HEADER HYDROLASE 16-JUN-08 3DGY TITLE CRYSTAL STRUCTURE OF RIBONUCLEASE SA2 WITH GUANOSINE-2'-CYCLOPHOSPHATE 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: NOVA BLUE; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PEH200 KEYWDS RIBONUCLEASE, HYDROLASE, PROTEIN-MONONUCLEOTIDE COMPLEX, GUANOSINE- KEYWDS 2 2'-MONOPHOSPHATE, MONONUCLEOTIDE EXPDTA X-RAY DIFFRACTION AUTHOR J.SEVCIK,V.BAUEROVA-HLINKOVA REVDAT 6 09-OCT-24 3DGY 1 REMARK REVDAT 5 01-NOV-23 3DGY 1 HETSYN REVDAT 4 29-JUL-20 3DGY 1 COMPND REMARK HETNAM SITE REVDAT 3 13-JUL-11 3DGY 1 VERSN REVDAT 2 04-AUG-09 3DGY 1 JRNL REVDAT 1 16-JUN-09 3DGY 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 33012 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) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1750 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2434 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE SET COUNT : 110 REMARK 3 BIN FREE R VALUE : 0.2790 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2217 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 277 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.11000 REMARK 3 B22 (A**2) : 2.28000 REMARK 3 B33 (A**2) : -1.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.16000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.133 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.126 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.091 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.295 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2336 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1619 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3181 ; 1.388 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3875 ; 0.931 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 271 ; 6.661 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 122 ;28.785 ;22.705 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 346 ;15.922 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;20.416 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 323 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2599 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 511 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 464 ; 0.210 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1695 ; 0.210 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1108 ; 0.179 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1181 ; 0.079 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 180 ; 0.181 ; 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): 14 ; 0.162 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 39 ; 0.204 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.178 ; 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): 1733 ; 0.809 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 555 ; 0.176 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2223 ; 0.986 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1157 ; 1.667 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 958 ; 2.389 ; 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 16 REMARK 3 ORIGIN FOR THE GROUP (A): 67.0556 -3.7823 -26.7731 REMARK 3 T TENSOR REMARK 3 T11: 0.0757 T22: -0.1392 REMARK 3 T33: -0.0354 T12: -0.1368 REMARK 3 T13: 0.0177 T23: -0.0116 REMARK 3 L TENSOR REMARK 3 L11: 5.8264 L22: 6.1342 REMARK 3 L33: 5.4718 L12: -1.0157 REMARK 3 L13: -3.0054 L23: 0.8760 REMARK 3 S TENSOR REMARK 3 S11: 0.2377 S12: 0.0642 S13: 0.3906 REMARK 3 S21: 0.0160 S22: -0.0989 S23: 0.2261 REMARK 3 S31: -0.8594 S32: 0.5166 S33: -0.1388 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 17 A 61 REMARK 3 ORIGIN FOR THE GROUP (A): 62.2561 -15.7888 -18.8526 REMARK 3 T TENSOR REMARK 3 T11: 0.0235 T22: -0.0731 REMARK 3 T33: 0.0105 T12: -0.0391 REMARK 3 T13: 0.0073 T23: -0.0008 REMARK 3 L TENSOR REMARK 3 L11: 2.3266 L22: 0.8905 REMARK 3 L33: 2.5950 L12: -0.5894 REMARK 3 L13: -0.5198 L23: 0.4263 REMARK 3 S TENSOR REMARK 3 S11: 0.0236 S12: -0.1757 S13: -0.0736 REMARK 3 S21: 0.1128 S22: -0.0384 S23: 0.0333 REMARK 3 S31: -0.0520 S32: 0.1936 S33: 0.0148 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 91 REMARK 