HEADER NUCLEAR PROTEIN 14-OCT-19 6L3Q TITLE CRYSTAL STRUCTURE OF CHAETOMIUM THERMOPHILUM UTP15 C TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: WD_REPEATS_REGION DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHAETOMIUM THERMOPHILUM VAR. THERMOPHILUM DSM SOURCE 3 1495; SOURCE 4 ORGANISM_TAXID: 759272; SOURCE 5 STRAIN: DSM 1495; SOURCE 6 GENE: CTHT_0063870; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS 90S PRERIBOSOME, NUCLEAR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.C.CHEN,K.Q.YE REVDAT 1 15-APR-20 6L3Q 0 JRNL AUTH R.C.CHEN,K.Q.YE JRNL TITL CRYSTAL STRUCTURE OF CHAETOMIUM THERMOPHILUM UTP15 C JRNL TITL 2 TERMINAL DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 20360 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.080 REMARK 3 FREE R VALUE TEST SET COUNT : 2053 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 36.2800 - 6.6511 0.96 1183 123 0.1726 0.1907 REMARK 3 2 6.6511 - 5.2844 1.00 1215 144 0.2065 0.2213 REMARK 3 3 5.2844 - 4.6180 1.00 1223 142 0.1815 0.2201 REMARK 3 4 4.6180 - 4.1964 1.00 1226 136 0.1733 0.1830 REMARK 3 5 4.1964 - 3.8960 1.00 1227 142 0.1691 0.1922 REMARK 3 6 3.8960 - 3.6665 1.00 1224 132 0.1836 0.2091 REMARK 3 7 3.6665 - 3.4831 1.00 1233 134 0.1971 0.3047 REMARK 3 8 3.4831 - 3.3316 1.00 1221 132 0.2189 0.2844 REMARK 3 9 3.3316 - 3.2034 1.00 1236 142 0.2128 0.3065 REMARK 3 10 3.2034 - 3.0929 1.00 1239 140 0.2309 0.3141 REMARK 3 11 3.0929 - 2.9962 1.00 1219 134 0.2345 0.2874 REMARK 3 12 2.9962 - 2.9106 1.00 1205 136 0.2439 0.3194 REMARK 3 13 2.9106 - 2.8340 1.00 1215 134 0.2326 0.2856 REMARK 3 14 2.8340 - 2.7649 1.00 1234 146 0.2584 0.3000 REMARK 3 15 2.7649 - 2.7021 1.00 1207 136 0.2587 0.3614 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.060 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.02 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 : 0.008 2035 REMARK 3 ANGLE : 1.062 2763 REMARK 3 CHIRALITY : 0.071 321 REMARK 3 PLANARITY : 0.005 353 REMARK 3 DIHEDRAL : 14.741 745 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SF FILE CONTAINS FRIEDEL PAIRS UNDER REMARK 3 I/F_MINUS AND I/F_PLUS COLUMNS. REMARK 4 REMARK 4 6L3Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1300012683. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0-8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20360 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 21.30 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.9300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.75 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 17.95 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M MGSO4, 0.1M MES, PH 6.5, REMARK 280 EVAPORATION, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.38733 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 19.69367 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 19.69367 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 39.38733 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: 2170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 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 SER A 418 REMARK 465 PRO A 419 REMARK 465 LYS A 420 REMARK 465 THR A 543 REMARK 465 GLY A 544 REMARK 465 GLY A 545 REMARK 465 MSE A 546 REMARK 465 VAL A 547 REMARK 465 