HEADER HYDROLASE 26-MAY-08 3D8Y TITLE RNASE A- 5'-DEOXY-5'-N-PIPERIDINOTHYMIDINE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE PANCREATIC; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RIBONUCLEASE A, RNASE 1, RNASE A; 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; SOURCE 5 TISSUE: PANCREAS KEYWDS RIBONUCLEASE, HYDROLASE, LIGAND BINDING, ENDONUCLEASE, GLYCATION, KEYWDS 2 GLYCOPROTEIN, NUCLEASE, SECRETED EXPDTA X-RAY DIFFRACTION AUTHOR D.D.LEONIDAS,S.E.ZOGRAPHOS,N.G.OIKONOMAKOS REVDAT 4 01-NOV-23 3D8Y 1 REMARK REVDAT 3 29-JAN-14 3D8Y 1 JRNL REVDAT 2 13-JUL-11 3D8Y 1 VERSN REVDAT 1 10-FEB-09 3D8Y 0 JRNL AUTH A.SAMANTA,D.D.LEONIDAS,S.DASGUPTA,T.PATHAK,S.E.ZOGRAPHOS, JRNL AUTH 2 N.G.OIKONOMAKOS JRNL TITL MORPHOLINO, PIPERIDINO, AND PYRROLIDINO DERIVATIVES OF JRNL TITL 2 PYRIMIDINE NUCLEOSIDES AS INHIBITORS OF RIBONUCLEASE A: JRNL TITL 3 SYNTHESIS, BIOCHEMICAL, AND CRYSTALLOGRAPHIC EVALUATION JRNL REF J.MED.CHEM. V. 52 932 2009 JRNL REFN ISSN 0022-2623 JRNL PMID 19173562 JRNL DOI 10.1021/JM800724T REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0037 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) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 23272 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 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 : 1258 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) : 1.72 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1539 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.29 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 90 REMARK 3 BIN FREE R VALUE : 0.2700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1901 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 213 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 19.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.39000 REMARK 3 B22 (A**2) : 0.73000 REMARK 3 B33 (A**2) : -0.34000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.17000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.129 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.124 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.080 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.603 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2003 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2713 ; 1.204 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 246 ; 5.862 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ;36.195 ;25.222 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 341 ;11.593 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;10.506 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 298 ; 0.076 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1506 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 891 ; 0.184 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1387 ; 0.292 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 175 ; 0.134 ; 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): 65 ; 0.230 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 28 ; 0.176 ; 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): 