HEADER RIBOSOMAL PROTEIN 15-JUN-20 6ZDT TITLE CRYSTAL STRUCTURE OF EUKARYOTIC FIBRILLARIN WITH NOP56 N-TERMINAL TITLE 2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RRNA 2'-O-METHYLTRANSFERASE FIBRILLARIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NOP1SHORT; COMPND 5 SYNONYM: HISTONE-GLUTAMINE METHYLTRANSFERASE,U3 SMALL NUCLEOLAR RNA- COMPND 6 ASSOCIATED PROTEIN NOP1,U3 SNORNA-ASSOCIATED PROTEIN NOP1; COMPND 7 EC: 2.1.1.-; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: CYSTEINE 314 WAS FOUND TO BE OXIDIZED.; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: NUCLEOLAR PROTEIN 56; COMPND 12 CHAIN: B; COMPND 13 FRAGMENT: 56NTD; COMPND 14 SYNONYM: RIBOSOME BIOSYNTHESIS PROTEIN SIK1,SUPPRESSOR OF I KAPPA B COMPND 15 PROTEIN 1; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 ATCC: 204508; SOURCE 6 GENE: NOP1, LOT3, YDL014W, D2870; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PROKARYOTIC EXPRESSION VECTOR; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETM11; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 13 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 14 ORGANISM_TAXID: 4932; SOURCE 15 ATCC: 204508; SOURCE 16 GENE: NOP56, SIK1, YLR197W, L8167.9; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PROKARYOTIC EXPRESSION VECTOR; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PETM11 KEYWDS 2'-O-METHYLATION, METHYLTRANSFERASE, BOX C/D SNORNP ENZYME, RIBOSOME KEYWDS 2 BIOGENESIS, RIBOSOMAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.HOEFLER,P.LUKAT,T.CARLOMAGNO,W.BLANKENFELDT REVDAT 4 13-NOV-24 6ZDT 1 REMARK REVDAT 3 24-JAN-24 6ZDT 1 REMARK REVDAT 2 31-MAR-21 6ZDT 1 JRNL REVDAT 1 03-FEB-21 6ZDT 0 JRNL AUTH S.HOFLER,P.LUKAT,W.BLANKENFELDT,T.CARLOMAGNO JRNL TITL HIGH-RESOLUTION STRUCTURE OF EUKARYOTIC FIBRILLARIN JRNL TITL 2 INTERACTING WITH NOP56 AMINO-TERMINAL DOMAIN. JRNL REF RNA V. 27 496 2021 JRNL REFN ESSN 1469-9001 JRNL PMID 33483369 JRNL DOI 10.1261/RNA.077396.120 REMARK 2 REMARK 2 RESOLUTION. 1.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18RC4_3812 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 44211 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 2184 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.8300 - 4.3000 1.00 2835 138 0.1681 0.2156 REMARK 3 2 4.3000 - 3.4100 1.00 2688 152 0.1444 0.1868 REMARK 3 3 3.4100 - 2.9800 1.00 2625 167 0.1652 0.2056 REMARK 3 4 2.9800 - 2.7100 1.00 2620 150 0.1675 0.1965 REMARK 3 5 2.7100 - 2.5200 1.00 2625 151 0.1586 0.1959 REMARK 3 6 2.5200 - 2.3700 1.00 2638 122 0.1555 0.1930 REMARK 3 7 2.3700 - 2.2500 1.00 2626 130 0.1501 0.2010 REMARK 3 8 2.2500 - 2.1500 1.00 2614 131 0.1507 0.2109 REMARK 3 9 2.1500 - 2.0700 1.00 2581 139 0.1619 0.2111 REMARK 3 10 2.0700 - 2.0000 1.00 2611 149 0.1681 0.2176 REMARK 3 11 2.0000 - 1.9300 1.00 2576 129 0.1730 0.2025 REMARK 3 12 1.9300 - 1.8800 1.00 2588 119 0.1746 0.2353 REMARK 3 13 1.8800 - 1.8300 1.00 2617 137 0.1846 0.2292 REMARK 3 14 1.8300 - 1.7900 1.00 2608 