HEADER HYDROLASE 16-MAY-08 3D5I TITLE CRYSTAL STRUCTURE OF RIBONUCLEASE SA2 WITH EXO-2',3'- TITLE 2 CYCLOPHOSPHOROTIOATE 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: R8/26; 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, EXO-2', KEYWDS 2 3'-CYCLOPHOSPHOROTIOATE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.BAUEROVA-HLINKOVA,J.SEVCIK REVDAT 5 09-OCT-24 3D5I 1 REMARK REVDAT 4 01-NOV-23 3D5I 1 REMARK REVDAT 3 13-JUL-11 3D5I 1 VERSN REVDAT 2 04-AUG-09 3D5I 1 JRNL REVDAT 1 26-MAY-09 3D5I 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) : 19.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 16896 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) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 913 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) : 1052 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.08 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 45 REMARK 3 BIN FREE R VALUE : 0.3720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2233 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 169 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 38.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.07000 REMARK 3 B22 (A**2) : 2.56000 REMARK 3 B33 (A**2) : -1.51000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.04000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.279 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.229 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.159 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.228 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2339 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1618 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3188 ; 1.555 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3874 ; 1.707 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 274 ; 6.623 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 124 ;30.865 ;22.823 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 346 ;16.304 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;25.711 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 320 ; 0.144 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2628 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 514 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 481 ; 0.207 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1723 ; 0.219 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1095 ; 0.181 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1182 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 156 ; 0.193 ; 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): 25 ; 0.150 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 56 ; 0.239 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.179 ; 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): 1749 ; 0.805 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 561 ; 0.130 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2243 ; 0.953 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1152 ; 1.607 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 945 ; 2.434 ; 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 4 A 34 REMARK 3 ORIGIN FOR THE GROUP (A): 65.9747 -1.7064 -26.5082 REMARK 3 T TENSOR REMARK 3 T11: 0.0385 T22: 