HEADER DNA BINDING PROTEIN 31-MAR-17 5VC8 TITLE CRYSTAL STRUCTURE OF THE WHSC1 PWWP1 DOMAIN CAVEAT 5VC8 THE DEPOSITOR NOTES THAT THE DNA COORDINATES OF THIS ENTRY CAVEAT 2 5VC8 ARE UNRELIABLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE NSD2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MULTIPLE MYELOMA SET DOMAIN-CONTAINING PROTEIN,MMSET,NUCLEAR COMPND 5 SET DOMAIN-CONTAINING PROTEIN 2,PROTEIN TRITHORAX-5,WOLF-HIRSCHHORN COMPND 6 SYNDROME CANDIDATE 1 PROTEIN; COMPND 7 EC: 2.1.1.43; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DODECA-2-DEOXY-NUCLEOTIDE, POORLY RESOLVED BY ELECTRON COMPND 11 DENSITY; COMPND 12 CHAIN: W, X, Y; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: DNA (5'-D(P*CP*TP*(DN))-3'); COMPND 16 CHAIN: Z; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: INTERPRETATION OF WEAK ELECTRON DENSITY IN TERMS OF AN COMPND 19 UNIDENTIFIED FRAGMENT OF THE DODECADEOXYNUCLEOTIDE. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NSD2, KIAA1090, MMSET, TRX5, WHSC1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-V2R-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28-MHL; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630 KEYWDS PWWP DOMAIN, STRUCTURAL GENOMICS CONSORTIUM, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.QIN,W.TEMPEL,A.DONG,C.BOUNTRA,J.WEIGELT,C.H.ARROWSMITH,A.M.EDWARDS, AUTHOR 2 J.MIN,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 2 04-AUG-21 5VC8 1 JRNL REVDAT 1 28-JUN-17 5VC8 0 JRNL AUTH M.ZHANG,Y.YANG,M.ZHOU,A.DONG,X.YAN,P.LOPPNAU,J.MIN,Y.LIU JRNL TITL HISTONE AND DNA BINDING ABILITY STUDIES OF THE NSD SUBFAMILY JRNL TITL 2 OF PWWP DOMAINS. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 569 199 2021 JRNL REFN ESSN 1090-2104 JRNL PMID 34271259 JRNL DOI 10.1016/J.BBRC.2021.07.017 REMARK 2 REMARK 2 RESOLUTION. 1.80 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 71350 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.730 REMARK 3 FREE R VALUE TEST SET COUNT : 2661 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 37.1221 - 4.7999 1.00 3639 130 0.2028 0.2285 REMARK 3 2 4.7999 - 3.8110 1.00 3610 128 0.1658 0.1707 REMARK 3 3 3.8110 - 3.3297 1.00 3545 219 0.1812 0.1997 REMARK 3 4 3.3297 - 3.0254 1.00 3621 138 0.2031 0.2738 REMARK 3 5 3.0254 - 2.8086 1.00 3624 131 0.2215 0.2406 REMARK 3 6 2.8086 - 2.6431 1.00 3738 23 0.2130 0.3833 REMARK 3 7 2.6431 - 2.5107 1.00 3552 197 0.2226 0.2418 REMARK 3 8 2.5107 - 2.4015 1.00 3564 201 0.2080 0.2573 REMARK 3 9 2.4015 - 2.3090 1.00 3751 0 0.2007 0.0000 REMARK 3 10 2.3090 - 2.2294 1.00 3481 255 0.2001 0.2382 REMARK 3 11 2.2294 - 2.1597 1.00 3763 0 0.1872 0.0000 REMARK 3 12 2.1597 - 2.0979 1.00 3488 269 0.1969 0.2160 REMARK 3 13 2.0979 - 2.0427 1.00 3760 0 0.1977 0.0000 REMARK 3 14 2.0427 - 1.9929 1.00 3456 304 0.2041 0.2573 REMARK 3 15 1.9929 - 1.9476 1.00 3761 0 0.2127 0.0000 REMARK 3 16 1.9476 - 1.9061 1.00 3617 146 0.2223 0.2844 REMARK 3 17 1.9061 - 1.8680 1.00 3555 180 0.2453 0.2639 REMARK 3 18 1.8680 - 1.8327 1.00 3749 0 0.2643 0.0000 REMARK 3 19 1.8327 - 1.8000 1.00 3415 340 0.3013 0.3368 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.19 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.25 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 : 0.007 2860 REMARK 3 ANGLE : 0.824 4032 REMARK 3 CHIRALITY : 0.053 433 REMARK 3 PLANARITY : 0.006 381 REMARK 3 DIHEDRAL : 22.317 1539 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 32.8921 -26.6351 -4.9496 REMARK 3 T TENSOR REMARK 3 T11: 0.1747 T22: 0.1570 REMARK 3 T33: 0.1651 T12: 0.0153 REMARK 3 T13: 0.0272 T23: -0.0024 REMARK 3 L TENSOR REMARK 3 L11: 2.4566 L22: 2.3879 REMARK 3 L33: 3.5022 L12: -0.1494 REMARK 3 L13: -0.8966 L23: 0.0138 REMARK 3 S TENSOR REMARK 3 S11: -0.1860 S12: -0.0724 S13: -0.1333 REMARK 3 S21: 0.0952 S22: -0.0150 S23: -0.1334 REMARK 3 S31: 0.0953 S32: 0.1686 S33: 0.1645 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 15.9558 -12.2484 2.3396 REMARK 3 T TENSOR REMARK 3 T11: 0.2066 T22: 0.1510 REMARK 3 T33: 0.2278 T12: 0.0081 REMARK 3 T13: 0.0430 T23: -0.0018 REMARK 3 L TENSOR REMARK 3 L11: 2.9284 L22: 2.3201 REMARK 3 L33: 3.4991 L12: -0.9418 REMARK 3 L13: -0.8275 L23: 0.4160 REMARK 3 S TENSOR REMARK 3 S11: -0.0258 S12: -0.0359 S13: -0.0394 REMARK 3 S21: 0.1564 S22: -0.0010 S23: 0.2042 REMARK 3 S31: -0.0567 S32: -0.0975 S33: -0.0036 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN W REMARK 3 ORIGIN FOR THE GROUP (A): 3.1785 -30.2804 -28.3216 REMARK 3 T TENSOR REMARK 3 T11: 0.5280 T22: 1.0199 REMARK 3 T33: 0.8703 T12: -0.3728 REMARK 3 T13: 0.1429 T23: -0.1641 REMARK 3 L TENSOR REMARK 3 L11: 0.0103 L22: 3.6809 REMARK 3 L33: 0.3632 L12: -0.1213 REMARK 3 L13: 0.0082 L23: 0.7853 REMARK 3 S TENSOR REMARK 3 S11: -0.5339 S12: -0.0394 S13: -0.0864 REMARK 3 S21: -0.6341 S22: 0.2980 S23: 1.1111 REMARK 3 S31: 0.3693 S32: -0.8830 S33: -0.2402 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN X REMARK 3 ORIGIN FOR THE GROUP (A): 2.6532 -30.5593 -26.8582 REMARK 3 T TENSOR REMARK 3 T11: 0.6149 T22: 1.1419 REMARK 3 T33: 1.4568 T12: -0.3542 REMARK 3 T13: 0.1158 T23: -0.1832 REMARK 3 L TENSOR REMARK 3 L11: 2.7441 L22: 3.7439 REMARK 3 L33: 0.3905 L12: 3.1571 REMARK 3 L13: 0.0397 L23: -0.1629 REMARK 3 S TENSOR REMARK 3 S11: 0.1310 S12: 0.0899 S13: -0.0339 REMARK 3 S21: 0.1416 S22: 0.3650 S23: 1.3253 