HEADER RNA BINDING PROTEIN 08-FEB-21 7NG2 TITLE CRYSTAL STRUCTURE OF TOXOPLASMA CPSF4-YTH DOMAIN IN APO FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC FINGER (CCCH TYPE) MOTIF-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CPSF4; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TOXOPLASMA GONDII (STRAIN ATCC 50611 / ME49); SOURCE 3 ORGANISM_TAXID: 508771; SOURCE 4 STRAIN: ATCC 50611 / ME49; SOURCE 5 GENE: TGME49_201200; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-RIL KEYWDS YTH, CLEAVAGE AND POLYADENYLATION, RNA, M6A, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.SWALE,M.W.BOWLER REVDAT 3 31-JAN-24 7NG2 1 REMARK REVDAT 2 28-JUL-21 7NG2 1 JRNL REVDAT 1 21-JUL-21 7NG2 0 JRNL AUTH D.C.FARHAT,M.W.BOWLER,G.COMMUNIE,D.PONTIER,L.BELMUDES,C.MAS, JRNL AUTH 2 C.CORRAO,Y.COUTE,A.BOUGDOUR,T.LAGRANGE,M.A.HAKIMI,C.SWALE JRNL TITL A PLANT-LIKE MECHANISM COUPLING M6A READING TO JRNL TITL 2 POLYADENYLATION SAFEGUARDS TRANSCRIPTOME INTEGRITY AND JRNL TITL 3 DEVELOPMENTAL GENE PARTITIONING IN TOXOPLASMA . JRNL REF ELIFE V. 10 2021 JRNL REFN ESSN 2050-084X JRNL PMID 34263725 JRNL DOI 10.7554/ELIFE.68312 REMARK 2 REMARK 2 RESOLUTION. 1.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1 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) : 1.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 49441 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 2500 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 3.2200 - 2.5600 1.00 2722 146 0.1822 0.2275 REMARK 3 2 2.5600 - 2.2300 1.00 2651 158 0.1680 0.1935 REMARK 3 3 2.2300 - 2.0300 1.00 2669 130 0.1571 0.1678 REMARK 3 4 2.0300 - 1.8900 1.00 2668 130 0.1666 0.1968 REMARK 3 5 1.8900 - 1.7700 1.00 2617 138 0.1627 0.1709 REMARK 3 6 1.7700 - 1.6900 1.00 2606 138 0.1374 0.1772 REMARK 3 7 1.6900 - 1.6100 1.00 2600 135 0.1434 0.1763 REMARK 3 8 1.6100 - 1.5500 1.00 2570 155 0.1594 0.1969 REMARK 3 9 1.5500 - 1.5000 1.00 2589 138 0.1790 0.2241 REMARK 3 10 1.5000 - 1.4500 1.00 2603 141 0.1845 0.2388 REMARK 3 11 1.4500 - 1.4100 1.00 2595 147 0.1842 0.2206 REMARK 3 12 1.4100 - 1.3700 1.00 2581 131 0.1856 0.2319 REMARK 3 13 1.3700 - 1.3400 1.00 2585 105 0.1965 0.2188 REMARK 3 14 1.3400 - 1.3100 1.00 2576 139 0.2285 0.2496 REMARK 3 15 1.3100 - 1.2800 1.00 2551 151 0.2682 0.2868 REMARK 3 16 1.2800 - 1.2500 0.97 2451 151 0.3126 0.3160 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) : 18.873 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.56 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 1337 REMARK 3 ANGLE : 0.771 1822 REMARK 3 CHIRALITY : 0.079 193 REMARK 3 PLANARITY : 0.005 240 REMARK 3 DIHEDRAL : 14.570 496 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: NULL REMARK 4 REMARK 4 7NG2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1292113904. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PHENIX REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49444 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.230 REMARK 200 RESOLUTION RANGE LOW (A) : 34.