129 0.1911 0.2335 REMARK 3 15 1.7900 - 1.7400 1.00 2588 109 0.2015 0.2411 REMARK 3 16 1.7400 - 1.7100 1.00 2587 132 0.2131 0.2277 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.157 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.456 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.56 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 3198 REMARK 3 ANGLE : 0.686 4337 REMARK 3 CHIRALITY : 0.052 490 REMARK 3 PLANARITY : 0.004 567 REMARK 3 DIHEDRAL : 19.400 1232 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 13 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 96 THROUGH 145 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.6585 -15.1701 11.9827 REMARK 3 T TENSOR REMARK 3 T11: 0.1769 T22: 0.1868 REMARK 3 T33: 0.2053 T12: 0.0228 REMARK 3 T13: 0.0140 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: 1.3667 L22: 1.5016 REMARK 3 L33: 1.4009 L12: 0.6048 REMARK 3 L13: 1.1364 L23: -0.1892 REMARK 3 S TENSOR REMARK 3 S11: 0.0909 S12: -0.0155 S13: -0.1223 REMARK 3 S21: -0.1097 S22: 0.0521 S23: -0.0689 REMARK 3 S31: 0.2034 S32: 0.0295 S33: 0.0145 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 146 THROUGH 165 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.8267 3.4863 23.5292 REMARK 3 T TENSOR REMARK 3 T11: 0.1869 T22: 0.2278 REMARK 3 T33: 0.2243 T12: -0.0087 REMARK 3 T13: 0.0053 T23: -0.0050 REMARK 3 L TENSOR REMARK 3 L11: 0.2085 L22: 0.5577 REMARK 3 L33: 0.9552 L12: 0.0065 REMARK 3 L13: -0.3662 L23: 0.4209 REMARK 3 S TENSOR REMARK 3 S11: 0.0464 S12: -0.2913 S13: 0.1854 REMARK 3 S21: 0.2832 S22: -0.0696 S23: -0.0648 REMARK 3 S31: -0.0466 S32: 0.0595 S33: 0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 86 THROUGH 109 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.7942 27.7995 6.3778 REMARK 3 T TENSOR REMARK 3 T11: 0.3308 T22: 0.2465 REMARK 3 T33: 0.3865 T12: 0.0638 REMARK 3 T13: -0.0590 T23: 0.0265 REMARK 3 L TENSOR REMARK 3 L11: 0.5425 L22: 0.3088 REMARK 3 L33: 0.4964 L12: -0.2459 REMARK 3 L13: 0.1006 L23: 0.2708 REMARK 3 S TENSOR REMARK 3 S11: -0.0789 S12: -0.1031 S13: 0.4843 REMARK 3 S21: -0.1901 S22: -0.0499 S23: 0.5022 REMARK 3 S31: -0.3245 S32: -0.4445 S33: -0.0204 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 110 THROUGH 168 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.7399 23.2406 10.9103 REMARK 3 T TENSOR REMARK 3 T11: 0.2604 T22: 0.2065 REMARK 3 T33: 0.2274 T12: 0.0087 REMARK 3 T13: -0.0041 T23: -0.0205 REMARK 3 L TENSOR REMARK 3 L11: 0.8640 L22: 1.0400 REMARK 3 L33: 0.6733 L12: 0.1478 REMARK 3 L13: 0.2619 L23: -0.6029 REMARK 3 S TENSOR REMARK 3 S11: -0.0806 S12: -0.0915 S13: 0.2075 REMARK 3 S21: 0.0185 S22: 0.0832 S23: 0.0444 REMARK 3 S31: -0.2518 S32: -0.1034 S33: 0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 169 THROUGH 233 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.9859 9.2499 15.1097 REMARK 3 T TENSOR REMARK 3 T11: 0.1449 T22: 0.1933 REMARK 3 T33: 0.1666 T12: -0.0036 REMARK 3 T13: 0.0080 T23: -0.0067 REMARK 3 L TENSOR