1274 ; 0.553 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2023 ; 0.948 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 810 ; 1.572 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 690 ; 2.498 ; 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 : 14 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 15 REMARK 3 ORIGIN FOR THE GROUP (A): 30.8912 9.0038 9.6770 REMARK 3 T TENSOR REMARK 3 T11: 0.0563 T22: 0.0332 REMARK 3 T33: 0.0048 T12: -0.0023 REMARK 3 T13: 0.0500 T23: 0.0498 REMARK 3 L TENSOR REMARK 3 L11: 2.5009 L22: 3.6343 REMARK 3 L33: 7.9714 L12: -0.4859 REMARK 3 L13: -0.4321 L23: 0.5066 REMARK 3 S TENSOR REMARK 3 S11: 0.1793 S12: 0.1058 S13: 0.2624 REMARK 3 S21: -0.0357 S22: -0.0126 S23: -0.2608 REMARK 3 S31: -0.6591 S32: 0.0724 S33: -0.1667 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 16 A 23 REMARK 3 ORIGIN FOR THE GROUP (A): 24.6760 -4.4083 -1.7844 REMARK 3 T TENSOR REMARK 3 T11: 0.1207 T22: 0.4099 REMARK 3 T33: 0.0580 T12: 0.1401 REMARK 3 T13: 0.2133 T23: 0.0186 REMARK 3 L TENSOR REMARK 3 L11: 36.4039 L22: 33.0370 REMARK 3 L33: 37.3076 L12: -29.4277 REMARK 3 L13: -30.1112 L23: 35.0505 REMARK 3 S TENSOR REMARK 3 S11: -1.4557 S12: 2.6373 S13: -2.2651 REMARK 3 S21: 1.8524 S22: -0.7638 S23: 2.3247 REMARK 3 S31: 1.4040 S32: -2.6640 S33: 2.2195 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 24 A 58 REMARK 3 ORIGIN FOR THE GROUP (A): 32.0782 2.1574 5.1426 REMARK 3 T TENSOR REMARK 3 T11: 0.0220 T22: 0.0653 REMARK 3 T33: -0.0060 T12: -0.0108 REMARK 3 T13: 0.0139 T23: 0.0370 REMARK 3 L TENSOR REMARK 3 L11: 3.6531 L22: 1.2050 REMARK 3 L33: 3.6997 L12: -0.9110 REMARK 3 L13: -2.6074 L23: 0.6325 REMARK 3 S TENSOR REMARK 3 S11: 0.1747 S12: 0.3730 S13: 0.1864 REMARK 3 S21: -0.2197 S22: 0.0573 S23: -0.1382 REMARK 3 S31: -0.1493 S32: -0.1318 S33: -0.2320 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 59 A 77 REMARK 3 ORIGIN FOR THE GROUP (A): 28.3211 -1.7148 24.1818 REMARK 3 T TENSOR REMARK 3 T11: 0.0396 T22: 0.0165 REMARK 3 T33: 0.0175 T12: -0.0054 REMARK 3 T13: -0.0003 T23: 0.0101 REMARK 3 L TENSOR REMARK 3 L11: 7.8390 L22: 3.2824 REMARK 3 L33: 3.5072 L12: 0.7881 REMARK 3 L13: 1.4775 L23: -0.4597 REMARK 3 S TENSOR REMARK 3 S11: -0.1087 S12: -0.0862 S13: -0.0731 REMARK 3 S21: 0.1549 S22: 0.1084 S23: -0.1139 REMARK 3 S31: 0.0043 S32: -0.2821 S33: 0.0003 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 78 A 99 REMARK 3 ORIGIN FOR THE GROUP (A): 38.2631 -4.9017 1.6439 REMARK 3 T TENSOR REMARK 3 T11: 0.0376 T22: 0.0315 REMARK 3 T33: -0.0125 T12: -0.0145 REMARK 3 T13: 0.0294 T23: -0.0641 REMARK 3 L TENSOR REMARK 3 L11: 12.2190 L22: 0.6802 REMARK 3 L33: 7.3804 L12: 1.5950 REMARK 3 L13: -6.8811 L23: -1.0595 REMARK 3 S TENSOR REMARK 3 S11: -0.3540 S12: 0.3652 S13: -0.4671 REMARK 3 S21: -0.1720 S22: 0.1759 S23: -0.2898 REMARK 3 S31: 0.7304 S32: 0.1587 S33: 0.1781 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 106 REMARK 3 ORIGIN FOR THE GROUP (A): 25.8308 -8.8961 10.0774 REMARK 3 T TENSOR REMARK 3 T11: 0.0198 T22: 0.0441 REMARK 3 T33: -0.0508 T12: -0.0916 