HEADER ONCOPROTEIN 22-MAR-18 6G24 TITLE X-RAY STRUCTURE OF NSD3-PWWP1 IN COMPLEX WITH COMPOUND 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE NSD3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NUCLEAR SET DOMAIN-CONTAINING PROTEIN 3,PROTEIN WHISTLE, COMPND 5 WHSC1-LIKE 1 ISOFORM 9 WITH METHYLTRANSFERASE ACTIVITY TO LYSINE, COMPND 6 WOLF-HIRSCHHORN SYNDROME CANDIDATE 1-LIKE PROTEIN 1,WHSC1-LIKE COMPND 7 PROTEIN 1; COMPND 8 EC: 2.1.1.43; 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: NSD3, WHSC1L1, DC28; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, PWWP DOMAIN, ONCOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.BOETTCHER,B.J.MUELLAUER,A.WEISS-PUXBAUM,A.ZOEPHEL REVDAT 3 08-MAY-24 6G24 1 REMARK REVDAT 2 15-JAN-20 6G24 1 JRNL REVDAT 1 26-JUN-19 6G24 0 JRNL AUTH J.BOTTCHER,D.DILWORTH,U.REISER,R.A.NEUMULLER,M.SCHLEICHER, JRNL AUTH 2 M.PETRONCZKI,M.ZEEB,N.MISCHERIKOW,A.ALLALI-HASSANI, JRNL AUTH 3 M.M.SZEWCZYK,F.LI,S.KENNEDY,M.VEDADI,D.BARSYTE-LOVEJOY, JRNL AUTH 4 P.J.BROWN,K.V.M.HUBER,C.M.ROGERS,C.I.WELLS,O.FEDOROV, JRNL AUTH 5 K.RUMPEL,A.ZOEPHEL,M.MAYER,T.WUNBERG,D.BOSE,S.ZAHN,H.ARNHOF, JRNL AUTH 6 H.BERGER,C.REISER,A.HORMANN,T.KRAMMER,M.CORCOKOVIC,B.SHARPS, JRNL AUTH 7 S.WINKLER,D.HARING,X.L.COCKCROFT,J.E.FUCHS,B.MULLAUER, JRNL AUTH 8 A.WEISS-PUXBAUM,T.GERSTBERGER,G.BOEHMELT,C.R.VAKOC, JRNL AUTH 9 C.H.ARROWSMITH,M.PEARSON,D.B.MCCONNELL JRNL TITL FRAGMENT-BASED DISCOVERY OF A CHEMICAL PROBE FOR THE PWWP1 JRNL TITL 2 DOMAIN OF NSD3. JRNL REF NAT.CHEM.BIOL. V. 15 822 2019 JRNL REFN ESSN 1552-4469 JRNL PMID 31285596 JRNL DOI 10.1038/S41589-019-0310-X REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.7 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 7982 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 411 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.35 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.46 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2068 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2233 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1965 REMARK 3 BIN R VALUE (WORKING SET) : 0.2197 REMARK 3 BIN FREE R VALUE : 0.2949 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.98 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 103 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1033 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 85 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.71380 REMARK 3 B22 (A**2) : -1.99280 REMARK 3 B33 (A**2) : 2.70660 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.310 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.276 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.195 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.246 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.188 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1079 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1455 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 383 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 27 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 153 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1079 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 129 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1214 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 0.90 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.30 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.14 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): -8.5264 -8.8642 12.4553 REMARK 3 T TENSOR REMARK 3 T11: -0.1108 T22: -0.1423 REMARK 3 T33: -0.0802 T12: 0.0112 REMARK 3 T13: 0.0107 T23: 0.0228 REMARK 3 L TENSOR REMARK 3 L11: 4.1775 L22: 4.4033 REMARK 3 L33: 2.1349 L12: 1.3052 REMARK 3 L13: -0.3644 L23: 1.0040 REMARK 3 S TENSOR REMARK 3 S11: -0.1506 S12: 0.0832 S13: -0.0801 REMARK 3 S21: -0.0975 S22: 0.1775 S23: -0.0772 REMARK 3 S31: -0.0509 S32: 0.0556 S33: -0.0268 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6G24 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1200009305. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-003 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541800 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7983 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.103 REMARK 200 RESOLUTION RANGE LOW (A) : 28.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : 0.05700 REMARK 200 FOR THE DATA SET : 22.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.57000 REMARK 200 R SYM FOR SHELL (I) : 0.57000 REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM MORPHEUS BUFFER 3, 30% REMARK 280 P550MME_P20K, 10% MORPHEUS ETHYLENE GLYCOLS, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 22.60650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.87700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.37050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.87700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.60650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.37050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 SER A 263 REMARK 465 THR A 264 REMARK 465 GLY A 265 REMARK 465 LYS A 345 REMARK 465 GLN A 346 REMARK 465 ALA A 347 REMARK 465 SER A 348 REMARK 465 ASN A 349 REMARK 465 HIS A 350 REMARK 465 SER A 351 REMARK 465 GLU A 352 REMARK 465 LYS A 353 REMARK 465 GLN A 354 REMARK 465 LYS A 397 REMARK 465 GLN A 398 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 PRO A 317 109.36 -58.26 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 EH2 A 401 DBREF 6G24 A 263 398 UNP Q9BZ95 NSD3_HUMAN 263 398 SEQRES 1 A 136 SER THR GLY VAL LYS PHE GLN VAL GLY ASP LEU VAL TRP SEQRES 2 A 136 SER LYS VAL GLY THR TYR PRO TRP TRP PRO CYS MET VAL SEQRES 3 A 136 SER SER ASP PRO GLN LEU GLU VAL HIS THR LYS ILE ASN SEQRES 4 A 136 THR ARG GLY ALA ARG GLU TYR HIS VAL GLN PHE PHE SER SEQRES 5 A 136 ASN GLN PRO GLU ARG ALA TRP VAL HIS GLU LYS ARG VAL SEQRES 6 A 136 ARG GLU TYR LYS GLY HIS LYS GLN TYR GLU GLU LEU LEU SEQRES 7 A 136 ALA GLU ALA THR LYS GLN ALA SER ASN HIS SER GLU LYS SEQRES 8 A 136 GLN LYS ILE ARG LYS PRO ARG PRO GLN ARG GLU ARG ALA SEQRES 9 A 136 GLN TRP ASP ILE GLY ILE ALA HIS ALA GLU LYS ALA LEU SEQRES 10 A 136 LYS MET THR ARG GLU GLU ARG ILE GLU GLN TYR THR PHE SEQRES 11 A 136 ILE TYR ILE ASP LYS GLN HET EH2 A 401 16 HETNAM EH2 2-[(~{E})-2-THIOPHEN-2-YLETHENYL]BENZOIC ACID FORMUL 2 EH2 C13 H10 O2 S FORMUL 3 HOH *85(H2 O) HELIX 1 AA1 GLY A 332 LYS A 334 5 3 HELIX 2 AA2 GLN A 335 GLU A 342 1 8 HELIX 3 AA3 PRO A 361 LYS A 380 1 20 HELIX 4 AA4 THR A 382 THR A 391 1 10 SHEET 1 AA1 3 THR A 298 ILE A 300 0 SHEET 2 AA1 3 ARG A 306 PHE A 312 -1 O GLU A 307 N LYS A 299 SHEET 3 AA1 3 ARG A 319 HIS A 323 -1 O VAL A 322 N TYR A 308 SHEET 1 AA2 5 THR A 298 ILE A 300 0 SHEET 2 AA2 5 ARG A 306 PHE A 312 -1 O GLU A 307 N LYS A 299 SHEET 3 AA2 5 TRP A 284 VAL A 288 -1 N MET A 287 O GLN A 311 SHEET 4 AA2 5 LEU A 273 SER A 276 -1 N VAL A 274 O CYS A 286 SHEET 5 AA2 5 VAL A 327 GLU A 329 -1 O ARG A 328 N TRP A 275 SITE 1 AC1 13 LYS A 277 PHE A 313 SER A 314 ASN A 315 SITE 2 AC1 13 LYS A 358 ARG A 360 GLN A 367 ILE A 370 SITE 3 AC1 13 GLY A 371 HIS A 374 TYR A 390 HOH A 505 SITE 4 AC1 13 HOH A 517 CRYST1 45.213 46.741 63.754 90.00 90.00 90.00 P 21 21 21 4 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 0.022118 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021394 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015685 0.00000