HEADER TRANSFERASE 31-JUL-24 9GBF TITLE X-RAY STRUCTURE OF PHDVC5HCH TANDEM DOMAIN OF NSD2 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: 2.1.1.357; COMPND 8 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: NSD2, KIAA1090, MMSET, TRX5, WHSC1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HISTONE LYSINE METHYL TRANSFERASE, NUCLEAR RECEPTOR BINDING SET KEYWDS 2 DOMAIN, MYELOMA, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.MUSCO,P.COCOMAZZI,A.BERARDI,S.KNAPP,A.KRAMER REVDAT 3 22-JAN-25 9GBF 1 JRNL REVDAT 2 25-DEC-24 9GBF 1 JRNL REVDAT 1 18-DEC-24 9GBF 0 JRNL AUTH A.BERARDI,C.L.KAESTNER,M.GHITTI,G.QUILICI,P.COCOMAZZI,J.LI, JRNL AUTH 2 F.BALLABIO,C.ZUCCHELLI,S.KNAPP,J.D.LICHT,G.MUSCO JRNL TITL THE C-TERMINAL PHDVC5HCH TANDEM DOMAIN OF NSD2 IS A JRNL TITL 2 COMBINATORIAL READER OF UNMODIFIED H3K4 AND TRI-METHYLATED JRNL TITL 3 H3K27 THAT REGULATES TRANSCRIPTION OF CELL ADHESION GENES IN JRNL TITL 4 MULTIPLE MYELOMA. JRNL REF NUCLEIC ACIDS RES. V. 53 2025 JRNL REFN ESSN 1362-4962 JRNL PMID 39656918 JRNL DOI 10.1093/NAR/GKAE1121 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.V.AFONINE,R.W.GROSSE-KUNSTLEVE,N.ECHOLS,J.J.HEADD, REMARK 1 AUTH 2 N.W.MORIARTY,M.MUSTYAKIMOV,T.C.TERWILLIGER,A.URZHUMTSEV, REMARK 1 AUTH 3 P.H.ZWART,P.D.ADAMS REMARK 1 TITL TOWARDS AUTOMATED CRYSTALLOGRAPHIC STRUCTURE REFINEMENT WITH REMARK 1 TITL 2 PHENIX.REFINE. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 68 352 2012 REMARK 1 REFN ESSN 1399-0047 REMARK 1 PMID 22505256 REMARK 1 DOI 10.1107/S0907444912001308 REMARK 1 REFERENCE 2 REMARK 1 AUTH D.LIEBSCHNER,P.V.AFONINE,M.L.BAKER,G.BUNKOCZI,V.B.CHEN, REMARK 1 AUTH 2 T.I.CROLL,B.HINTZE,L.W.HUNG,S.JAIN,A.J.MCCOY,N.W.MORIARTY, REMARK 1 AUTH 3 R.D.OEFFNER,B.K.POON,M.G.PRISANT,R.J.READ,J.S.RICHARDSON, REMARK 1 AUTH 4 D.C.RICHARDSON,M.D.SAMMITO,O.V.SOBOLEV,D.H.STOCKWELL, REMARK 1 AUTH 5 T.C.TERWILLIGER,A.G.URZHUMTSEV,L.L.VIDEAU,C.J.WILLIAMS, REMARK 1 AUTH 6 P.D.ADAMS REMARK 1 TITL MACROMOLECULAR STRUCTURE DETERMINATION USING X-RAYS, REMARK 1 TITL 2 NEUTRONS AND ELECTRONS: RECENT DEVELOPMENTS IN PHENIX. REMARK 1 REF ACTA CRYSTALLOGR D STRUCT V. 75 861 2019 REMARK 1 REF 2 BIOL REMARK 1 REFN ISSN 2059-7983 REMARK 1 PMID 31588918 REMARK 1 DOI 10.1107/S2059798319011471 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 4.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 67.6 REMARK 3 NUMBER OF REFLECTIONS : 17294 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1730 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 4.9700 - 3.6600 0.97 1926 215 0.1669 0.2061 REMARK 3 2 3.6600 - 2.9100 0.96 1866 207 0.1800 0.2208 REMARK 3 3 2.9100 - 2.5400 0.99 1904 211 0.1866 0.2294 REMARK 3 4 2.5400 - 2.3100 0.99 1898 212 0.1796 0.2214 REMARK 3 5 2.3100 - 2.1400 0.95 1815 201 0.1863 0.2574 REMARK 3 6 2.1400 - 2.0200 0.94 1821 202 0.2187 0.2615 REMARK 3 7 2.0200 - 1.9200 0.80 1517 169 0.2410 0.2416 REMARK 3 8 1.9200 - 1.8300 0.65 1243 138 0.2494 0.2610 REMARK 3 9 1.8300 - 1.7600 0.47 898 100 0.2462 0.2917 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) : 0.157 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.779 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.28 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.95 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 : 0.019 1398 REMARK 3 ANGLE : 1.607 1874 REMARK 3 CHIRALITY : 0.069 177 REMARK 3 PLANARITY : 0.026 243 REMARK 3 DIHEDRAL : 11.430 192 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1238 THROUGH 1268 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.0193 -1.8993 1.6613 REMARK 3 T TENSOR REMARK 3 T11: 0.1616 T22: 0.1709 REMARK 3 T33: 0.2055 T12: 0.0003 REMARK 3 T13: -0.0032 T23: -0.0171 REMARK 3 L TENSOR REMARK 3 L11: 1.1464 L22: 3.0122 REMARK 3 L33: 2.1461 L12: 0.8707 REMARK 3 L13: -0.2039 L23: 2.1288 REMARK 3 S TENSOR REMARK 3 S11: -0.0492 S12: 0.0751 S13: -0.0719 REMARK 3 S21: -0.3511 S22: -0.1522 S23: 0.5086 REMARK 3 S31: 0.0389 S32: -0.2012 S33: 0.0007 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1269 THROUGH 1280 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.1835 -0.3904 12.1949 REMARK 3 T TENSOR REMARK 3 T11: 0.3377 T22: 0.3193 REMARK 3 T33: 0.2207 T12: -0.0460 REMARK 3 T13: 0.0320 T23: 0.0015 REMARK 3 L TENSOR REMARK 3 L11: 1.4252 L22: 0.2673 REMARK 3 L33: 0.6886 L12: 0.3714 REMARK 3 L13: 0.3149 L23: 0.0127 REMARK 3 S TENSOR REMARK 3 S11: -0.0427 S12: -1.0290 S13: 0.0953 REMARK 3 S21: 0.3448 S22: -0.0625 S23: 0.3959 REMARK 3 S31: 0.3710 S32: -0.4274 S33: -0.0660 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1281 THROUGH 1308 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.9303 3.2240 3.7511 REMARK 3 T TENSOR REMARK 3 T11: 0.1436 T22: 0.2418 REMARK 3 T33: 0.1901 T12: -0.0039 REMARK 3 T13: 0.0159 T23: 0.0191 REMARK 3 L TENSOR REMARK 3 L11: 1.3654 L22: 2.5852 REMARK 3 L33: 1.4570 L12: -0.3918 REMARK 3 L13: -0.2731 L23: 0.1850 REMARK 3 S TENSOR REMARK 3 S11: -0.0340 S12: -0.0065 S13: -0.1820 REMARK 3 S21: -0.0443 S22: 0.1920 S23: -0.7374 REMARK 3 S31: 0.1481 S32: 0.5750 S33: 0.0462 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1313 THROUGH 1326 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.8451 -2.5743 -6.6923 REMARK 3 T TENSOR REMARK 3 T11: 0.5775 T22: 0.5193 REMARK 3 T33: 0.5304 T12: -0.0425 REMARK 3 T13: 0.2033 T23: 0.0348 REMARK 3 L TENSOR REMARK 3 L11: 0.0676 L22: 0.5379 REMARK 3 L33: 0.1182 L12: 0.1354 REMARK 3 L13: 0.0711 L23: 0.0677 REMARK 3 S TENSOR REMARK 3 S11: -0.3329 S12: 0.6312 S13: 0.2317 