HEADER TRANSFERASE/NUCLEAR PROTEIN 17-AUG-12 4GNG TITLE CRYSTAL STRUCTURE OF NSD3 TANDEM PHD5-C5HCH DOMAINS COMPLEXED WITH TITLE 2 H3K9ME3 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE NSD3; COMPND 3 CHAIN: A, D; COMPND 4 FRAGMENT: UNP RESIDUES 1310-1413; COMPND 5 SYNONYM: NUCLEAR SET DOMAIN-CONTAINING PROTEIN 3, PROTEIN WHISTLE, COMPND 6 WHSC1-LIKE 1 ISOFORM 9 WITH METHYLTRANSFERASE ACTIVITY TO LYSINE, COMPND 7 WOLF-HIRSCHHORN SYNDROME CANDIDATE 1-LIKE PROTEIN 1, WHSC1-LIKE COMPND 8 PROTEIN 1; COMPND 9 EC: 2.1.1.43; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: HISTONE H3.3; COMPND 13 CHAIN: B, F; COMPND 14 FRAGMENT: UNP RESIDUES 2-16; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: WHSC1L1, NSD3, DC28; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 OTHER_DETAILS: SYNTHETIC KEYWDS ZINC FINGER, TRANSCRIPTION, HISTONE, LYSINE METHYALTION, NUCLEAR KEYWDS 2 PROTEIN, TRANSFERASE-NUCLEAR PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR F.LI,C.HE,J.WU,Y.SHI REVDAT 3 08-NOV-23 4GNG 1 REMARK SEQADV LINK REVDAT 2 04-SEP-13 4GNG 1 JRNL REVDAT 1 02-JAN-13 4GNG 0 JRNL AUTH C.HE,F.LI,J.ZHANG,J.WU,Y.SHI JRNL TITL THE METHYLTRANSFERASE NSD3 HAS CHROMATIN-BINDING MOTIFS, JRNL TITL 2 PHD5-C5HCH, THAT ARE DISTINCT FROM OTHER NSD (NUCLEAR JRNL TITL 3 RECEPTOR SET DOMAIN) FAMILY MEMBERS IN THEIR HISTONE H3 JRNL TITL 4 RECOGNITION. JRNL REF J.BIOL.CHEM. V. 288 4692 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 23269674 JRNL DOI 10.1074/JBC.M112.426148 REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 34289 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1733 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.73 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.78 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2362 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE SET COUNT : 122 REMARK 3 BIN FREE R VALUE : 0.3040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1656 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 294 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.091 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.093 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.057 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.735 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1754 ; 0.009 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2373 ; 1.314 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 218 ; 6.331 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 80 ;37.041 ;24.750 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 282 ;12.425 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;28.428 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 239 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1358 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 4GNG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074403. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97837 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34350 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 50.