REMARK 3 L11: 0.7625 L22: 1.3417 REMARK 3 L33: 0.5356 L12: -0.0826 REMARK 3 L13: -0.0235 L23: 0.0103 REMARK 3 S TENSOR REMARK 3 S11: -0.0441 S12: -0.0416 S13: 0.1154 REMARK 3 S21: -0.0066 S22: 0.0512 S23: -0.1272 REMARK 3 S31: -0.0156 S32: 0.0162 S33: 0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 234 THROUGH 260 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.0688 3.1857 3.9075 REMARK 3 T TENSOR REMARK 3 T11: 0.2289 T22: 0.2372 REMARK 3 T33: 0.2309 T12: -0.0201 REMARK 3 T13: 0.0580 T23: -0.0007 REMARK 3 L TENSOR REMARK 3 L11: 0.2045 L22: 0.4513 REMARK 3 L33: 0.6475 L12: -0.0526 REMARK 3 L13: 0.3013 L23: 0.0658 REMARK 3 S TENSOR REMARK 3 S11: 0.0008 S12: -0.0234 S13: 0.1380 REMARK 3 S21: -0.2463 S22: 0.0034 S23: -0.2199 REMARK 3 S31: -0.0124 S32: 0.2133 S33: 0.0000 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 261 THROUGH 281 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.5034 8.5006 -2.2073 REMARK 3 T TENSOR REMARK 3 T11: 0.3192 T22: 0.2620 REMARK 3 T33: 0.2505 T12: -0.0663 REMARK 3 T13: 0.0598 T23: -0.0044 REMARK 3 L TENSOR REMARK 3 L11: 0.0675 L22: 0.4097 REMARK 3 L33: 0.4883 L12: -0.0927 REMARK 3 L13: -0.0278 L23: 0.4221 REMARK 3 S TENSOR REMARK 3 S11: -0.3017 S12: 0.3969 S13: -0.1445 REMARK 3 S21: -0.5689 S22: 0.2784 S23: -0.3569 REMARK 3 S31: -0.0658 S32: 0.0136 S33: -0.0042 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 282 THROUGH 296 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.6501 6.1379 -10.2856 REMARK 3 T TENSOR REMARK 3 T11: 0.5128 T22: 0.3979 REMARK 3 T33: 0.2925 T12: -0.0934 REMARK 3 T13: 0.1432 T23: -0.0193 REMARK 3 L TENSOR REMARK 3 L11: 0.0635 L22: 0.2542 REMARK 3 L33: 0.0892 L12: -0.0619 REMARK 3 L13: 0.0112 L23: 0.1154 REMARK 3 S TENSOR REMARK 3 S11: -0.4699 S12: 0.0316 S13: 0.0004 REMARK 3 S21: -0.7454 S22: 0.3056 S23: -0.4990 REMARK 3 S31: -0.0167 S32: 0.1304 S33: -0.0953 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 297 THROUGH 326 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.7630 10.3373 -5.9804 REMARK 3 T TENSOR REMARK 3 T11: 0.4098 T22: 0.2764 REMARK 3 T33: 0.2054 T12: -0.0802 REMARK 3 T13: 0.0230 T23: 0.0237 REMARK 3 L TENSOR REMARK 3 L11: 0.4681 L22: 1.0701 REMARK 3 L33: 1.0716 L12: -0.5226 REMARK 3 L13: -0.5574 L23: 0.1567 REMARK 3 S TENSOR REMARK 3 S11: -0.1383 S12: 0.2038 S13: -0.0292 REMARK 3 S21: -1.1464 S22: 0.0089 S23: -0.2935 REMARK 3 S31: 0.0721 S32: 0.2011 S33: 0.0273 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID -1 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.8372 -19.2222 10.0355 REMARK 3 T TENSOR REMARK 3 T11: 0.2214 T22: 0.1774 REMARK 3 T33: 0.2010 T12: 0.0149 REMARK 3 T13: -0.0012 T23: -0.0183 REMARK 3 L TENSOR REMARK 3 L11: 0.4031 L22: 0.4682 REMARK 3 L33: 0.3727 L12: -0.2981 REMARK 3 L13: 0.1733 L23: -0.2985 REMARK 3 S TENSOR REMARK 3 S11: 0.0475 S12: 0.0483 S13: -0.1653 REMARK 3 S21: -0.0831 S22: 0.0064 S23: 0.0305 REMARK 3 S31: 0.1239 S32: 0.1318 S33: 0.0001 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 