HEADER RNA BINDING PROTEIN 12-AUG-19 6TZN TITLE STRUCTURE OF S. POMBE TELOMERASE ACCESSORY PROTEIN POF8 C-TERMINAL TITLE 2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN POF8; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RNA RECOGNITION MOTIF 2 - RRM2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE (STRAIN 972 / ATCC SOURCE 3 24843); SOURCE 4 ORGANISM_COMMON: FISSION YEAST; SOURCE 5 ORGANISM_TAXID: 284812; SOURCE 6 STRAIN: 972 / ATCC 24843; SOURCE 7 GENE: POF8, SPAC17G6.17; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET SUMO KEYWDS RRM, LARP7, RNA BINDING PROTEIN, LSM BINDING EXPDTA X-RAY DIFFRACTION AUTHOR R.S.BASU,D.CASCIO,C.D.EICHHORN,J.FEIGON REVDAT 4 13-MAR-24 6TZN 1 JRNL REVDAT 3 14-JUL-21 6TZN 1 JRNL REVDAT 2 18-NOV-20 6TZN 1 JRNL REVDAT 1 19-AUG-20 6TZN 0 JRNL AUTH R.BASU,C.D.EICHHORN,R.CHENG,R.D.PETERSON,J.FEIGON JRNL TITL STRUCTURE OF S. POMBE TELOMERASE PROTEIN POF8 C-TERMINAL JRNL TITL 2 DOMAIN IS AN XRRM CONSERVED AMONG LARP7 PROTEINS. JRNL REF RNA BIOL. V. 18 1181 2021 JRNL REFN ESSN 1555-8584 JRNL PMID 33131423 JRNL DOI 10.1080/15476286.2020.1836891 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.S.BASU,C.D.EICHHORN,R.C.CHENG,J.FEIGON REMARK 1 TITL STRUCTURE OF S. POMBE TELOMERASE ACCESSORY PROTEIN POF8 REMARK 1 TITL 2 C-TERMINAL DOMAIN IS CONSERVED AMONG LARP7 PROTEINS REMARK 1 REF BIORXIV 2019 REMARK 1 REFN ISSN 2692-8205 REMARK 1 DOI 10.1101/739532 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 29647 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2964 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 49.6700 - 3.7245 0.95 1336 149 0.1638 0.1881 REMARK 3 2 3.7245 - 2.9563 0.97 1275 141 0.1762 0.1861 REMARK 3 3 2.9563 - 2.5827 0.98 1287 143 0.1808 0.2060 REMARK 3 4 2.5827 - 2.3465 0.99 1275 142 0.1715 0.2017 REMARK 3 5 2.3465 - 2.1783 0.98 1270 141 0.1557 0.1789 REMARK 3 6 2.1783 - 2.0499 1.00 1271 142 0.1528 0.2036 REMARK 3 7 2.0499 - 1.9472 1.00 1284 142 0.1524 0.1929 REMARK 3 8 1.9472 - 1.8625 1.00 1286 143 0.1488 0.1930 REMARK 3 9 1.8625 - 1.7908 0.99 1254 139 0.1451 0.1978 REMARK 3 10 1.7908 - 1.7290 1.00 1289 144 0.1430 0.1933 REMARK 3 11 1.7290 - 1.6749 1.00 1260 140 0.1391 0.1760 REMARK 3 12 1.6749 - 1.6270 1.00 1272 141 0.1326 0.1517 REMARK 3 13 1.6270 - 1.5842 1.00 1250 139 0.1267 0.1900 REMARK 3 14 1.5842 - 1.5455 1.00 1257 139 0.1385 0.1957 REMARK 3 15 1.5455 - 1.5104 1.00 1254 138 0.1362 0.1733 REMARK 3 16 1.5104 - 1.4783 1.00 1267 141 0.1351 0.1971 REMARK 3 17 1.4783 - 1.4487 1.00 1273 142 0.1581 0.2050 REMARK 3 18 1.4487 - 1.4213 1.00 1263 140 0.1776 0.2570 REMARK 3 19 1.4213 - 1.3960 1.00 1228 137 0.1861 0.2628 REMARK 3 20 1.3960 - 1.3723 1.00 1277 142 0.2148 0.2746 REMARK 3 21 1.3723 - 1.3502 0.98 1255 139 0.2615 0.3088 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.91 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 : 0.005 960 REMARK 3 ANGLE : 0.713 1298 REMARK 3 CHIRALITY : 0.085 143 REMARK 3 PLANARITY : 0.004 167 REMARK 3 DIHEDRAL : 2.531 590 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -16.2144 18.3329 -8.7570 REMARK 3 T TENSOR REMARK 3 T11: 0.1383 T22: 0.1235 REMARK 3 T33: 0.1340 T12: -0.0118 REMARK 3 T13: 0.0101 T23: 0.0095 REMARK 3 L TENSOR REMARK 3 L11: 3.7672 L22: 1.4048 REMARK 3 L33: 1.9469 L12: -0.3258 REMARK 3 L13: 0.3500 L23: -0.1815 REMARK 3 S TENSOR REMARK 3 S11: -0.0428 S12: -0.0845 S13: -0.0855 REMARK 3 S21: 0.0485 S22: 0.0040 S23: -0.0571 REMARK 3 S31: 0.0348 S32: 0.0461 S33: 0.0301 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 6TZN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1000243194. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-AUG-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29661 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 49.675 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 4.590 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.24 REMARK 200 R MERGE FOR SHELL (I) : 0.74100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.950 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHASER 1.3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG 3350, 0.1 M NANO3, 0.1 M TRIS, REMARK 280 PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 23.43333 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 46.86667 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 46.86667 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 23.43333 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL 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 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 LYS A 282 REMARK 465 ASP A 283 REMARK 465 GLU A 284 REMARK 465 ASP A 285 REMARK 465 ASN A 286 REMARK 465 LEU A 287 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 ASP A 288 CB CG OD1 OD2 REMARK 470 LYS A 291 CD CE NZ REMARK 470 ASN A 323 CG OD1 ND2 REMARK 470 ILE A 324 CG2 REMARK 470 GLU A 327 CD OE1 OE2 REMARK 470 ARG A 334 CD NE CZ NH1 NH2 REMARK 470 LYS A 363 CG CD CE NZ REMARK 470 LYS A 376 CD CE NZ REMARK 470 LYS A 394 CE NZ REMARK 470 LYS A 402 CG CD CE NZ 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 ASN A 292 31.84 71.45 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 NO3 A 501 DBREF 6TZN A 282 402 UNP O13795 POF8_SCHPO 282 402 SEQRES 1 A 121 LYS ASP GLU ASP ASN LEU ASP PHE THR LYS ASN LEU LEU SEQRES 2 A 121 THR ARG ILE LYS ASN LEU HIS PRO LEU THR ASN LYS SER SEQRES 3 A 121 THR ILE HIS SER LEU LEU SER TYR VAL PHE SER ARG GLN SEQRES 4 A 121 THR GLN ASN ILE ALA CYS GLU PRO MET TYR ILE ASP TYR SEQRES 5 A 121 ARG LYS ASP GLU THR GLU ALA ILE ILE ARG TRP LYS THR SEQRES 6 A 121 PRO LEU HIS ALA GLU THR CYS ILE ASN ALA PHE ARG THR SEQRES 7 A 121 GLN GLU ARG LYS GLN ASN SER HIS ASP ASP ILE ARG ALA SEQRES 8 A 121 HIS ARG LYS LYS GLY SER SER ARG PRO PHE LEU ILE ALA SEQRES 9 A 121 GLU LEU ILE THR GLY GLU GLU GLU LYS ASN TYR TRP ARG SEQRES 10 A 121 MET LEU LYS LYS HET NO3 A 501 4 HETNAM NO3 NITRATE ION FORMUL 2 NO3 N O3 1- FORMUL 3 HOH *78(H2 O) HELIX 1 AA1 ASN A 305 THR A 321 1 17 HELIX 2 AA2 THR A 346 GLN A 360 1 15 HELIX 3 AA3 THR A 389 LYS A 401 1 13 SHEET 1 AA1 4 PRO A 328 ASP A 332 0 SHEET 2 AA1 4 GLU A 339 TRP A 344 -1 O ILE A 341 N ASP A 332 SHEET 3 AA1 4 LEU A 294 LYS A 298 -1 N THR A 295 O ILE A 342 SHEET 4 AA1 4 ILE A 384 LEU A 387 -1 O GLU A 386 N ARG A 296 SITE 1 AC1 7 TYR A 330 ARG A 343 ASP A 368 ASP A 369 SITE 2 AC1 7 ILE A 370 ARG A 371 TRP A 397 CRYST1 57.360 57.360 70.300 90.00 90.00 120.00 P 31 2 1 6 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 0.017434 0.010065 0.000000 0.00000 SCALE2 0.000000 0.020131 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014225 0.00000