REMARK 3 S21: -1.6921 S22: 0.7937 S23: -1.8496 REMARK 3 S31: 0.8286 S32: 0.1292 S33: 0.0249 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1236 THROUGH 1268 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.5967 5.5518 30.1543 REMARK 3 T TENSOR REMARK 3 T11: 0.1338 T22: 0.1147 REMARK 3 T33: 0.1635 T12: 0.0068 REMARK 3 T13: -0.0023 T23: -0.0281 REMARK 3 L TENSOR REMARK 3 L11: 1.5945 L22: 3.0069 REMARK 3 L33: 1.3147 L12: -0.1764 REMARK 3 L13: 0.0932 L23: 2.0055 REMARK 3 S TENSOR REMARK 3 S11: 0.0232 S12: -0.2493 S13: 0.1512 REMARK 3 S21: 0.3542 S22: -0.2105 S23: 0.3986 REMARK 3 S31: -0.0407 S32: -0.1673 S33: -0.0116 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1269 THROUGH 1280 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.2942 3.0309 19.7346 REMARK 3 T TENSOR REMARK 3 T11: 0.2923 T22: 0.3229 REMARK 3 T33: 0.3539 T12: -0.0509 REMARK 3 T13: -0.1367 T23: 0.1188 REMARK 3 L TENSOR REMARK 3 L11: 0.2633 L22: 0.0732 REMARK 3 L33: 0.5894 L12: -0.1089 REMARK 3 L13: -0.3300 L23: 0.2098 REMARK 3 S TENSOR REMARK 3 S11: -0.4301 S12: 0.1518 S13: 0.4992 REMARK 3 S21: -0.0714 S22: 0.4273 S23: 0.5913 REMARK 3 S31: -0.1138 S32: -0.5611 S33: -0.0799 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1281 THROUGH 1308 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.5276 0.2916 22.2647 REMARK 3 T TENSOR REMARK 3 T11: 0.1316 T22: 0.1609 REMARK 3 T33: 0.1119 T12: 0.0045 REMARK 3 T13: 0.0053 T23: 0.0001 REMARK 3 L TENSOR REMARK 3 L11: 1.8505 L22: 1.7670 REMARK 3 L33: 1.8161 L12: -0.0661 REMARK 3 L13: 0.8357 L23: -0.9469 REMARK 3 S TENSOR REMARK 3 S11: -0.0430 S12: 0.0576 S13: 0.0387 REMARK 3 S21: -0.2854 S22: 0.0504 S23: -0.0976 REMARK 3 S31: 0.1809 S32: 0.3558 S33: 0.0034 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1309 THROUGH 1328 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.6829 5.9663 32.1314 REMARK 3 T TENSOR REMARK 3 T11: 0.2579 T22: 0.4483 REMARK 3 T33: 0.4984 T12: 0.0632 REMARK 3 T13: -0.0809 T23: -0.0607 REMARK 3 L TENSOR REMARK 3 L11: 0.6184 L22: 0.8677 REMARK 3 L33: 2.0050 L12: 0.0192 REMARK 3 L13: 0.1179 L23: -0.1577 REMARK 3 S TENSOR REMARK 3 S11: -0.1273 S12: -0.5343 S13: 0.5595 REMARK 3 S21: 0.2416 S22: 0.1518 S23: -0.6908 REMARK 3 S31: 0.2637 S32: 0.8876 S33: -0.0078 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 9GBF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1292140580. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-18 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 : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.998 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 : XDS REMARK 200 DATA SCALING SOFTWARE : STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17296 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.601 REMARK 200 RESOLUTION RANGE LOW (A) : 36.