27 THROUGH 47 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.7919 -14.1003 0.6385 REMARK 3 T TENSOR REMARK 3 T11: 0.3568 T22: 0.3304 REMARK 3 T33: 0.2731 T12: -0.0150 REMARK 3 T13: 0.0008 T23: -0.0561 REMARK 3 L TENSOR REMARK 3 L11: 0.1300 L22: 0.8448 REMARK 3 L33: 0.2224 L12: -0.0597 REMARK 3 L13: -0.0739 L23: 0.0039 REMARK 3 S TENSOR REMARK 3 S11: -0.0349 S12: 0.3997 S13: -0.1979 REMARK 3 S21: -0.8238 S22: 0.1673 S23: 0.4117 REMARK 3 S31: 0.2662 S32: -0.0858 S33: 0.0444 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 48 THROUGH 58 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.1488 -14.9065 22.3478 REMARK 3 T TENSOR REMARK 3 T11: 0.2575 T22: 0.2302 REMARK 3 T33: 0.1966 T12: -0.0340 REMARK 3 T13: 0.0482 T23: 0.0021 REMARK 3 L TENSOR REMARK 3 L11: 0.9477 L22: 0.2195 REMARK 3 L33: 0.6616 L12: 0.0537 REMARK 3 L13: 0.4610 L23: 0.0605 REMARK 3 S TENSOR REMARK 3 S11: 0.4349 S12: 0.0185 S13: -0.3331 REMARK 3 S21: 0.2306 S22: -0.0184 S23: -0.0077 REMARK 3 S31: 0.3999 S32: -0.3373 S33: 0.0724 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 59 THROUGH 95 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.9608 -19.2503 21.0490 REMARK 3 T TENSOR REMARK 3 T11: 0.2592 T22: 0.1964 REMARK 3 T33: 0.2261 T12: 0.0097 REMARK 3 T13: -0.0187 T23: 0.0020 REMARK 3 L TENSOR REMARK 3 L11: 0.7525 L22: 0.6825 REMARK 3 L33: 1.2698 L12: -0.4299 REMARK 3 L13: 0.0871 L23: -0.5475 REMARK 3 S TENSOR REMARK 3 S11: 0.0742 S12: 0.0167 S13: -0.2076 REMARK 3 S21: 0.2413 S22: 0.0778 S23: -0.1175 REMARK 3 S31: 0.3392 S32: 0.0967 S33: 0.0002 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6ZDT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1292109231. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-SEP-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033198 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44280 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.710 REMARK 200 RESOLUTION RANGE LOW (A) : 48.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.71 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.10 REMARK 200 R MERGE FOR SHELL (I) : 1.01600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 2IPX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M LICL, 0.1 M HEPES, 19 % PEG 400, REMARK 280 CRYO: 10% 2,3-BUTANEDIOL, PH 7.8, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 285K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 34.50200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 59.14300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.50200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 59.14300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 443 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 480 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 GLY A 80 REMARK 465 ALA A 81 REMARK 465 MET A 82 REMARK 465 GLY A 83 REMARK 465 ALA A 84 REMARK 465 LYS A 85 REMARK 465 PRO A 128 REMARK 465 SER A 129 REMARK 465 LYS A 130 REMARK 465 