3 ORIGIN FOR THE GROUP (A): 66.5854 -11.1994 -18.6462 REMARK 3 T TENSOR REMARK 3 T11: 0.0266 T22: -0.0441 REMARK 3 T33: 0.0055 T12: -0.0647 REMARK 3 T13: 0.0021 T23: -0.0139 REMARK 3 L TENSOR REMARK 3 L11: 5.2736 L22: 1.6037 REMARK 3 L33: 2.8635 L12: 1.2995 REMARK 3 L13: 0.9234 L23: 0.1245 REMARK 3 S TENSOR REMARK 3 S11: 0.2232 S12: -0.0425 S13: -0.3492 REMARK 3 S21: 0.1072 S22: -0.0533 S23: -0.2138 REMARK 3 S31: -0.1454 S32: 0.3995 S33: -0.1699 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 92 A 97 REMARK 3 ORIGIN FOR THE GROUP (A): 60.2174 -2.4020 -28.6953 REMARK 3 T TENSOR REMARK 3 T11: 0.1552 T22: -0.1166 REMARK 3 T33: -0.0293 T12: -0.0303 REMARK 3 T13: 0.0132 T23: 0.0214 REMARK 3 L TENSOR REMARK 3 L11: 5.9241 L22: 7.2201 REMARK 3 L33: 31.3904 L12: -5.5963 REMARK 3 L13: 9.5492 L23: -3.4590 REMARK 3 S TENSOR REMARK 3 S11: 0.4271 S12: -0.1602 S13: -0.0415 REMARK 3 S21: -0.3803 S22: -0.2576 S23: 0.7134 REMARK 3 S31: -1.0108 S32: -1.5079 S33: -0.1695 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): 66.0059 -37.3564 13.1487 REMARK 3 T TENSOR REMARK 3 T11: -0.0004 T22: -0.0763 REMARK 3 T33: -0.0566 T12: 0.0510 REMARK 3 T13: 0.0400 T23: 0.0093 REMARK 3 L TENSOR REMARK 3 L11: 9.1713 L22: 1.7448 REMARK 3 L33: 2.6542 L12: -1.7258 REMARK 3 L13: 1.6654 L23: -0.8893 REMARK 3 S TENSOR REMARK 3 S11: 0.0353 S12: 0.5452 S13: -0.2078 REMARK 3 S21: -0.0714 S22: -0.0523 S23: 0.0986 REMARK 3 S31: 0.5775 S32: -0.0898 S33: 0.0170 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 34 REMARK 3 ORIGIN FOR THE GROUP (A): 51.4088 -33.5751 19.6782 REMARK 3 T TENSOR REMARK 3 T11: -0.1391 T22: -0.0045 REMARK 3 T33: 0.1156 T12: -0.0344 REMARK 3 T13: 0.0865 T23: -0.0200 REMARK 3 L TENSOR REMARK 3 L11: 9.4862 L22: 17.8156 REMARK 3 L33: 17.7423 L12: -0.9845 REMARK 3 L13: 1.7102 L23: -17.7507 REMARK 3 S TENSOR REMARK 3 S11: -0.0553 S12: 0.4723 S13: -0.2221 REMARK 3 S21: 0.2746 S22: 0.3685 S23: 1.0705 REMARK 3 S31: 0.3455 S32: -1.0700 S33: -0.3132 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 35 B 58 REMARK 3 ORIGIN FOR THE GROUP (A): 65.6688 -31.2665 27.0567 REMARK 3 T TENSOR REMARK 3 T11: -0.0226 T22: -0.0217 REMARK 3 T33: -0.0531 T12: 0.0634 REMARK 3 T13: 0.0215 T23: 0.0431 REMARK 3 L TENSOR REMARK 3 L11: 5.7715 L22: 3.4342 REMARK 3 L33: 2.5666 L12: -1.4256 REMARK 3 L13: -0.4074 L23: 0.9167 REMARK 3 S TENSOR REMARK 3 S11: -0.2417 S12: -0.6542 S13: -0.2366 REMARK 3 S21: 0.5056 S22: 0.1042 S23: -0.0621 REMARK 3 S31: 0.1662 S32: 0.2505 S33: 0.1374 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 59 B 97 REMARK 3 ORIGIN FOR THE GROUP (A): 65.0414 -38.1581 18.7274 REMARK 3 T TENSOR REMARK 3 T11: -0.0286 T22: -0.0737 REMARK 3 T33: 0.0402 T12: 0.0519 REMARK 3 T13: 0.0576 T23: 0.0260 REMARK 3 L TENSOR REMARK 3 L11: 2.6445 L22: 2.2963 REMARK 3 L33: 3.4872 L12: 0.1792 REMARK 3 L13: 0.0562 L23: -0.5635 REMARK 3 S TENSOR REMARK 3 S11: -0.0917 S12: -0.1070 S13: -0.3520 REMARK 3 S21: -0.0086 S22: -0.1159 S23: 0.1149 REMARK 3 S31: 0.4357 S32: 0.0643 S33: 0.2076 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): 64.3258 -17.0737 11.6113 REMARK 3 T TENSOR REMARK 3 T11: -0.0579 T22: 0.0018 REMARK 3 T33: -0.0674 T12: 0.0288 REMARK 3 T13: -0.0266 T23: 0.0528 REMARK 3 L TENSOR REMARK 3 L11: 7.0319 L22: 1.9461 REMARK 3 L33: 2.9158 L12: -1.3740 REMARK 3 L13: -0.8529 L23: -0.2386 REMARK 3 S TENSOR REMARK 3 S11: 0.0375 S12: 0.2829 S13: 0.1172 REMARK 3 S21: 0.0987 S22: -0.2570 S23: -0.2341 REMARK 3 S31: -0.3240 S32: 0.1321 S33: 0.2195 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 53 REMARK 3 ORIGIN FOR THE GROUP (A): 59.1627 -24.5436 -3.9522 REMARK 3 T TENSOR REMARK 3 T11: -0.1099 T22: 0.2045 REMARK 3 T33: -0.0603 T12: 0.0907 REMARK 3 T13: -0.0072 T23: -0.0824 REMARK 3 L TENSOR REMARK 3 L11: 0.7353 L22: 6.5556 REMARK 3 L33: 6.7851 L12: 1.5541 REMARK 3 L13: 0.5263 L23: -2.4535 REMARK 3 S TENSOR REMARK 3 S11: 0.0559 S12: 0.0945 S13: -0.1982 REMARK 3 S21: -0.5652 S22: -0.5030 S23: 0.3682 REMARK 3 S31: 0.1725 S32: -0.7000 S33: 0.4472 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 54 C 82 REMARK 3 ORIGIN FOR THE GROUP (A): 62.9896 -17.9031 5.8660 REMARK 