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.3 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG SMEAR MEDIUM, 0.1M HEPES, PH REMARK 280 7.5, 0.05M MAGNESIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 22.62450 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 ARG A 1229 REMARK 465 ALA A 1230 REMARK 465 LYS A 1231 REMARK 465 GLY A 1232 REMARK 465 GLU A 1233 REMARK 465 GLY A 1234 REMARK 465 LYS A 1235 REMARK 465 ARG A 1236 REMARK 465 GLN A 1237 REMARK 465 ASP A 1309 REMARK 465 GLY A 1310 REMARK 465 THR A 1311 REMARK 465 ALA A 1312 REMARK 465 THR A 1316 REMARK 465 PRO A 1317 REMARK 465 ASP A 1318 REMARK 465 GLY A 1319 REMARK 465 ASP A 1327 REMARK 465 LEU A 1328 REMARK 465 GLY A 1329 REMARK 465 ALA A 1330 REMARK 465 ALA A 1331 REMARK 465 ARG B 1229 REMARK 465 ALA B 1230 REMARK 465 LYS B 1231 REMARK 465 GLY B 1232 REMARK 465 GLU B 1233 REMARK 465 GLY B 1234 REMARK 465 LYS B 1235 REMARK 465 GLY B 1310 REMARK 465 THR B 1311 REMARK 465 ALA B 1312 REMARK 465 GLY B 1329 REMARK 465 ALA B 1330 REMARK 465 ALA B 1331 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 ARG A1320 CG CD NE CZ NH1 NH2 REMARK 470 LEU B1270 CG CD1 CD2 REMARK 470 LYS B1272 CG CD CE NZ REMARK 470 LYS B1305 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP B1247 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 CYS B1280 CA - CB - SG ANGL. DEV. = 7.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 GLU A1325 2.14 -60.47 REMARK 500 PHE B1258 10.71 58.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A1273 0.10 SIDE CHAIN REMARK 500 ARG B1273 0.14 SIDE CHAIN REMARK 500 ARG B1320 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1404 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1242 SG REMARK 620 2 CYS A1245 SG 111.6 REMARK 620 3 HIS A1264 ND1 102.8 99.0 REMARK 620 4 CYS A1267 SG 118.0 108.4 115.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1254 SG REMARK 620 2 CYS A1259 SG 110.2 REMARK 620 3 CYS A1280 SG 106.0 118.4 REMARK 620 4 HIS A1283 NE2 107.1 107.8 106.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1405 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO A1281 O REMARK 620 2 HIS A1284 O 78.9 REMARK 620 3 ASP A1286 OD1 140.0 101.2 REMARK 620 4 PRO A1300 O 88.1 156.1 101.6 REMARK 620 5 SER A1302 OG 98.6 76.4 120.6 85.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1285 SG REMARK 620 2 CYS A1288 SG 111.2 REMARK 620 3 CYS A1304 SG 111.8 109.8 REMARK 620 4 HIS A1307 ND1 112.9 112.4 98.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1296 SG REMARK 620 2 CYS A1299 SG 120.1 REMARK 620 3 CYS A1323 SG 111.0 109.2 REMARK 620 4 HIS A1326 NE2 104.8 110.3 99.