REMARK 3 S31: 0.3048 S32: -0.8164 S33: -0.5698 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN Y REMARK 3 ORIGIN FOR THE GROUP (A): -27.4137 -55.3612 -29.6477 REMARK 3 T TENSOR REMARK 3 T11: 1.0937 T22: 1.2053 REMARK 3 T33: 2.0255 T12: -0.5581 REMARK 3 T13: 0.2011 T23: -0.2184 REMARK 3 L TENSOR REMARK 3 L11: 3.7581 L22: 3.1942 REMARK 3 L33: 0.1207 L12: 3.2762 REMARK 3 L13: 0.0215 L23: -0.0885 REMARK 3 S TENSOR REMARK 3 S11: 0.1743 S12: -0.0285 S13: 0.3942 REMARK 3 S21: -0.1583 S22: 0.1758 S23: -0.1090 REMARK 3 S31: 0.0838 S32: -0.1166 S33: -0.3314 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE NUCLEIC ACID COMPONENT OF THIS REMARK 3 MODEL IS BASED ON WEAK AND DISCONTINUOUS DENSITY. IT HAS BEEN REMARK 3 INCLUDED AS AN INTERPRETATIVE GUIDE TO SOME FEATURES IN THE REMARK 3 DIFFERENCE MAPS, BUT MUST BE CONSIDERED UNRELIABLE. MOREOVER, REMARK 3 THE CURRENT DEFINITION OF THE ASYMMETRIC UNIT DOES NOT AIM TO REMARK 3 REFLECT A BIOLOGICALLY RELEVANT PROTEIN:DNA INTERFACE. THE POOR REMARK 3 FIT OF THE SIDE CHAINS OF WHSC1 RESIDUES GLU-278 TO ELECTRON REMARK 3 DENSITY MAPS SUGGESTS THAT THESE RESIDUES HAVE BEEN MUTATED REMARK 3 RELATIVE TO THE PROVIDED AMINO ACID SEQUENCE. THE STRUCTURE WAS REMARK 3 SOLVED BY SINGLE WAVELENGTH ANOMALOUS DIFFRACTION USING AN REMARK 3 ISOMORPHOUS CRYSTAL AND DATA COLLECTED AT APS BEAM LINE 23-IDB. REMARK 4 REMARK 4 5VC8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-APR-17. REMARK 100 THE DEPOSITION ID IS D_1000227127. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 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 : XIA2, XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.31 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38039 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 37.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.30 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.30 REMARK 200 R MERGE FOR SHELL (I) : 1.06000 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: SAD REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM IODIDE,0.1M MAGNESIUM REMARK 280 NITRATE, 25%PEG3350, VAPOR DIFFUSION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 57.70000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 41.49500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 41.49500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 86.55000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 41.49500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 41.49500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.85000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 