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10800 REMARK 200 FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.55600 REMARK 200 R SYM FOR SHELL (I) : 0.55600 REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4GNE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES PH 6.5, 20% PEG 3350, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 283K 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 28.10000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.61500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.98000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.61500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.10000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.98000 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, F 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 1307 REMARK 465 ASN A 1308 REMARK 465 ALA A 1309 REMARK 465 ARG A 1310 REMARK 465 LYS A 1311 REMARK 465 ILE A 1312 REMARK 465 LYS A 1313 REMARK 465 THR A 1314 REMARK 465 GLU A 1315 REMARK 465 PRO A 1316 REMARK 465 LYS A 1317 REMARK 465 GLN A 1318 REMARK 465 THR B 11 REMARK 465 GLY B 12 REMARK 465 GLY B 13 REMARK 465 LYS B 14 REMARK 465 ALA B 15 REMARK 465 SER D 1307 REMARK 465 ASN D 1308 REMARK 465 ALA D 1309 REMARK 465 ARG D 1310 REMARK 465 LYS D 1311 REMARK 465 ILE D 1312 REMARK 465 LYS D 1313 REMARK 465 THR D 1314 REMARK 465 GLU D 1315 REMARK 465 PRO D 1316 REMARK 465 THR F 11 REMARK 465 GLY F 12 REMARK 465 GLY F 13 REMARK 465 LYS F 14 REMARK 465 ALA F 15 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 A1400 17.93 58.96 REMARK 500 GLU D1400 17.86 59.60 REMARK 500 ALA D1412 73.81 -154.35 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 A1501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1324 SG REMARK 620 2 CYS A1327 SG 112.3 REMARK 620 3 HIS A1346 ND1 103.7 95.6 REMARK 620 4 CYS A1349 SG 115.9 111.9 115.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1336 SG REMARK 620 2 CYS A1341 SG 110.5 REMARK 620 3 CYS A1362 SG 107.7 120.0 REMARK 620 4 HIS A1365 NE2 108.9 107.4 101.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1367 SG REMARK 620 2 CYS A1370 SG 118.9 REMARK 620 3 CYS A1386 SG 111.3 101.9 REMARK 620 4 HIS A1389 ND1 110.7 112.4 99.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1378 SG REMARK 620 2 CYS A1381 SG 125.0 REMARK 620 3 CYS A1405 SG 111.5 104.8 REMARK 620 4 HIS A1408 NE2 99.5 110.1 104.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D1501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D1324 SG REMARK 620 2 CYS D1327 SG 112.3 REMARK 620 3 HIS D1346 ND1 102.1 98.0 REMARK 620 4 CYS D1349 SG 115.5 112.1 115.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D1502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D1336 SG REMARK 620 2 CYS D1341 SG 111.9 REMARK 620 3 CYS D1362 SG 109.0 119.4 REMARK 620 4 HIS D1365 NE2 104.2 108.0 102.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D1504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D1367 SG REMARK 620 2 CYS D1370 SG 118.1 REMARK 620 3 CYS D1386 SG 111.7 106.9 REMARK 620 4 HIS D1389 ND1 111.2 107.0 100.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D1503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D1378 SG REMARK 620 2 CYS D1381 SG 122.7 REMARK 620 3 CYS D1405 SG 112.4 106.2 REMARK 620 4 HIS D1408 NE2 99.2 113.6 100.