3 T TENSOR REMARK 3 T11: -0.0559 T22: 0.0492 REMARK 3 T33: -0.0547 T12: 0.0766 REMARK 3 T13: -0.0054 T23: 0.0347 REMARK 3 L TENSOR REMARK 3 L11: 3.9819 L22: 4.7170 REMARK 3 L33: 5.1465 L12: 0.4106 REMARK 3 L13: -0.6042 L23: 0.3863 REMARK 3 S TENSOR REMARK 3 S11: 0.2756 S12: 0.3653 S13: 0.2317 REMARK 3 S21: 0.1046 S22: -0.4288 S23: -0.1538 REMARK 3 S31: -0.4532 S32: -0.1838 S33: 0.1532 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 83 C 97 REMARK 3 ORIGIN FOR THE GROUP (A): 69.9765 -19.9960 3.4564 REMARK 3 T TENSOR REMARK 3 T11: -0.1266 T22: 0.0412 REMARK 3 T33: -0.0310 T12: 0.0433 REMARK 3 T13: 0.0374 T23: 0.0753 REMARK 3 L TENSOR REMARK 3 L11: 11.1100 L22: 3.0566 REMARK 3 L33: 11.8604 L12: -5.3552 REMARK 3 L13: 4.0861 L23: -1.3759 REMARK 3 S TENSOR REMARK 3 S11: 0.3909 S12: 0.5776 S13: -0.5801 REMARK 3 S21: -0.0112 S22: -0.3129 S23: 0.0066 REMARK 3 S31: -0.4067 S32: 0.2572 S33: -0.0780 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 3DGY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000048025. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-03 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 : 34762 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 98.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.31700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 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: 1PY3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.94 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 50.74450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.65650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.74450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.65650 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 215 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 220 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 GLY B 63 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 ASN C 65 REMARK 465 ASP C 66 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 PRO A 62 O HOH A 209 2.15 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 70 NE - CZ - NH2 ANGL. DEV. = -4.1 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 HIS C 86 42.26 72.42 REMARK 500 REMARK 500 REMARK: NULL 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: 3D4A RELATED DB: PDB REMARK 900 STRUCTURE OF RIBONUCLEASE SA2 WITH 3'-GMP REMARK 900 RELATED ID: 3D5I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RIBONUCLEASE SA2 WITH EXO-2',3'- REMARK 900 CYCLOPHOSPHOROTIOATE REMARK 900 RELATED ID: 1GMP RELATED DB: PDB REMARK 900 STRUCTURE OF RIBONUCLEASE SA WITH 2'-GMP REMARK 900 RELATED ID: 2SAR RELATED DB: PDB REMARK 900 STRUCTURE OF RIBONUCLEASE SA WITH 3'-GMP REMARK 900 RELATED ID: 3DH2 RELATED DB: PDB DBREF 3DGY A 1 97 UNP Q53752 Q53752_STRAU 67 163 DBREF 3DGY B 1 97 UNP Q53752 Q53752_STRAU 67 163 DBREF 3DGY 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 BGC A 99 12 HET SO4 A 98 5 HET SO4 B 100 5 HET 2GP B 98 24 HET SO4 C 198 5 HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM SO4 SULFATE ION HETNAM 2GP GUANOSINE-2'-MONOPHOSPHATE HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 4 BGC C6 H12 O6 FORMUL 5 SO4 3(O4 S 2-) FORMUL 7 2GP C10 H14 N5 O8 P FORMUL 9 HOH *277(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 ASN B 27 1 14 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 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 VAL A 73 O TYR A 81 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 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 HIS B 55 O THR B 74 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 ARG C 71 O SER C 83 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 2.04 SSBOND 2 CYS B 9 CYS B 97 1555 1555 2.06 SSBOND 3 CYS C 9 CYS C 97 1555 1555 2.05 CISPEP 1 GLY A 28 PRO A 29 0 -2.69 CISPEP 2 GLY B 28 PRO B 29 0 -12.67 CISPEP 3 GLY C 28 PRO C 29 0 4.26 CISPEP 4 PRO C 62 GLY C 63 0 -17.66 CRYST1 101.489 67.313 57.234 90.00 100.63 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 0.009853 0.000000 0.001849 0.00000 SCALE2 0.000000 0.014856 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017777 0.00000