41.49500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.49500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 86.55000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 41.49500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.49500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 28.85000 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 57.70000 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 300 REMARK: UNRELIABLE DNA COORDINATES DOES NOT ALLOW FOR HIGHER-LEVEL REMARK 300 BIOLOGICAL ASSEMBLY PREDICTION. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, W, X, Y, Z 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 210 REMARK 465 GLY A 211 REMARK 465 ARG A 212 REMARK 465 ASP A 213 REMARK 465 LYS A 214 REMARK 465 ASP A 215 REMARK 465 GLY A 254 REMARK 465 GLN A 255 REMARK 465 LYS A 256 REMARK 465 LYS A 257 REMARK 465 SER A 258 REMARK 465 LEU A 347 REMARK 465 TYR A 348 REMARK 465 VAL A 349 REMARK 465 GLY A 350 REMARK 465 GLY B 210 REMARK 465 GLY B 211 REMARK 465 ARG B 212 REMARK 465 ASP B 213 REMARK 465 LYS B 214 REMARK 465 ASP B 215 REMARK 465 HIS B 216 REMARK 465 PRO B 302 REMARK 465 THR B 303 REMARK 465 LYS B 304 REMARK 465 ALA B 305 REMARK 465 GLU B 306 REMARK 465 LYS B 307 REMARK 465 ILE B 308 REMARK 465 LYS B 309 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 HIS A 216 N CB CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 217 CG CD1 CD2 REMARK 470 LYS A 219 CE NZ REMARK 470 LYS A 253 NZ REMARK 470 GLU A 278 OE1 OE2 REMARK 470 LYS A 279 CG CD CE NZ REMARK 470 GLU A 285 CD OE1 OE2 REMARK 470 GLU A 291 OE1 OE2 REMARK 470 LYS A 292 CE NZ REMARK 470 LYS A 304 CE NZ REMARK 470 LYS A 312 CD CE NZ REMARK 470 GLU A 331 OE1 OE2 REMARK 470 LYS A 343 NZ REMARK 470 THR A 345 OG1 CG2 REMARK 470 PHE A 346 CA C O CB CG CD1 CD2 REMARK 470 PHE A 346 CE1 CE2 CZ REMARK 470 LEU B 217 CG CD1 CD2 REMARK 470 LYS B 219 CD CE NZ REMARK 470 LYS B 253 NZ REMARK 470 LYS B 256 CG CD CE NZ REMARK 470 LYS B 257 CD CE NZ REMARK 470 GLU B 278 OE1 OE2 REMARK 470 LYS B 279 CG CD CE NZ REMARK 470 GLU B 285 CD OE1 OE2 REMARK 470 GLU B 291 CG CD OE1 OE2 REMARK 470 LYS B 292 CD CE NZ REMARK 470 GLU B 296 CG CD OE1 OE2 REMARK 470 LYS B 299 CE NZ REMARK 470 GLN B 300 CG CD OE1 NE2 REMARK 470 ALA B 301 CA C O CB REMARK 470 LYS B 312 CG CD CE NZ REMARK 470 SER B 315 OG REMARK 470 LYS B 317 CG CD CE NZ REMARK 470 GLU B 331 CG CD OE1 OE2 REMARK 470 LYS B 343 CD CE NZ REMARK 470 DN Z 2 C5' C4' O4' C3' O3' C2' C1' 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 HIS B 247 -11.87 73.33 REMARK 500 ALA B 259 50.69 -118.48 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 Di-nucleotide DT Z 1 and DN Z 2 DBREF 5VC8 A 211 350 UNP O96028 NSD2_HUMAN 