0.0705 REMARK 3 T33: -0.0187 T12: -0.0374 REMARK 3 T13: 0.0238 T23: -0.0084 REMARK 3 L TENSOR REMARK 3 L11: 1.4520 L22: 3.7635 REMARK 3 L33: 2.5446 L12: 1.3244 REMARK 3 L13: -0.2979 L23: -0.6399 REMARK 3 S TENSOR REMARK 3 S11: 0.0426 S12: 0.0458 S13: -0.0690 REMARK 3 S21: 0.0608 S22: -0.0516 S23: 0.1552 REMARK 3 S31: -0.1537 S32: 0.3764 S33: 0.0090 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 35 A 61 REMARK 3 ORIGIN FOR THE GROUP (A): 59.9950 -1.5900 -14.2669 REMARK 3 T TENSOR REMARK 3 T11: 0.0852 T22: 0.0825 REMARK 3 T33: 0.0224 T12: -0.0485 REMARK 3 T13: 0.0054 T23: 0.0055 REMARK 3 L TENSOR REMARK 3 L11: 2.0196 L22: 1.6965 REMARK 3 L33: 3.0087 L12: -0.5467 REMARK 3 L13: -0.9865 L23: 0.7606 REMARK 3 S TENSOR REMARK 3 S11: -0.0147 S12: -0.4095 S13: 0.0311 REMARK 3 S21: 0.2002 S22: 0.0456 S23: 0.0344 REMARK 3 S31: -0.0249 S32: 0.2003 S33: -0.0309 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 68 REMARK 3 ORIGIN FOR THE GROUP (A): 78.1359 -6.7073 -19.3622 REMARK 3 T TENSOR REMARK 3 T11: 0.0050 T22: 0.3404 REMARK 3 T33: 0.1703 T12: 0.0250 REMARK 3 T13: -0.1293 T23: 0.0367 REMARK 3 L TENSOR REMARK 3 L11: 32.7287 L22: 35.1654 REMARK 3 L33: 15.6626 L12: 21.8428 REMARK 3 L13: -19.1742 L23: -3.2474 REMARK 3 S TENSOR REMARK 3 S11: -2.2208 S12: 1.7880 S13: -0.2925 REMARK 3 S21: 1.1373 S22: 2.1349 S23: -3.1757 REMARK 3 S31: 0.6778 S32: -0.4603 S33: 0.0858 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 97 REMARK 3 ORIGIN FOR THE GROUP (A): 63.4243 3.5787 -20.6650 REMARK 3 T TENSOR REMARK 3 T11: 0.0715 T22: 0.0916 REMARK 3 T33: 0.0251 T12: -0.0588 REMARK 3 T13: 0.0137 T23: -0.0009 REMARK 3 L TENSOR REMARK 3 L11: 1.6356 L22: 1.1658 REMARK 3 L33: 2.2116 L12: 0.0033 REMARK 3 L13: -0.7362 L23: 0.4633 REMARK 3 S TENSOR REMARK 3 S11: 0.0264 S12: -0.0789 S13: 0.2324 REMARK 3 S21: -0.0827 S22: -0.0249 S23: -0.0326 REMARK 3 S31: -0.4374 S32: 0.1712 S33: -0.0016 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 30 REMARK 3 ORIGIN FOR THE GROUP (A): 62.8832 -24.3248 13.6041 REMARK 3 T TENSOR REMARK 3 T11: 0.0519 T22: 0.0150 REMARK 3 T33: 0.0254 T12: 0.0363 REMARK 3 T13: 0.0384 T23: 0.0219 REMARK 3 L TENSOR REMARK 3 L11: 7.3459 L22: 1.5923 REMARK 3 L33: 4.0373 L12: -0.7858 REMARK 3 L13: 2.9495 L23: -0.7275 REMARK 3 S TENSOR REMARK 3 S11: -0.0681 S12: 0.3211 S13: -0.1336 REMARK 3 S21: -0.1454 S22: 0.0821 S23: 0.1632 REMARK 3 S31: 0.4503 S32: -0.1735 S33: -0.0140 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 31 B 60 REMARK 3 ORIGIN FOR THE GROUP (A): 62.9215 -20.8651 25.9962 REMARK 3 T TENSOR REMARK 3 T11: 0.0186 T22: 0.0585 REMARK 3 T33: 0.0036 T12: 0.0613 REMARK 3 T13: 0.0364 T23: 0.0677 REMARK 3 L TENSOR REMARK 3 L11: 3.8333 L22: 5.2250 REMARK 3 L33: 6.9522 L12: -1.2614 REMARK 3 L13: 2.4159 L23: 1.8907 REMARK 3 S TENSOR REMARK 3 S11: -0.0315 S12: -0.5533 S13: -0.3724 REMARK 3 S21: 0.5763 S22: 0.0584 S23: 0.2843 REMARK 3 S31: 0.3716 S32: -0.1382 S33: -0.0269 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 61 B 68 REMARK 3 ORIGIN FOR THE GROUP (A): 53.7863 -36.3517 21.0971 REMARK 3 T TENSOR REMARK 3 T11: -0.0315 T22: 0.3661 REMARK 3 T33: 0.2932 T12: -0.0429 REMARK 3 T13: 0.1456 T23: -0.1497 REMARK 3 L TENSOR REMARK 3 L11: 16.6346 L22: 26.0237 REMARK 3 L33: 20.9329 L12: 