HEADER DNA BINDING PROTEIN/DNA 21-DEC-20 7L4X TITLE YTH DOMAIN OF HUMAN YTHDC1 WITH DSDNA COMPRISING SINGLE N6MA JOINED BY TITLE 2 TWO SIX-BP DNA DUPLEXES IN P3221 CRYSTAL COMPND MOL_ID: 1; COMPND 2 MOLECULE: YTH DOMAIN-CONTAINING PROTEIN 1; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: SPLICING FACTOR YT521,YT521-B; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: SSDNA W/N6A; COMPND 8 CHAIN: E; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: YTHDC1, KIAA1966, YT521; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS N6-METHYLADENINE BINDING PROTEIN DOMAIN, SSDNA, DNA BINDING PROTEIN, KEYWDS 2 PROTEIN-DNA COMPLEX, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.R.HORTON,X.CHENG REVDAT 3 18-OCT-23 7L4X 1 REMARK REVDAT 2 01-DEC-21 7L4X 1 JRNL REVDAT 1 03-NOV-21 7L4X 0 JRNL AUTH D.YU,J.R.HORTON,J.YANG,T.HAJIAN,M.VEDADI,C.A.SAGUM, JRNL AUTH 2 M.T.BEDFORD,R.M.BLUMENTHAL,X.ZHANG,X.CHENG JRNL TITL HUMAN METTL3-METTL14 RNA ADENINE METHYLTRANSFERASE COMPLEX JRNL TITL 2 IS ACTIVE ON DOUBLE-STRANDED DNA CONTAINING LESIONS. JRNL REF NUCLEIC ACIDS RES. V. 49 11629 2021 JRNL REFN ESSN 1362-4962 JRNL PMID 34086966 JRNL DOI 10.1093/NAR/GKAB460 REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 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) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 19702 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 990 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 36.4900 - 3.4300 1.00 2827 150 0.1572 0.1963 REMARK 3 2 3.4300 - 2.7200 1.00 2695 137 0.2246 0.2394 REMARK 3 3 2.7200 - 2.3800 1.00 2670 143 0.2314 0.2435 REMARK 3 4 2.3800 - 2.1600 1.00 2658 137 0.2205 0.2881 REMARK 3 5 2.1600 - 2.0000 1.00 2635 143 0.2436 0.2909 REMARK 3 6 2.0000 - 1.8900 1.00 2620 139 0.2378 0.2776 REMARK 3 7 1.8900 - 1.7900 0.99 2607 141 0.3335 0.3834 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) : 0.228 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.381 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.37 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.89 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 : 0.004 1653 REMARK 3 ANGLE : 0.706 2283 REMARK 3 CHIRALITY : 0.045 246 REMARK 3 PLANARITY : 0.005 243 REMARK 3 DIHEDRAL : 17.966 644 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 7L4X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1000253700. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-SEP-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19738 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 36.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 17.50 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 1.43900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 6WEA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% V/V 2-PROPANOL, 0.1M SODIUM REMARK 280 CITRATE TRIBASIC DIHYDRATE, 0.1M SODIUM CACODYLATE PH 4.6, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 292K 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 72.63733 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 36.31867 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 36.31867 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 72.63733 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, E 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 APPLY THE FOLLOWING TO CHAINS: E REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 36.31867 REMARK 350 APPLY THE FOLLOWING TO CHAINS: E REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 72.63733 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 B 778 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 HIS B 509 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 SER B 424 OG REMARK 470 GLU B 452 CG CD OE1 OE2 REMARK 470 GLU B 467 CG CD OE1 OE2 REMARK 470 GLU B 496 CG CD OE1 OE2 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 SER B 424 107.51 -40.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 7L4X B 345 509 UNP Q96MU7 YTDC1_HUMAN 345 509 DBREF 7L4X E 1 13 PDB 7L4X 7L4X 1 13 SEQADV 7L4X GLY B 344 UNP Q96MU7 EXPRESSION TAG SEQRES 1 B 166 GLY THR SER LYS LEU LYS TYR VAL LEU GLN ASP ALA ARG SEQRES 2 B 166 PHE PHE LEU ILE LYS SER ASN ASN HIS GLU ASN VAL SER SEQRES 3 B 166 LEU ALA LYS ALA LYS GLY VAL TRP SER THR LEU PRO VAL SEQRES 4 B 166 ASN GLU LYS LYS LEU ASN LEU ALA PHE ARG SER ALA ARG SEQRES 5 B 166 SER VAL ILE LEU ILE PHE SER VAL ARG GLU SER GLY LYS SEQRES 6 B 166 PHE GLN GLY PHE ALA ARG LEU SER SER GLU SER HIS HIS SEQRES 7 B 166 GLY GLY SER PRO ILE HIS TRP VAL LEU PRO ALA GLY MET SEQRES 8 B 166 SER ALA LYS MET LEU GLY GLY VAL PHE LYS ILE ASP TRP SEQRES 9 B 166 ILE CYS ARG ARG GLU LEU PRO PHE THR LYS SER ALA HIS SEQRES 10 B 166 LEU THR ASN PRO TRP ASN GLU HIS LYS PRO VAL LYS ILE SEQRES 11 B 166 GLY ARG ASP GLY GLN GLU ILE GLU LEU GLU CYS GLY THR SEQRES 12 B 166 GLN LEU CYS LEU LEU PHE PRO PRO ASP GLU SER ILE ASP SEQRES 13 B 166 LEU TYR GLN VAL ILE HIS LYS MET ARG HIS SEQRES 1 E 13 DC DA DG DC DT DG 6MA DG DT DC DG DA DC HET 6MA E 7 22 HET EDO B 601 4 HET EDO B 602 4 HET EDO B 603 4 HETNAM 6MA N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 6MA C11 H16 N5 O6 P FORMUL 3 EDO 3(C2 H6 O2) FORMUL 6 HOH *103(H2 O) HELIX 1 AA1 THR B 345 GLN B 353 1 9 HELIX 2 AA2 HIS B 365 GLY B 375 1 11 HELIX 3 AA3 LEU B 380 ALA B 394 1 15 HELIX 4 AA4 ALA B 436 GLY B 440 5 5 HELIX 5 AA5 THR B 456 SER B 458 5 3 HELIX 6 AA6 GLU B 481 PHE B 492 1 12 HELIX 7 AA7 LEU B 500 ARG B 508 1 9 SHEET 1 AA1 6 VAL B 376 TRP B 377 0 SHEET 2 AA1 6 PHE B 443 CYS B 449 -1 O PHE B 443 N TRP B 377 SHEET 3 AA1 6 GLY B 411 LEU B 415 -1 N ARG B 414 O ASP B 446 SHEET 4 AA1 6 SER B 396 VAL B 403 -1 N LEU B 399 O ALA B 413 SHEET 5 AA1 6 ALA B 355 SER B 362 1 N ARG B 356 O ILE B 398 SHEET 6 AA1 6 GLU B 479 ILE B 480 -1 O ILE B 480 N PHE B 357 SHEET 1 AA2 2 LYS B 408 PHE B 409 0 SHEET 2 AA2 2 LEU B 453 PRO B 454 -1 O LEU B 453 N PHE B 409 LINK O3' DG E 6 P 6MA E 7 1555 1555 1.61 LINK O3' 6MA E 7 P DG E 8 1555 1555 1.60 CRYST1 56.744 56.744 108.956 90.00 90.00 120.00 P 32 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 0.017623 0.010175 0.000000 0.00000 SCALE2 0.000000 0.020349 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009178 0.00000