211 350 DBREF 5VC8 B 211 350 UNP O96028 NSD2_HUMAN 211 350 DBREF 5VC8 W 1 12 PDB 5VC8 5VC8 1 12 DBREF 5VC8 X 1 12 PDB 5VC8 5VC8 1 12 DBREF 5VC8 Y 1 12 PDB 5VC8 5VC8 1 12 DBREF 5VC8 Z 0 2 PDB 5VC8 5VC8 0 2 SEQADV 5VC8 GLY A 210 UNP O96028 EXPRESSION TAG SEQADV 5VC8 GLY B 210 UNP O96028 EXPRESSION TAG SEQRES 1 A 141 GLY GLY ARG ASP LYS ASP HIS LEU LEU LYS TYR ASN VAL SEQRES 2 A 141 GLY ASP LEU VAL TRP SER LYS VAL SER GLY TYR PRO TRP SEQRES 3 A 141 TRP PRO CYS MSE VAL SER ALA ASP PRO LEU LEU HIS SER SEQRES 4 A 141 TYR THR LYS LEU LYS GLY GLN LYS LYS SER ALA ARG GLN SEQRES 5 A 141 TYR HIS VAL GLN PHE PHE GLY ASP ALA PRO GLU ARG ALA SEQRES 6 A 141 TRP ILE PHE GLU LYS SER LEU VAL ALA PHE GLU GLY GLU SEQRES 7 A 141 GLY GLN PHE GLU LYS LEU CYS GLN GLU SER ALA LYS GLN SEQRES 8 A 141 ALA PRO THR LYS ALA GLU LYS ILE LYS LEU LEU LYS PRO SEQRES 9 A 141 ILE SER GLY LYS LEU ARG ALA GLN TRP GLU MSE GLY ILE SEQRES 10 A 141 VAL GLN ALA GLU GLU ALA ALA SER MSE SER VAL GLU GLU SEQRES 11 A 141 ARG LYS ALA LYS PHE THR PHE LEU TYR VAL GLY SEQRES 1 B 141 GLY GLY ARG ASP LYS ASP HIS LEU LEU LYS TYR ASN VAL SEQRES 2 B 141 GLY ASP LEU VAL TRP SER LYS VAL SER GLY TYR PRO TRP SEQRES 3 B 141 TRP PRO CYS MSE VAL SER ALA ASP PRO LEU LEU HIS SER SEQRES 4 B 141 TYR THR LYS LEU LYS GLY GLN LYS LYS SER ALA ARG GLN SEQRES 5 B 141 TYR HIS VAL GLN PHE PHE GLY ASP ALA PRO GLU ARG ALA SEQRES 6 B 141 TRP ILE PHE GLU LYS SER LEU VAL ALA PHE GLU GLY GLU SEQRES 7 B 141 GLY GLN PHE GLU LYS LEU CYS GLN GLU SER ALA LYS GLN SEQRES 8 B 141 ALA PRO THR LYS ALA GLU LYS ILE LYS LEU LEU LYS PRO SEQRES 9 B 141 ILE SER GLY LYS LEU ARG ALA GLN TRP GLU MSE GLY ILE SEQRES 10 B 141 VAL GLN ALA GLU GLU ALA ALA SER MSE SER VAL GLU GLU SEQRES 11 B 141 ARG LYS ALA LYS PHE THR PHE LEU TYR VAL GLY SEQRES 1 W 12 DG DA DG DA DT DC DG DA DT DC DT DC SEQRES 1 X 12 DG DA DG DA DT DC DG DA DT DC DT DC SEQRES 1 Y 12 DG DA DG DA DT DC DG DA DT DC DT DC SEQRES 1 Z 3 DC DT DN MODRES 5VC8 MSE A 239 MET MODIFIED RESIDUE MODRES 5VC8 MSE A 324 MET MODIFIED RESIDUE MODRES 5VC8 MSE A 335 MET MODIFIED RESIDUE MODRES 5VC8 MSE B 239 MET MODIFIED RESIDUE MODRES 5VC8 MSE B 324 MET MODIFIED RESIDUE MODRES 5VC8 MSE B 335 MET MODIFIED RESIDUE HET MSE A 239 8 HET MSE A 324 13 HET MSE A 335 8 HET MSE B 239 8 HET MSE B 324 8 HET MSE B 335 8 HET DN Z 2 4 HET UNX A 401 1 HET UNX A 402 1 HET UNX A 403 1 HET UNX A 404 1 HET UNX A 405 1 HET UNX A 406 1 HET UNX A 407 1 HET UNX A 408 1 HET UNX A 409 1 HET UNX A 410 1 HET UNX A 411 1 HET UNX A 412 1 HET UNX A 413 1 HET UNX A 414 1 HET UNX A 415 1 HET UNX A 416 1 HET UNX A 417 1 HET UNX A 418 1 HET UNX A 419 1 HET UNX A 420 1 HET UNX B 401 1 HET UNX B 