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 MASTER 415 0 46 11 16 0 2 6 0 0 0 26 END