18.6105 REMARK 3 L13: 16.0716 L23: 12.6776 REMARK 3 S TENSOR REMARK 3 S11: 0.6778 S12: -2.3389 S13: -1.3948 REMARK 3 S21: 1.2767 S22: -1.8987 S23: 0.5839 REMARK 3 S31: 0.9252 S32: -2.5466 S33: 1.2209 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 69 B 97 REMARK 3 ORIGIN FOR THE GROUP (A): 66.8576 -24.5310 18.3130 REMARK 3 T TENSOR REMARK 3 T11: -0.0088 T22: 0.0690 REMARK 3 T33: 0.0598 T12: 0.0413 REMARK 3 T13: 0.0206 T23: 0.0158 REMARK 3 L TENSOR REMARK 3 L11: 2.4618 L22: 2.4261 REMARK 3 L33: 2.3501 L12: -1.1188 REMARK 3 L13: 0.7784 L23: 0.9674 REMARK 3 S TENSOR REMARK 3 S11: 0.0754 S12: 0.0895 S13: -0.3220 REMARK 3 S21: -0.0051 S22: -0.0829 S23: 0.0841 REMARK 3 S31: 0.2568 S32: 0.1339 S33: 0.0075 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 26 REMARK 3 ORIGIN FOR THE GROUP (A): 69.2630 -6.7100 12.1602 REMARK 3 T TENSOR REMARK 3 T11: -0.0347 T22: 0.1077 REMARK 3 T33: 0.0169 T12: -0.0221 REMARK 3 T13: -0.0167 T23: 0.0412 REMARK 3 L TENSOR REMARK 3 L11: 4.7781 L22: 1.7220 REMARK 3 L33: 5.2520 L12: -1.1922 REMARK 3 L13: 0.4619 L23: -0.2726 REMARK 3 S TENSOR REMARK 3 S11: 0.0362 S12: 0.1764 S13: 0.2206 REMARK 3 S21: 0.0733 S22: -0.0191 S23: -0.2910 REMARK 3 S31: -0.1613 S32: 0.5155 S33: -0.0171 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 27 C 34 REMARK 3 ORIGIN FOR THE GROUP (A): 54.6652 -1.7443 11.6948 REMARK 3 T TENSOR REMARK 3 T11: 0.0335 T22: 0.1257 REMARK 3 T33: -0.0415 T12: 0.0606 REMARK 3 T13: -0.0198 T23: 0.0159 REMARK 3 L TENSOR REMARK 3 L11: 7.4868 L22: 10.5259 REMARK 3 L33: 11.6099 L12: -1.1577 REMARK 3 L13: -5.6140 L23: -4.6681 REMARK 3 S TENSOR REMARK 3 S11: 0.3603 S12: 0.3976 S13: 0.5123 REMARK 3 S21: -0.6499 S22: -0.2618 S23: -0.0659 REMARK 3 S31: -0.4668 S32: -0.1012 S33: -0.0984 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 35 C 81 REMARK 3 ORIGIN FOR THE GROUP (A): 60.4824 -8.0005 2.3799 REMARK 3 T TENSOR REMARK 3 T11: -0.0143 T22: 0.1908 REMARK 3 T33: -0.0248 T12: 0.0794 REMARK 3 T13: 0.0096 T23: 0.0154 REMARK 3 L TENSOR REMARK 3 L11: 3.0362 L22: 1.3906 REMARK 3 L33: 5.8256 L12: -0.4518 REMARK 3 L13: -0.6553 L23: 0.9050 REMARK 3 S TENSOR REMARK 3 S11: 0.1897 S12: 0.3179 S13: 0.0951 REMARK 3 S21: -0.0814 S22: -0.2848 S23: 0.0040 REMARK 3 S31: -0.4183 S32: -0.4534 S33: 0.0951 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 82 C 97 REMARK 3 ORIGIN FOR THE GROUP (A): 69.6987 -7.7936 3.6893 REMARK 3 T TENSOR REMARK 3 T11: -0.0386 T22: 0.1268 REMARK 3 T33: -0.0286 T12: 0.0103 REMARK 3 T13: 0.0082 T23: 0.0262 REMARK 3 L TENSOR REMARK 3 L11: 11.8187 L22: 3.9930 REMARK 3 L33: 13.8306 L12: -4.8165 REMARK 3 L13: 4.0057 L23: -4.4566 REMARK 3 S TENSOR REMARK 3 S11: 0.5464 S12: 0.5523 S13: -0.1531 REMARK 3 S21: -0.0221 S22: -0.3539 S23: -0.1492 REMARK 3 S31: -0.2003 S32: 0.1951 S33: -0.1926 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 3D5I 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_1000047617. 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 : 19754 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 (%) : 90.2 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.0000 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 (%) : 65.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.21200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.700 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 (%): 57.