402 1 HET UNX B 403 1 HET UNX B 404 1 HET UNX B 405 1 HET UNX B 406 1 HET UNX B 407 1 HET UNX B 408 1 HET UNX B 409 1 HET UNX B 410 1 HET UNX B 411 1 HET UNX B 412 1 HET UNX B 413 1 HET UNX B 414 1 HET UNX B 415 1 HET UNX B 416 1 HET UNX B 417 1 HET UNX B 418 1 HET UNX B 419 1 HETNAM MSE SELENOMETHIONINE HETNAM DN UNKNOWN 2'-DEOXYNUCLEOTIDE HETNAM UNX UNKNOWN ATOM OR ION FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 6 DN C5 H11 O6 P FORMUL 7 UNX 39(X) FORMUL 46 HOH *106(H2 O) HELIX 1 AA1 GLY A 286 GLY A 288 5 3 HELIX 2 AA2 GLN A 289 ALA A 301 1 13 HELIX 3 AA3 THR A 303 LYS A 312 1 10 HELIX 4 AA4 SER A 315 SER A 334 1 20 HELIX 5 AA5 SER A 336 THR A 345 1 10 HELIX 6 AA6 GLY B 254 LYS B 256 5 3 HELIX 7 AA7 GLY B 286 GLY B 288 5 3 HELIX 8 AA8 GLN B 289 GLN B 300 1 12 HELIX 9 AA9 SER B 315 SER B 334 1 20 HELIX 10 AB1 SER B 336 PHE B 344 1 9 HELIX 11 AB2 THR B 345 VAL B 349 5 5 SHEET 1 AA1 3 THR A 250 LYS A 251 0 SHEET 2 AA1 3 GLN A 261 PHE A 266 -1 O GLN A 261 N LYS A 251 SHEET 3 AA1 3 ARG A 273 PHE A 277 -1 O ILE A 276 N TYR A 262 SHEET 1 AA2 5 THR A 250 LYS A 251 0 SHEET 2 AA2 5 GLN A 261 PHE A 266 -1 O GLN A 261 N LYS A 251 SHEET 3 AA2 5 TRP A 236 VAL A 240 -1 N MSE A 239 O GLN A 265 SHEET 4 AA2 5 LEU A 225 SER A 228 -1 N VAL A 226 O CYS A 238 SHEET 5 AA2 5 LEU A 281 ALA A 283 -1 O VAL A 282 N TRP A 227 SHEET 1 AA3 3 THR B 250 LEU B 252 0 SHEET 2 AA3 3 ARG B 260 PHE B 266 -1 O GLN B 261 N LYS B 251 SHEET 3 AA3 3 ARG B 273 PHE B 277 -1 O ALA B 274 N VAL B 264 SHEET 1 AA4 5 THR B 250 LEU B 252 0 SHEET 2 AA4 5 ARG B 260 PHE B 266 -1 O GLN B 261 N LYS B 251 SHEET 3 AA4 5 TRP B 236 VAL B 240 -1 N MSE B 239 O GLN B 265 SHEET 4 AA4 5 LEU B 225 SER B 228 -1 N VAL B 226 O CYS B 238 SHEET 5 AA4 5 LEU B 281 ALA B 283 -1 O VAL B 282 N TRP B 227 LINK C CYS A 238 N MSE A 239 1555 1555 1.34 LINK C MSE A 239 N VAL A 240 1555 1555 1.34 LINK C GLU A 323 N MSE A 324 1555 1555 1.33 LINK C MSE A 324 N GLY A 325 1555 1555 1.34 LINK C SER A 334 N MSE A 335 1555 1555 1.33 LINK C MSE A 335 N SER A 336 1555 1555 1.33 LINK C CYS B 238 N MSE B 239 1555 1555 1.33 LINK C MSE B 239 N VAL B 240 1555 1555 1.34 LINK C GLU B 323 N MSE B 324 1555 1555 1.33 LINK C MSE B 324 N GLY B 325 1555 1555 1.34 LINK C SER B 334 N MSE B 335 1555 1555 1.32 LINK C MSE B 335 N SER B 336 1555 1555 1.33 LINK O3' DT Z 1 P DN Z 2 1555 1555 1.61 SITE 1 AC1 5 GLY A 316 ARG A 319 DG W 3 DA W 4 SITE 2 AC1 5 DC Z 0 CRYST1 82.990 82.990 115.400 90.00 90.00 90.00 P 43 21 2 24 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 0.012050 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012050 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008666 0.00000