REMARK 3 T13: -0.0152 T23: -0.0294 REMARK 3 L TENSOR REMARK 3 L11: 3.9349 L22: 6.2769 REMARK 3 L33: 14.9584 L12: 1.8504 REMARK 3 L13: -5.7609 L23: 3.2301 REMARK 3 S TENSOR REMARK 3 S11: -0.3067 S12: 0.4053 S13: -0.5797 REMARK 3 S21: -0.4994 S22: -0.0180 S23: -0.0636 REMARK 3 S31: 0.6364 S32: -0.6369 S33: 0.3248 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 : A 107 A 124 REMARK 3 ORIGIN FOR THE GROUP (A): 29.3384 3.8836 19.2891 REMARK 3 T TENSOR REMARK 3 T11: 0.0216 T22: 0.0270 REMARK 3 T33: 0.0306 T12: -0.0012 REMARK 3 T13: -0.0095 T23: 0.0166 REMARK 3 L TENSOR REMARK 3 L11: 2.7751 L22: 6.4276 REMARK 3 L33: 2.9978 L12: -0.5878 REMARK 3 L13: -0.8904 L23: 0.4287 REMARK 3 S TENSOR REMARK 3 S11: -0.0414 S12: 0.0158 S13: 0.1277 REMARK 3 S21: -0.1090 S22: 0.1480 S23: -0.0292 REMARK 3 S31: -0.0720 S32: -0.2145 S33: -0.1065 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 1 B 11 REMARK 3 ORIGIN FOR THE GROUP (A): 16.4270 -7.5853 30.6470 REMARK 3 T TENSOR REMARK 3 T11: 0.0188 T22: 0.0287 REMARK 3 T33: 0.0220 T12: -0.0113 REMARK 3 T13: 0.0221 T23: -0.0547 REMARK 3 L TENSOR REMARK 3 L11: 5.6191 L22: 2.8902 REMARK 3 L33: 9.6574 L12: 1.6836 REMARK 3 L13: 3.2600 L23: 1.0017 REMARK 3 S TENSOR REMARK 3 S11: -0.1259 S12: 0.5582 S13: -0.7439 REMARK 3 S21: 0.0818 S22: 0.3629 S23: -0.1777 REMARK 3 S31: 0.8365 S32: 0.4059 S33: -0.2370 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 12 B 27 REMARK 3 ORIGIN FOR THE GROUP (A): 10.0138 6.7533 22.9552 REMARK 3 T TENSOR REMARK 3 T11: 0.0827 T22: 0.0928 REMARK 3 T33: 0.0119 T12: -0.1295 REMARK 3 T13: -0.0758 T23: 0.1728 REMARK 3 L TENSOR REMARK 3 L11: 5.7675 L22: 1.2949 REMARK 3 L33: 0.5448 L12: 0.2958 REMARK 3 L13: 1.0722 L23: 0.7200 REMARK 3 S TENSOR REMARK 3 S11: -0.4762 S12: 1.0033 S13: 1.0351 REMARK 3 S21: -0.5041 S22: 0.1222 S23: -0.0452 REMARK 3 S31: -0.3943 S32: 0.2710 S33: 0.3540 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 28 B 39 REMARK 3 ORIGIN FOR THE GROUP (A): 9.4490 -5.4996 19.7119 REMARK 3 T TENSOR REMARK 3 T11: -0.0242 T22: 0.2213 REMARK 3 T33: -0.1510 T12: -0.0902 REMARK 3 T13: 0.0388 T23: -0.0477 REMARK 3 L TENSOR REMARK 3 L11: 14.1904 L22: 8.7934 REMARK 3 L33: 3.5255 L12: 1.0203 REMARK 3 L13: 4.2596 L23: 3.8893 REMARK 3 S TENSOR REMARK 3 S11: -0.1776 S12: 1.2401 S13: -0.6352 REMARK 3 S21: -0.6201 S22: 0.0621 S23: -0.0186 REMARK 3 S31: -0.0938 S32: 0.2988 S33: 0.1155 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 40 B 72 REMARK 3 ORIGIN FOR THE GROUP (A): 10.2914 0.1803 38.3077 REMARK 3 T TENSOR REMARK 3 T11: 0.0226 T22: -0.0109 REMARK 3 T33: 0.0687 T12: -0.0125 REMARK 3 T13: -0.0016 T23: 0.0090 REMARK 3 L TENSOR REMARK 3 L11: 2.2914 L22: 0.9188 REMARK 3 L33: 1.0728 L12: 0.1956 REMARK 3 L13: 0.5941 L23: 0.9611 REMARK 3 S TENSOR REMARK 3 S11: -0.1130 S12: -0.0050 S13: 0.0185 REMARK 3 S21: -0.0551 S22: 0.0407 S23: 0.0675 REMARK 3 S31: -0.0285 S32: -0.0231 S33: 0.0723 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 73 B 84 REMARK 3 ORIGIN FOR THE GROUP (A): 8.4894 6.9381 37.7501 REMARK 3 T TENSOR REMARK 3 T11: 0.0342 T22: -0.0310 REMARK 3 T33: 0.0636 T12: -0.0131 REMARK 3 T13: -0.0615 T23: 0.0162 REMARK 3 L TENSOR REMARK 3 L11: 1.1365 L22: 1.9684 REMARK 3 L33: 0.7068 L12: 0.7486 REMARK 3 L13: -0.0431 L23: 0.9916 REMARK 3 S TENSOR REMARK 3 S11: -0.2324 S12: 0.0411 S13: 0.2569 REMARK 3 S21: -0.2544 S22: 0.0427 S23: 0.1618 REMARK 3 S31: -0.2200 S32: -0.0879 S33: 0.1897 REMARK 3 REMARK 3 TLS GROUP : 13 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 85 B 103 REMARK 3 ORIGIN FOR THE GROUP (A): -0.2166 -0.6189 20.3413 REMARK 3 T TENSOR REMARK 3 T11: 0.1006 T22: 0.1117 REMARK 3 T33: 0.0469 T12: -0.0222 REMARK 3 T13: -0.0317 T23: 0.0078 REMARK 3 L TENSOR REMARK 3 L11: 3.2904 L22: 2.3192 REMARK 3 L33: 4.5709 L12: 0.6440 REMARK 3 L13: 1.3543 L23: 1.8429 REMARK 3 S TENSOR REMARK 3 S11: -0.3187 S12: 0.4896 S13: 0.0828 REMARK 3 S21: -0.4292 S22: -0.0020 S23: 0.1910 REMARK 3 S31: -0.3254 S32: 0.0695 S33: 0.3207 REMARK 3 REMARK 3 TLS GROUP : 14 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 104 B 124 REMARK 3 ORIGIN FOR THE GROUP (A): 11.5847 -1.4926 39.8662 REMARK 3 T TENSOR REMARK 3 T11: 0.0286 T22: -0.0016 REMARK 3 T33: 0.0465 T12: -0.0228 REMARK 3 T13: 0.0034 T23: 0.0115 REMARK 3 L TENSOR REMARK 3 L11: 3.0394 L22: 2.3769 REMARK 3 L33: 2.7257 L12: -0.1113 REMARK 3 L13: 0.9038 L23: -0.0312 REMARK 3 S TENSOR REMARK 3 S11: -0.0629 S12: 0.0537 S13: -0.1011 REMARK 3 S21: -0.1153 S22: -0.0033 S23: 0.1639 REMARK 3 S31: 0.0326 S32: -0.0368 S33: 0.0662 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3D8Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000047741. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24530 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07800 REMARK 200 FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.47000 REMARK 200 FOR SHELL : 3.000 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 2G8Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM CITRATE, PH 5.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K 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 50.08050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.21050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.08050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.21050 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 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 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 207 O HOH B 281 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 SER A 16 CB SER A 16 OG 0.294 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 ALA A 19 68.30 165.59 REMARK 500 SER A 21 75.54 17.14 REMARK 500 GLN A 60 -139.53 -97.52 REMARK 500 GLN B 60 -132.88 -104.60 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 FLC A 125 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FLC A 126 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE T3S A 127 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3D8Z RELATED DB: PDB DBREF 3D8Y A 1 124 UNP P61823 RNAS1_BOVIN 27 150 DBREF 3D8Y B 1 124 UNP P61823 RNAS1_BOVIN 27 150 SEQRES 1 A 124 LYS GLU THR ALA ALA ALA LYS PHE