GLU A 548 REMARK 465 SER A 549 REMARK 465 LEU A 550 REMARK 465 MSE A 551 REMARK 465 MSE A 552 REMARK 465 SER A 553 REMARK 465 VAL A 554 REMARK 465 GLU A 555 REMARK 465 ALA A 556 REMARK 465 GLN A 557 REMARK 465 SER B 418 REMARK 465 PRO B 419 REMARK 465 LYS B 420 REMARK 465 SER B 553 REMARK 465 VAL B 554 REMARK 465 GLU B 555 REMARK 465 ALA B 556 REMARK 465 GLN B 557 DBREF 6L3Q A 419 557 UNP G0SEI5 G0SEI5_CHATD 419 557 DBREF 6L3Q B 419 557 UNP G0SEI5 G0SEI5_CHATD 419 557 SEQADV 6L3Q SER A 418 UNP G0SEI5 EXPRESSION TAG SEQADV 6L3Q SER B 418 UNP G0SEI5 EXPRESSION TAG SEQRES 1 A 140 SER PRO LYS LEU LYS PRO TRP GLN LYS ALA PHE ARG GLN SEQRES 2 A 140 GLY ARG TYR ALA ALA ALA VAL ASP ASP VAL LEU ASN THR SEQRES 3 A 140 THR ALA PRO SER TYR ASP PRO VAL ILE ALA LEU THR LEU SEQRES 4 A 140 LEU THR ALA LEU ARG HIS ARG SER ALA LEU ARG GLU ALA SEQRES 5 A 140 LEU GLN GLY ARG ASP GLU LEU SER VAL ILE ASN ILE LEU SEQRES 6 A 140 ARG TRP ALA GLY LYS TYR VAL ALA ASP PRO ARG TYR ARG SEQRES 7 A 140 SER ILE CYS VAL ASP VAL ALA PHE HIS LEU ILE ASP LEU SEQRES 8 A 140 TYR ALA GLU HIS VAL GLY GLY SER ALA GLU LEU ALA THR SEQRES 9 A 140 GLN PHE GLN GLN LEU LEU ALA LYS VAL ASN ARG GLU VAL SEQRES 10 A 140 GLU LYS ALA GLU LEU ALA ILE VAL THR GLY GLY MSE VAL SEQRES 11 A 140 GLU SER LEU MSE MSE SER VAL GLU ALA GLN SEQRES 1 B 140 SER PRO LYS LEU LYS PRO TRP GLN LYS ALA PHE ARG GLN SEQRES 2 B 140 GLY ARG TYR ALA ALA ALA VAL ASP ASP VAL LEU ASN THR SEQRES 3 B 140 THR ALA PRO SER TYR ASP PRO VAL ILE ALA LEU THR LEU SEQRES 4 B 140 LEU THR ALA LEU ARG HIS ARG SER ALA LEU ARG GLU ALA SEQRES 5 B 140 LEU GLN GLY ARG ASP GLU LEU SER VAL ILE ASN ILE LEU SEQRES 6 B 140 ARG TRP ALA GLY LYS TYR VAL ALA ASP PRO ARG TYR ARG SEQRES 7 B 140 SER ILE CYS VAL ASP VAL ALA PHE HIS LEU ILE ASP LEU SEQRES 8 B 140 TYR ALA GLU HIS VAL GLY GLY SER ALA GLU LEU ALA THR SEQRES 9 B 140 GLN PHE GLN GLN LEU LEU ALA LYS VAL ASN ARG GLU VAL SEQRES 10 B 140 GLU LYS ALA GLU LEU ALA ILE VAL THR GLY GLY MSE VAL SEQRES 11 B 140 GLU SER LEU MSE MSE SER VAL GLU ALA GLN MODRES 6L3Q MSE B 546 MET MODIFIED RESIDUE MODRES 6L3Q MSE B 551 MET MODIFIED RESIDUE MODRES 6L3Q MSE B 552 MET MODIFIED RESIDUE HET MSE B 546 8 HET MSE B 551 8 HET MSE B 552 8 HETNAM MSE SELENOMETHIONINE FORMUL 2 MSE 3(C5 H11 N O2 SE) FORMUL 3 HOH *20(H2 O) HELIX 1 AA1 LYS A 422 GLN A 430 1 9 HELIX 2 AA2 ARG A 432 LEU A 441 1 10 HELIX 3 AA3 ASP A 449 ARG A 463 1 15 HELIX 4 AA4 ALA A 465 GLN A 471 1 7 HELIX 5 AA5 ASP A 474 LYS A 487 1 14 HELIX 6 AA6 TYR A 494 ALA A 510 1 17 HELIX 7 AA7 GLU A 511 VAL A 513 5 3 HELIX 8 AA8 SER A 516 VAL A 542 1 27 HELIX 9 AA9 LYS B 422 GLN B 430 1 9 HELIX 10 AB1 ARG B 432 LEU B 441 1 10 HELIX 11 AB2 ASP B 449 ARG B 463 1 15 HELIX 12 AB3 ALA B 465 GLN B 471 1 7 HELIX 13 AB4 ASP B 474 VAL B 489 1 16 HELIX 14 AB5 TYR B 494 ALA B 510 1 17 HELIX 15 AB6 ALA B 517 MSE B 551 1 35 LINK C GLY B 545 N MSE B 546 1555 1555 1.33 LINK C MSE B 546 N VAL B 547 1555 1555 1.33 LINK C LEU B 550 N MSE B 551 1555 1555 1.33 LINK C MSE B 551 N MSE B 552 1555 1555 1.33 CRYST1 106.188 106.188 59.081 90.00 90.00 120.00 P 32 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 0.009417 0.005437 0.000000 0.00000 SCALE2 0.000000 0.010874 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016926 0.00000