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4R3I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 % PEG 4000, 20% ISOPROPANOL AND REMARK 280 0.1M TRI-SODIUM CITRATE PH 5.6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 101.30000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.09000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.09000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 50.65000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.09000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.09000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 151.95000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.09000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.09000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 50.65000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.09000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.09000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 151.95000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 101.30000 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 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 GLY A 590 REMARK 465 THR A 591 REMARK 465 GLY A 592 REMARK 465 ILE A 593 REMARK 465 ASP A 594 REMARK 465 PRO A 595 REMARK 465 ALA A 596 REMARK 465 THR A 597 REMARK 465 ARG A 598 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 PHE A 515 60.57 34.94 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 IPA A 601 DBREF 7NG2 A 434 598 UNP S8F6K2 S8F6K2_TOXGM 434 598 SEQADV 7NG2 GLY A 433 UNP S8F6K2 EXPRESSION TAG SEQRES 1 A 166 GLY ASP PRO PHE GLY HIS VAL ALA SER PRO GLN SER THR SEQRES 2 A 166 LYS ARG PHE PHE ILE ILE LYS SER ASN ARG MET SER ASN SEQRES 3 A 166 ILE TYR THR SER ILE GLN HIS GLY VAL TRP ALA THR SER SEQRES 4 A 166 LYS GLY ASN SER ARG LYS LEU SER ASN ALA PHE THR SER SEQRES 5 A 166 THR ASP HIS VAL LEU LEU LEU PHE SER ALA ASN GLU SER SEQRES 6 A 166 GLY GLY PHE GLN GLY PHE GLY ARG MET MET SER LEU PRO SEQRES 7 A 166 ASP PRO GLN LEU PHE PRO GLY ILE TRP GLY PRO VAL GLN SEQRES 8 A 166 LEU ARG LEU GLY SER ASN PHE ARG VAL MET TRP LEU LYS SEQRES 9 A 166 GLN CYS LYS ILE GLU PHE GLU GLU LEU GLY LYS VAL THR SEQRES 10 A 166 ASN PRO TRP ASN ASP ASP LEU PRO LEU ARG LYS SER ARG SEQRES 11 A 166 ASP GLY THR GLU VAL PRO PRO ALA LEU GLY SER LEU LEU SEQRES 12 A 166 CYS THR TRP MET SER GLN ARG PRO SER GLU ASP LEU LEU SEQRES 13 A 166 ALA GLY THR GLY ILE ASP PRO ALA THR ARG HET IPA A 601 4 HETNAM IPA ISOPROPYL ALCOHOL HETSYN IPA 2-PROPANOL FORMUL 2 IPA C3 H8 O FORMUL 3 HOH *149(H2 O) HELIX 1 AA1 ARG A 455 GLY A 466 1 12 HELIX 2 AA2 SER A 471 THR A 485 1 15 HELIX 3 AA3 TRP A 519 LEU A 526 5 8 HELIX 4 AA4 GLU A 543 GLY A 546 5 4 HELIX 5 AA5 PRO A 557 SER A 561 5 5 HELIX 6 AA6 PRO A 568 ARG A 582 1 15 SHEET 1 AA1 6 VAL A 467 TRP A 468 0 SHEET 2 AA1 6 PHE A 530 GLU A 541 -1 O PHE A 530 N TRP A 468 SHEET 3 AA1 6 GLY A 499 MET A 506 -1 N PHE A 503 O LEU A 535 SHEET 4 AA1 6 HIS A 487 ALA A 494 -1 N LEU A 490 O GLY A 504 SHEET 5 AA1 6 LYS A 446 SER A 453 1 N ARG A 447 O LEU A 489 SHEET 6 AA1 6 GLU A 566 VAL A 567 -1 O VAL A 567 N PHE A 448 SITE 1 AC1 5 ASN A 458 ALA A 469 TRP A 519 LEU A 526 SITE 2 AC1 5 HOH A 726 CRYST1 40.180 40.180 202.600 90.00 90.00 90.00 P 41 21 2 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 0.024888 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024888 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004936 0.00000