GLU A 131 REMARK 465 ASP A 132 REMARK 465 GLY A 133 REMARK 465 ASP A 277 REMARK 465 SER A 278 REMARK 465 THR A 279 REMARK 465 VAL A 280 REMARK 465 LYS A 327 REMARK 465 LEU B 142 REMARK 465 SER B 166 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 102 CG CD CE NZ REMARK 470 GLU A 126 CG CD OE1 OE2 REMARK 470 GLU A 127 CG CD OE1 OE2 REMARK 470 LYS A 138 CG CD CE NZ REMARK 470 LYS A 272 CG CD CE NZ REMARK 470 GLU A 283 CG CD OE1 OE2 REMARK 470 ARG A 311 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 326 CG CD CE NZ REMARK 470 MET B 1 CG SD CE REMARK 470 LYS B 32 CG CD CE NZ 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 PHE B 139 O HOH B 201 1.93 REMARK 500 OD CSO A 314 O HOH A 401 2.01 REMARK 500 O HOH B 257 O HOH B 348 2.02 REMARK 500 O HOH B 204 O HOH B 289 2.05 REMARK 500 O HOH A 405 O HOH A 476 2.05 REMARK 500 OD1 ASN B 95 O HOH B 202 2.08 REMARK 500 O HOH A 539 O HOH A 543 2.16 REMARK 500 O HOH A 588 O HOH B 328 2.17 REMARK 500 O HOH A 483 O HOH A 545 2.18 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 CSO A 314 O - C - N ANGL. DEV. = -13.9 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 TYR A 118 36.73 -149.41 REMARK 500 PHE A 163 -0.78 64.29 REMARK 500 ALA A 176 -133.98 54.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 CSO A 314 25.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 593 DISTANCE = 5.96 ANGSTROMS DBREF 6ZDT A 83 327 UNP P15646 FBRL_YEAST 83 327 DBREF 6ZDT B 1 166 UNP Q12460 NOP56_YEAST 1 166 SEQADV 6ZDT GLY A 80 UNP P15646 EXPRESSION TAG SEQADV 6ZDT ALA A 81 UNP P15646 EXPRESSION TAG SEQADV 6ZDT MET A 82 UNP P15646 EXPRESSION TAG SEQADV 6ZDT GLY B -1 UNP Q12460 EXPRESSION TAG SEQADV 6ZDT ALA B 0 UNP Q12460 EXPRESSION TAG SEQRES 1 A 248 GLY ALA MET GLY ALA LYS VAL VAL ILE GLU PRO HIS ARG SEQRES 2 A 248 HIS ALA GLY VAL TYR ILE ALA ARG GLY LYS GLU ASP LEU SEQRES 3 A 248 LEU VAL THR LYS ASN MET ALA PRO GLY GLU SER VAL TYR SEQRES 4 A 248 GLY GLU LYS ARG ILE SER VAL GLU GLU PRO SER LYS GLU SEQRES 5 A 248 ASP GLY VAL PRO PRO THR LYS VAL GLU TYR ARG VAL TRP SEQRES 6 A 248 ASN PRO PHE ARG SER LYS LEU ALA ALA GLY ILE MET GLY SEQRES 7 A 248 GLY LEU ASP GLU LEU PHE ILE ALA PRO GLY LYS LYS VAL SEQRES 8 A 248 LEU TYR LEU GLY ALA ALA SER GLY THR SER VAL SER HIS SEQRES 9 A 248 VAL SER ASP VAL VAL GLY PRO GLU GLY VAL VAL TYR ALA SEQRES 10 A 248 VAL GLU PHE SER HIS ARG PRO GLY ARG GLU LEU ILE SER SEQRES 11 A 248 MET ALA LYS LYS ARG PRO ASN ILE ILE PRO ILE ILE GLU SEQRES 12 A 248 ASP ALA ARG HIS PRO GLN LYS TYR ARG MET LEU ILE GLY SEQRES 13 A 248 MET VAL ASP CYS VAL PHE ALA ASP VAL ALA GLN PRO ASP SEQRES 14 A 248 GLN ALA ARG ILE ILE ALA LEU ASN SER HIS MET PHE LEU SEQRES 15 A 248 LYS ASP GLN GLY GLY VAL VAL ILE SER ILE LYS ALA ASN SEQRES 16 A 248 CYS ILE ASP SER THR VAL ASP ALA GLU THR VAL PHE ALA SEQRES 17 A 248 ARG GLU VAL GLN LYS LEU ARG GLU GLU ARG ILE LYS PRO SEQRES 18 A 248 LEU GLU GLN LEU THR LEU GLU PRO TYR GLU ARG ASP HIS SEQRES 19 A 248 CSO ILE VAL VAL GLY ARG TYR MET