ARG VAL VAL THR GLY GLY TYR GLY SEQRES 7 A 97 GLU GLN TYR TRP SER PRO ASP HIS TYR ALA THR PHE GLN SEQRES 8 A 97 GLU ILE ASP PRO ARG CYS SEQRES 1 B 97 ALA ASP PRO ALA LEU ALA ASP VAL CYS ARG THR LYS LEU SEQRES 2 B 97 PRO SER GLN ALA GLN ASP THR LEU ALA LEU ILE ALA LYS SEQRES 3 B 97 ASN GLY PRO TYR PRO TYR ASN ARG ASP GLY VAL VAL PHE SEQRES 4 B 97 GLU ASN ARG GLU SER ARG LEU PRO LYS LYS GLY ASN GLY SEQRES 5 B 97 TYR TYR HIS GLU PHE THR VAL VAL THR PRO GLY SER ASN SEQRES 6 B 97 ASP ARG GLY THR ARG ARG VAL VAL THR GLY GLY TYR GLY SEQRES 7 B 97 GLU GLN TYR TRP SER PRO ASP HIS TYR ALA THR PHE GLN SEQRES 8 B 97 GLU ILE ASP PRO ARG CYS SEQRES 1 C 97 ALA ASP PRO ALA LEU ALA ASP VAL CYS ARG THR LYS LEU SEQRES 2 C 97 PRO SER GLN ALA GLN ASP THR LEU ALA LEU ILE ALA LYS SEQRES 3 C 97 ASN GLY PRO TYR PRO TYR ASN ARG ASP GLY VAL VAL PHE SEQRES 4 C 97 GLU ASN ARG GLU SER ARG LEU PRO LYS LYS GLY ASN GLY SEQRES 5 C 97 TYR TYR HIS GLU PHE THR VAL VAL THR PRO GLY SER ASN SEQRES 6 C 97 ASP ARG GLY THR ARG ARG VAL VAL THR GLY GLY TYR GLY SEQRES 7 C 97 GLU GLN TYR TRP SER PRO ASP HIS TYR ALA THR PHE GLN SEQRES 8 C 97 GLU ILE ASP PRO ARG CYS HET SO4 A 98 5 HET SO4 B 98 5 HET 3GP B 99 24 HETNAM SO4 SULFATE ION HETNAM 3GP GUANOSINE-3'-MONOPHOSPHATE FORMUL 4 SO4 2(O4 S 2-) FORMUL 6 3GP C10 H14 N5 O8 P FORMUL 7 HOH *133(H2 O) HELIX 1 1 THR A 11 LEU A 13 5 3 HELIX 2 2 PRO A 14 ASN A 27 1 14 HELIX 3 3 THR B 11 LEU B 13 5 3 HELIX 4 4 PRO B 14 LYS B 26 1 13 HELIX 5 5 THR C 11 LEU C 13 5 3 HELIX 6 6 PRO C 14 ASN C 27 1 14 SHEET 1 A 6 ALA A 6 CYS A 9 0 SHEET 2 A 6 GLN A 91 ASP A 94 1 O ASP A 94 N VAL A 8 SHEET 3 A 6 GLN A 80 SER A 83 -1 N TRP A 82 O GLN A 91 SHEET 4 A 6 ARG A 71 THR A 74 -1 N ARG A 71 O SER A 83 SHEET 5 A 6 TYR A 54 THR A 58 -1 N PHE A 57 O VAL A 72 SHEET 6 A 6 VAL A 38 PHE A 39 -1 N PHE A 39 O TYR A 54 SHEET 1 B 5 ALA B 6 CYS B 9 0 SHEET 2 B 5 GLN B 91 ASP B 94 1 O ASP B 94 N VAL B 8 SHEET 3 B 5 GLN B 80 SER B 83 -1 N TRP B 82 O GLN B 91 SHEET 4 B 5 ARG B 71 THR B 74 -1 N ARG B 71 O SER B 83 SHEET 5 B 5 HIS B 55 THR B 58 -1 N PHE B 57 O VAL B 72 SHEET 1 C 6 ALA C 6 CYS C 9 0 SHEET 2 C 6 GLN C 91 ASP C 94 1 O ASP C 94 N VAL C 8 SHEET 3 C 6 GLN C 80 SER C 83 -1 N TRP C 82 O GLN C 91 SHEET 4 C 6 ARG C 71 THR C 74 -1 N VAL C 73 O TYR C 81 SHEET 5 C 6 TYR C 54 THR C 58 -1 N PHE C 57 O VAL C 72 SHEET 6 C 6 VAL C 37 PHE C 39 -1 N VAL C 37 O GLU C 56 SSBOND 1 CYS A 9 CYS A 97 1555 1555 2.00 SSBOND 2 CYS B 9 CYS B 97 1555 1555 2.05 SSBOND 3 CYS C 9 CYS C 97 1555 1555 2.03 CISPEP 1 GLY A 28 PRO A 29 0 -2.47 CISPEP 2 GLY B 28 PRO B 29 0 7.89 CISPEP 3 GLY C 28 PRO C 29 0 4.33 SITE 1 AC1 7 ARG A 34 GLU A 56 ARG A 67 ARG A 71 SITE 2 AC1 7 HIS A 86 TYR A 87 ARG C 45 SITE 1 AC2 4 SER A 15 HOH A 139 GLU B 43 ARG B 45 SITE 1 AC3 12 VAL B 37 VAL B 38 PHE B 39 GLU B 40 SITE 2 AC3 12 ASN B 41 ARG B 42 GLU B 43 GLU B 56 SITE 3 AC3 12 ARG B 67 ARG B 71 HIS B 86 TYR B 87 CRYST1 101.521 65.913 56.966 90.00 100.92 90.00 C 1 2 1 12 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 0.009850 0.000000 0.001901 0.00000 SCALE2 0.000000 0.015172 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017878 0.00000