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B1242 SG REMARK 620 2 CYS B1245 SG 111.9 REMARK 620 3 HIS B1264 ND1 103.9 99.8 REMARK 620 4 CYS B1267 SG 113.6 111.1 115.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B1254 SG REMARK 620 2 CYS B1259 SG 111.2 REMARK 620 3 CYS B1280 SG 109.9 118.5 REMARK 620 4 HIS B1283 NE2 106.0 107.3 102.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B1405 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO B1281 O REMARK 620 2 HIS B1284 O 77.5 REMARK 620 3 ASP B1286 OD1 128.4 99.2 REMARK 620 4 PRO B1300 O 86.4 162.1 96.9 REMARK 620 5 SER B1302 OG 99.1 88.6 132.5 86.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1404 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B1285 SG REMARK 620 2 CYS B1288 SG 112.2 REMARK 620 3 CYS B1304 SG 112.4 111.0 REMARK 620 4 HIS B1307 ND1 109.2 108.0 103.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B1296 SG REMARK 620 2 CYS B1299 SG 118.1 REMARK 620 3 CYS B1323 SG 110.3 107.5 REMARK 620 4 HIS B1326 NE2 93.3 124.6 101.5 REMARK 620 N 1 2 3 DBREF 9GBF A 1229 1331 UNP O96028 NSD2_HUMAN 1229 1331 DBREF 9GBF B 1229 1331 UNP O96028 NSD2_HUMAN 1229 1331 SEQADV 9GBF SER A 1324 UNP O96028 CYS 1324 ENGINEERED MUTATION SEQADV 9GBF SER B 1324 UNP O96028 CYS 1324 ENGINEERED MUTATION SEQRES 1 A 103 ARG ALA LYS GLY GLU GLY LYS ARG GLN SER GLU ASP GLU SEQRES 2 A 103 CYS PHE ARG CYS GLY ASP GLY GLY GLN LEU VAL LEU CYS SEQRES 3 A 103 ASP ARG LYS PHE CYS THR LYS ALA TYR HIS LEU SER CYS SEQRES 4 A 103 LEU GLY LEU GLY LYS ARG PRO PHE GLY LYS TRP GLU CYS SEQRES 5 A 103 PRO TRP HIS HIS CYS ASP VAL CYS GLY LYS PRO SER THR SEQRES 6 A 103 SER PHE CYS HIS LEU CYS PRO ASN SER PHE CYS LYS GLU SEQRES 7 A 103 HIS GLN ASP GLY THR ALA PHE SER CYS THR PRO ASP GLY SEQRES 8 A 103 ARG SER TYR CYS SER GLU HIS ASP LEU GLY ALA ALA SEQRES 1 B 103 ARG ALA LYS GLY GLU GLY LYS ARG GLN SER GLU ASP GLU SEQRES 2 B 103 CYS PHE ARG CYS GLY ASP GLY GLY GLN LEU VAL LEU CYS SEQRES 3 B 103 ASP ARG LYS PHE CYS THR LYS ALA TYR HIS LEU SER CYS SEQRES 4 B 103 LEU GLY LEU GLY LYS ARG PRO PHE GLY LYS TRP GLU CYS SEQRES 5 B 103 PRO TRP HIS HIS CYS ASP VAL CYS GLY LYS PRO SER THR SEQRES 6 B 103 SER PHE CYS HIS LEU CYS PRO ASN SER PHE CYS LYS GLU SEQRES 7 B 103 HIS GLN ASP GLY THR ALA PHE SER CYS THR PRO ASP GLY SEQRES 8 B 103 ARG SER TYR CYS SER GLU HIS ASP LEU GLY ALA ALA HET ZN A1401 1 HET ZN A1402 1 HET ZN A1403 1 HET ZN A1404 1 HET NA A1405 1 HET PEG A1406 17 HET ZN B1401 1 HET ZN B1402 1 HET ZN B1403 1 HET ZN B1404 1 HET NA B1405 1 HET EPE B1406 32 HETNAM ZN ZINC ION HETNAM NA SODIUM ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 3 ZN 8(ZN 2+) FORMUL 7 NA 2(NA 1+) FORMUL 8 PEG C4 H10 O3 FORMUL 14 EPE C8 H18 N2 O4 S FORMUL 15 HOH *75(H2 O) HELIX 1 AA1 HIS A 1264 GLY A 1269 5 6 HELIX 2 AA2 CYS A 1280 