ARG SER GLY LEU LYS SEQRES 20 A 248 LYS SEQRES 1 B 168 GLY ALA MET ALA PRO ILE GLU TYR LEU LEU PHE GLU GLU SEQRES 2 B 168 PRO THR GLY TYR ALA VAL PHE LYS VAL LYS LEU GLN GLN SEQRES 3 B 168 ASP ASP ILE GLY SER ARG LEU LYS GLU VAL GLN GLU GLN SEQRES 4 B 168 ILE ASN ASP PHE GLY ALA PHE THR LYS LEU ILE GLU LEU SEQRES 5 B 168 VAL SER PHE ALA PRO PHE LYS GLY ALA ALA GLU ALA LEU SEQRES 6 B 168 GLU ASN ALA ASN ASP ILE SER GLU GLY LEU VAL SER GLU SEQRES 7 B 168 SER LEU LYS ALA ILE LEU ASP LEU ASN LEU PRO LYS ALA SEQRES 8 B 168 SER SER LYS LYS LYS ASN ILE THR LEU ALA ILE SER ASP SEQRES 9 B 168 LYS ASN LEU GLY PRO SER ILE LYS GLU GLU PHE PRO TYR SEQRES 10 B 168 VAL ASP CYS ILE SER ASN GLU LEU ALA GLN ASP LEU ILE SEQRES 11 B 168 ARG GLY VAL ARG LEU HIS GLY GLU LYS LEU PHE LYS GLY SEQRES 12 B 168 LEU GLN SER GLY ASP LEU GLU ARG ALA GLN LEU GLY LEU SEQRES 13 B 168 GLY HIS ALA TYR SER ARG ALA LYS VAL LYS PHE SER MODRES 6ZDT CSO A 314 CYS MODIFIED RESIDUE HET CSO A 314 11 HETNAM CSO S-HYDROXYCYSTEINE FORMUL 1 CSO C3 H7 N O3 S FORMUL 3 HOH *367(H2 O) HELIX 1 AA1 SER A 149 GLY A 158 1 10 HELIX 2 AA2 GLY A 178 GLY A 189 1 12 HELIX 3 AA3 SER A 200 LYS A 212 1 13 HELIX 4 AA4 HIS A 226 ILE A 234 5 9 HELIX 5 AA5 ASP A 248 PHE A 260 1 13 HELIX 6 AA6 ASN A 274 ILE A 276 5 3 HELIX 7 AA7 ALA A 282 GLU A 296 1 15 HELIX 8 AA8 ASP B 26 SER B 29 5 4 HELIX 9 AA9 ARG B 30 ASN B 39 1 10 HELIX 10 AB1 ASP B 40 THR B 45 1 6 HELIX 11 AB2 GLY B 58 GLU B 71 1 14 HELIX 12 AB3 SER B 75 LEU B 86 1 12 HELIX 13 AB4 ASP B 102 ASN B 104 5 3 HELIX 14 AB5 LEU B 105 PHE B 113 1 9 HELIX 15 AB6 ASN B 121 GLY B 135 1 15 HELIX 16 AB7 GLU B 136 PHE B 139 5 4 HELIX 17 AB8 GLY B 145 LYS B 164 1 20 SHEET 1 AA1 5 VAL A 87 PRO A 90 0 SHEET 2 AA1 5 VAL A 96 ARG A 100 -1 O ARG A 100 N VAL A 87 SHEET 3 AA1 5 ASP A 104 LYS A 109 -1 O LEU A 105 N ALA A 99 SHEET 4 AA1 5 LYS A 138 VAL A 143 -1 O ARG A 142 N THR A 108 SHEET 5 AA1 5 ARG A 122 GLU A 126 -1 N ILE A 123 O TYR A 141 SHEET 1 AA2 7 ILE A 217 ILE A 221 0 SHEET 2 AA2 7 VAL A 193 GLU A 198 1 N ALA A 196 O ILE A 220 SHEET 3 AA2 7 LYS A 169 LEU A 173 1 N TYR A 172 O TYR A 195 SHEET 4 AA2 7 VAL A 237 ALA A 242 1 O PHE A 241 N LEU A 173 SHEET 5 AA2 7 LEU A 261 LYS A 272 1 O LYS A 262 N VAL A 237 SHEET 6 AA2 7 HIS A 313 TYR A 320 -1 O TYR A 320 N GLY A 265 SHEET 7 AA2 7 ILE A 298 THR A 305 -1 N LEU A 301 O VAL A 317 SHEET 1 AA3 5 ILE B 48 PRO B 55 0 SHEET 2 AA3 5 GLY B 14 VAL B 20 -1 N LYS B 19 O GLU B 49 SHEET 3 AA3 5 TYR B 6 GLU B 11 -1 N LEU B 7 O PHE B 18 SHEET 4 AA3 5 ILE B 96 ALA B 99 1 O ALA B 99 N TYR B 6 SHEET 5 AA3 5 VAL B 116 ILE B 119 1 O ASP B 117 N ILE B 96 LINK C HIS A 313 N CSO A 314 1555 1555 1.32 LINK C CSO A 314 N ILE A 315 1555 1555 1.33 CISPEP 1 GLU A 307 PRO A 308 0 3.76 CRYST1 69.004 118.286 48.828 90.00 90.00 90.00 P 21 21 2 4 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 0.014492 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008454 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020480 0.00000