PDB Short entry for 6G29 HEADER ONCOPROTEIN 22-MAR-18 6G29 TITLE X-RAY STRUCTURE OF NSD3-PWWP1 IN COMPLEX WITH COMPOUND 6 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 6G29 1 REMARK REVDAT 2 15-JAN-20 6G29 1 JRNL REVDAT 1 26-JUN-19 6G29 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. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 14974 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 737 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.96 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2719 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2135 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2571 REMARK 3 BIN R VALUE (WORKING SET) : 0.2131 REMARK 3 BIN FREE R VALUE : 0.2209 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.44 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 148 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 : 1039 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 108 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.00310 REMARK 3 B22 (A**2) : 0.35060 REMARK 3 B33 (A**2) : -2.35370 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) : 0.230 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.121 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.105 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.113 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.101 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 : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1100 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1483 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 399 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 182 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1100 ; 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 : 1319 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 0.89 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.61 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 14.96 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): -8.3430 9.6866 -13.1781 REMARK 3 T TENSOR REMARK 3 T11: -0.1003 T22: -0.0941 REMARK 3 T33: -0.0889 T12: -0.0151 REMARK 3 T13: 0.0017 T23: 0.0100 REMARK 3 L TENSOR REMARK 3 L11: 3.0614 L22: 3.4871 REMARK 3 L33: 2.3432 L12: -0.8752 REMARK 3 L13: 0.5914 L23: 0.7117 REMARK 3 S TENSOR REMARK 3 S11: -0.0284 S12: -0.0165 S13: -0.0010 REMARK 3 S21: 0.1172 S22: 0.0524 S23: -0.1400 REMARK 3 S31: 0.0965 S32: -0.1315 S33: -0.0240 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6G29 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1200009314. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-OCT-15 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 : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.12 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15020 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.697 REMARK 200 RESOLUTION RANGE LOW (A) : 38.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : 0.04000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.85000 REMARK 200 R SYM FOR SHELL (I) : 0.85000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 46.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 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 22.00150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.14350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.71550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.14350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.00150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.71550 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: 8410 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 ALA A 343 REMARK 465 THR A 344 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EHK A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6G24 RELATED DB: PDB REMARK 900 RELATED ID: 6G25 RELATED DB: PDB REMARK 900 RELATED ID: 6G27 RELATED DB: PDB DBREF 6G29 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 EHK A 401 20 HETNAM EHK 5-METHYL-2-PIPERIDIN-4-YL-6-PYRIDIN-4-YL-PYRIDAZIN-3- HETNAM 2 EHK ONE FORMUL 2 EHK C15 H18 N4 O FORMUL 3 HOH *108(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 GLU A 318 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 10 VAL A 278 TYR A 281 TRP A 284 PHE A 312 SITE 2 AC1 10 SER A 314 GLN A 316 GLU A 318 GLN A 367 SITE 3 AC1 10 HOH A 536 HOH A 540 CRYST1 44.003 47.431 64.287 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 0.022726 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021083 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015555 0.00000