HIS A 1284 5 5 HELIX 3 AA3 CYS A 1304 GLN A 1308 5 5 HELIX 4 AA4 LEU B 1265 GLY B 1269 5 5 HELIX 5 AA5 CYS B 1280 HIS B 1284 5 5 SHEET 1 AA1 2 VAL A1252 LEU A1253 0 SHEET 2 AA1 2 ALA A1262 TYR A1263 -1 O TYR A1263 N VAL A1252 SHEET 1 AA2 2 SER A1294 PHE A1295 0 SHEET 2 AA2 2 SER A1302 PHE A1303 -1 O PHE A1303 N SER A1294 SHEET 1 AA3 2 VAL B1252 LEU B1253 0 SHEET 2 AA3 2 ALA B1262 TYR B1263 -1 O TYR B1263 N VAL B1252 SHEET 1 AA4 2 SER B1294 PHE B1295 0 SHEET 2 AA4 2 SER B1302 PHE B1303 -1 O PHE B1303 N SER B1294 SHEET 1 AA5 2 SER B1314 CYS B1315 0 SHEET 2 AA5 2 SER B1321 TYR B1322 -1 O TYR B1322 N SER B1314 LINK SG CYS A1242 ZN ZN A1404 1555 1555 2.30 LINK SG CYS A1245 ZN ZN A1404 1555 1555 2.28 LINK SG CYS A1254 ZN ZN A1401 1555 1555 2.32 LINK SG CYS A1259 ZN ZN A1401 1555 1555 2.26 LINK ND1 HIS A1264 ZN ZN A1404 1555 1555 2.11 LINK SG CYS A1267 ZN ZN A1404 1555 1555 2.25 LINK SG CYS A1280 ZN ZN A1401 1555 1555 2.30 LINK O PRO A1281 NA NA A1405 1555 1555 2.39 LINK NE2 HIS A1283 ZN ZN A1401 1555 1555 1.99 LINK O HIS A1284 NA NA A1405 1555 1555 2.51 LINK SG CYS A1285 ZN ZN A1403 1555 1555 2.30 LINK OD1 ASP A1286 NA NA A1405 1555 1555 2.34 LINK SG CYS A1288 ZN ZN A1403 1555 1555 2.21 LINK SG CYS A1296 ZN ZN A1402 1555 1555 2.26 LINK SG CYS A1299 ZN ZN A1402 1555 1555 2.30 LINK O PRO A1300 NA NA A1405 1555 1555 2.67 LINK OG SER A1302 NA NA A1405 1555 1555 2.65 LINK SG CYS A1304 ZN ZN A1403 1555 1555 2.21 LINK ND1 HIS A1307 ZN ZN A1403 1555 1555 2.05 LINK SG CYS A1323 ZN ZN A1402 1555 1555 2.25 LINK NE2 HIS A1326 ZN ZN A1402 1555 1555 2.06 LINK SG CYS B1242 ZN ZN B1401 1555 1555 2.32 LINK SG CYS B1245 ZN ZN B1401 1555 1555 2.26 LINK SG CYS B1254 ZN ZN B1402 1555 1555 2.31 LINK SG CYS B1259 ZN ZN B1402 1555 1555 2.28 LINK ND1 HIS B1264 ZN ZN B1401 1555 1555 2.02 LINK SG CYS B1267 ZN ZN B1401 1555 1555 2.32 LINK SG CYS B1280 ZN ZN B1402 1555 1555 2.32 LINK O PRO B1281 NA NA B1405 1555 1555 2.38 LINK NE2 HIS B1283 ZN ZN B1402 1555 1555 2.03 LINK O HIS B1284 NA NA B1405 1555 1555 2.43 LINK SG CYS B1285 ZN ZN B1404 1555 1555 2.33 LINK OD1 ASP B1286 NA NA B1405 1555 1555 2.45 LINK SG CYS B1288 ZN ZN B1404 1555 1555 2.28 LINK SG CYS B1296 ZN ZN B1403 1555 1555 2.29 LINK SG CYS B1299 ZN ZN B1403 1555 1555 2.31 LINK O PRO B1300 NA NA B1405 1555 1555 2.73 LINK OG SER B1302 NA NA B1405 1555 1555 2.43 LINK SG CYS B1304 ZN ZN B1404 1555 1555 2.28 LINK ND1 HIS B1307 ZN ZN B1404 1555 1555 2.10 LINK SG CYS B1323 ZN ZN B1403 1555 1555 2.29 LINK NE2 HIS B1326 ZN ZN B1403 1555 1555 2.05 CRYST1 36.131 45.249 60.646 90.00 99.65 90.00 P 1 21 1 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 0.027677 0.000000 0.004706 0.00000 SCALE2 0.000000 0.022100 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016726 0.00000