GLU ARG GLN HIS MET SEQRES 2 A 124 ASP SER SER THR SER ALA ALA SER SER SER ASN TYR CYS SEQRES 3 A 124 ASN GLN MET MET LYS SER ARG ASN LEU THR LYS ASP ARG SEQRES 4 A 124 CYS LYS PRO VAL ASN THR PHE VAL HIS GLU SER LEU ALA SEQRES 5 A 124 ASP VAL GLN ALA VAL CYS SER GLN LYS ASN VAL ALA CYS SEQRES 6 A 124 LYS ASN GLY GLN THR ASN CYS TYR GLN SER TYR SER THR SEQRES 7 A 124 MET SER 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 ALA ASN LYS SEQRES 9 A 124 HIS ILE ILE VAL ALA CYS GLU GLY ASN PRO TYR VAL PRO SEQRES 10 A 124 VAL HIS PHE ASP ALA SER VAL SEQRES 1 B 124 LYS GLU THR ALA ALA ALA LYS PHE GLU ARG GLN HIS MET SEQRES 2 B 124 ASP SER SER THR SER ALA ALA SER SER SER ASN TYR CYS SEQRES 3 B 124 ASN GLN MET MET LYS SER ARG ASN LEU THR LYS ASP ARG SEQRES 4 B 124 CYS LYS PRO VAL ASN THR PHE VAL HIS GLU SER LEU ALA SEQRES 5 B 124 ASP VAL GLN ALA VAL CYS SER GLN LYS ASN VAL ALA CYS SEQRES 6 B 124 LYS ASN GLY GLN THR ASN CYS TYR GLN SER TYR SER THR SEQRES 7 B 124 MET SER 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 ALA ASN LYS SEQRES 9 B 124 HIS ILE ILE VAL ALA CYS GLU GLY ASN PRO TYR VAL PRO SEQRES 10 B 124 VAL HIS PHE ASP ALA SER VAL HET FLC A 125 13 HET FLC A 126 13 HET T3S A 127 22 HETNAM FLC CITRATE ANION HETNAM T3S 5'-DEOXY-5'-PIPERIDIN-1-YLTHYMIDINE FORMUL 3 FLC 2(C6 H5 O7 3-) FORMUL 5 T3S C15 H23 N3 O4 FORMUL 6 HOH *213(H2 O) HELIX 1 1 THR A 3 MET A 13 1 11 HELIX 2 2 ASN A 24 ARG A 33 1 10 HELIX 3 3 SER A 50 ALA A 56 1 7 HELIX 4 4 VAL A 57 GLN A 60 5 4 HELIX 5 5 THR B 3 MET B 13 1 11 HELIX 6 6 ASN B 24 ARG B 33 1 10 HELIX 7 7 SER B 50 ALA B 56 1 7 HELIX 8 8 VAL B 57 GLN B 60 5 4 SHEET 1 A 5 VAL A 43 VAL A 47 0 SHEET 2 A 5 MET A 79 GLU A 86 -1 O CYS A 84 N ASN A 44 SHEET 3 A 5 TYR A 97 GLU A 111 -1 O THR A 100 N ASP A 83 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 CYS A 84 N ASN A 44 SHEET 3 B 4 TYR A 97 GLU A 111 -1 O THR A 100 N ASP A 83 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 GLU B 111 -1 O THR B 100 N ASP B 83 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 GLU B 111 -1 O THR B 100 N ASP B 83 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 2.04 SSBOND 2 CYS A 40 CYS A 95 1555 1555 2.02 SSBOND 3 CYS A 58 CYS A 110 1555 1555 2.02 SSBOND 4 CYS A 65 CYS A 72 1555 1555 2.03 SSBOND 5 CYS B 26 CYS B 84 1555 1555 2.04 SSBOND 6 CYS B 40 CYS B 95 1555 1555 2.02 SSBOND 7 CYS B 58 CYS B 110 1555 1555 2.05 SSBOND 8 CYS B 65 CYS B 72 1555 1555 2.04 CISPEP 1 TYR A 92 PRO A 93 0 3.92 CISPEP 2 ASN A 113 PRO A 114 0 8.64 CISPEP 3 TYR B 92 PRO B 93 0 6.27 CISPEP 4 ASN B 113 PRO B 114 0 6.28 SITE 1 AC1 7 LYS A 7 GLN A 11 HIS A 12 LYS A 41 SITE 2 AC1 7 HIS A 119 PHE A 120 LYS B 91 SITE 1 AC2 6 LYS A 7 ASN A 34 ASP A 38 ARG A 39 SITE 2 AC2 6 LYS A 41 LYS B 91 SITE 1 AC3 7 HIS A 12 LYS A 41 ASN A 44 THR A 45 SITE 2 AC3 7 LYS A 66 PHE A 120 ASP A 121 CRYST1 100.161 32.421 72.567 90.00 90.90 90.00 C 1 2 1 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 0.009984 0.000000 0.000157 0.00000 SCALE2 0.000000 0.030844 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013782 0.00000