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 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 50.61050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.38750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.61050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.38750 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 109 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 165 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 PRO A 3 REMARK 465 SER A 64 REMARK 465 ASN A 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 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 LYS C 48 CD CE NZ 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 34 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 34 NE - CZ - NH2 ANGL. DEV. = -4.9 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 PRO A 62 89.34 -47.68 REMARK 500 ASP C 85 43.72 -145.20 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 A 99 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 98 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SGP B 98 REMARK 900 REMARK 900 RELATED ENTRIES 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: 1RSN RELATED DB: PDB REMARK 900 STRUCTURE OF RIBONUCLEASE SA WITH EXO-2',3'-CYCLOPHOSPHOROTIOATE 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: 3D4A RELATED DB: PDB REMARK 900 RELATED ID: 3D5G RELATED DB: PDB DBREF 3D5I A 1 97 UNP Q53752 Q53752_STRAU 67 163 DBREF 3D5I B 1 97 UNP Q53752 Q53752_STRAU 67 163 DBREF 3D5I 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 A 99 5 HET SGP B 98 23 HET SO4 C 98 5 HETNAM SO4 SULFATE ION HETNAM SGP GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE FORMUL 4 SO4 3(O4 S 2-) FORMUL 6 SGP C10 H12 N5 O6 P S FORMUL 8 HOH *169(H2 O) HELIX 1 1 THR A 11 LEU A 13 5 3 HELIX 2 2 PRO A 14 LYS A 26 1 13 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 LYS C 26 1 13 SHEET 1 A 6 ASP A 7 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 37 PHE A 39 -1 N VAL A 37 O GLU A 56 SHEET 1 B 6 ALA B 6 CYS B 9 0 SHEET 2 B 6 GLN B 91 ASP B 94 1 O ASP B 94 N VAL B 8 SHEET 3 B 6 GLN B 80 SER B 83 -1 N TRP B 82 O GLN B 91 SHEET 4 B 6 ARG B 71 THR B 74 -1 N ARG B 71 O SER B 83 SHEET 5 B 6 TYR B 54 THR B 58 -1 N HIS B 55 O THR B 74 SHEET 6 B 6 VAL B 38 PHE B 39 -1 N PHE B 39 O TYR B 54 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 2.01 SSBOND 2 CYS B 9 CYS B 97 1555 1555 2.04 SSBOND 3 CYS C 9 CYS C 97 1555 1555 2.03 CISPEP 1 GLY A 28 PRO A 29 0 -5.57 CISPEP 2 GLY B 28 PRO B 29 0 11.74 CISPEP 3 GLY C 28 PRO C 29 0 2.64 SITE 1 AC1 8 ARG A 34 GLU A 56 ARG A 67 ARG A 71 SITE 2 AC1 8 HIS A 86 TYR A 87 HOH A 121 ARG C 45 SITE 1 AC2 4 SER A 15 HOH A 150 GLU B 43 ARG B 45 SITE 1 AC3 5 ARG A 42 ARG C 67 ARG C 71 HIS C 86 SITE 2 AC3 5 TYR C 87 SITE 1 AC4 14 ARG B 34 VAL B 38 PHE B 39 GLU B 40 SITE 2 AC4 14 ASN B 41 ARG B 42 GLU B 43 GLU B 56 SITE 3 AC4 14 ARG B 67 ARG B 71 HIS B 86 TYR B 87 SITE 4 AC4 14 HOH B 129 HOH B 162 CRYST1 101.221 66.775 57.070 90.00 100.80 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 0.009879 0.000000 0.001884 0.00000 SCALE2 0.000000 0.014976 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017838 0.00000