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 1501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 1502 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 1503 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 1504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GND RELATED DB: PDB REMARK 900 RELATED ID: 4GNE RELATED DB: PDB REMARK 900 RELATED ID: 4GNF RELATED DB: PDB DBREF 4GNG A 1310 1413 UNP Q9BZ95 NSD3_HUMAN 1310 1413 DBREF 4GNG B 1 15 UNP P84243 H33_HUMAN 2 16 DBREF 4GNG D 1310 1413 UNP Q9BZ95 NSD3_HUMAN 1310 1413 DBREF 4GNG F 1 15 UNP P84243 H33_HUMAN 2 16 SEQADV 4GNG SER A 1307 UNP Q9BZ95 EXPRESSION TAG SEQADV 4GNG ASN A 1308 UNP Q9BZ95 EXPRESSION TAG SEQADV 4GNG ALA A 1309 UNP Q9BZ95 EXPRESSION TAG SEQADV 4GNG SER D 1307 UNP Q9BZ95 EXPRESSION TAG SEQADV 4GNG ASN D 1308 UNP Q9BZ95 EXPRESSION TAG SEQADV 4GNG ALA D 1309 UNP Q9BZ95 EXPRESSION TAG SEQRES 1 A 107 SER ASN ALA ARG LYS ILE LYS THR GLU PRO LYS GLN MET SEQRES 2 A 107 HIS GLU ASP TYR CYS PHE GLN CYS GLY ASP GLY GLY GLU SEQRES 3 A 107 LEU VAL MET CYS ASP LYS LYS ASP CYS PRO LYS ALA TYR SEQRES 4 A 107 HIS LEU LEU CYS LEU ASN LEU THR GLN PRO PRO TYR GLY SEQRES 5 A 107 LYS TRP GLU CYS PRO TRP HIS GLN CYS ASP GLU CYS SER SEQRES 6 A 107 SER ALA ALA VAL SER PHE CYS GLU PHE CYS PRO HIS SER SEQRES 7 A 107 PHE CYS LYS ASP HIS GLU LYS GLY ALA LEU VAL PRO SER SEQRES 8 A 107 ALA LEU GLU GLY ARG LEU CYS CYS SER GLU HIS ASP PRO SEQRES 9 A 107 MET ALA PRO SEQRES 1 B 15 ALA ARG THR LYS GLN THR ALA ARG M3L SER THR GLY GLY SEQRES 2 B 15 LYS ALA SEQRES 1 D 107 SER ASN ALA ARG LYS ILE LYS THR GLU PRO LYS GLN MET SEQRES 2 D 107 HIS GLU ASP TYR CYS PHE GLN CYS GLY ASP GLY GLY GLU SEQRES 3 D 107 LEU VAL MET CYS ASP LYS LYS ASP CYS PRO LYS ALA TYR SEQRES 4 D 107 HIS LEU LEU CYS LEU ASN LEU THR GLN PRO PRO TYR GLY SEQRES 5 D 107 LYS TRP GLU CYS PRO TRP HIS GLN CYS ASP GLU CYS SER SEQRES 6 D 107 SER ALA ALA VAL SER PHE CYS GLU PHE CYS PRO HIS SER SEQRES 7 D 107 PHE CYS LYS ASP HIS GLU LYS GLY ALA LEU VAL PRO SER SEQRES 8 D 107 ALA LEU GLU GLY ARG LEU CYS CYS SER GLU HIS ASP PRO SEQRES 9 D 107 MET ALA PRO SEQRES 1 F 15 ALA ARG THR LYS GLN THR ALA ARG M3L SER THR GLY GLY SEQRES 2 F 15 LYS ALA MODRES 4GNG M3L B 9 LYS N-TRIMETHYLLYSINE MODRES 4GNG M3L F 9 LYS N-TRIMETHYLLYSINE HET M3L B 9 12 HET M3L F 9 12 HET ZN A1501 1 HET ZN A1502 1 HET ZN A1503 1 HET ZN A1504 1 HET GOL A1505 6 HET GOL B 101 6 HET GOL B 102 6 HET ZN D1501 1 HET ZN D1502 1 HET ZN D1503 1 HET ZN D1504 1 HETNAM M3L N-TRIMETHYLLYSINE HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 M3L 2(C9 H21 N2 O2 1+) FORMUL 5 ZN 8(ZN 2+) FORMUL 9 GOL 3(C3 H8 O3) FORMUL 16 HOH *294(H2 O) HELIX 1 1 LEU A 1347 ASN A 1351 5 5 HELIX 2 2 CYS A 1362 GLN A 1366 5 5 HELIX 3 3 LEU D 1347 ASN D 1351 5 5 HELIX 4 4 CYS D 1362 GLN D 1366 5 5 HELIX 5 5 CYS D 1386 GLU D 1390 5 5 SHEET 1 A 3 ALA A1344 TYR A1345 0 SHEET 2 A 3 GLU A1332 MET A1335 -1 N VAL A1334 O TYR A1345 SHEET 3 A 3 THR B 3 GLN B 5 -1 O LYS B 4 N LEU A1333 SHEET 1 B 2 SER A1376 PHE A1377 0 SHEET 2 B 2 SER A1384 PHE A1385 -1 O PHE A1385 N SER A1376 SHEET 1 C 2 VAL A1395 PRO A1396 0 SHEET 2 C 2 LEU A1403 CYS A1404 -1 O CYS A1404 N VAL A1395 SHEET 1 D 3 ALA D1344 TYR D1345 0 SHEET 2 D 3 GLU D1332 MET D1335 -1 N VAL D1334 O TYR D1345 SHEET 3 D 3 ARG F 2 GLN F 5 -1 O LYS F 4 N LEU D1333 SHEET 1 E 2 SER D1376 PHE D1377 0 SHEET 2 E 2 SER D1384 PHE D1385 -1 O PHE D1385 N SER D1376 SHEET 1 F 2 VAL D1395 PRO D1396 0 SHEET 2 F 2 LEU D1403 CYS D1404 -1 O CYS D1404 N VAL D1395 LINK C ARG B 8 N M3L B 9 1555 1555 1.33 LINK C M3L B 9 N SER B 10 1555 1555 1.34 LINK C ARG F 8 N M3L F 9 1555 1555 1.34 LINK C M3L F 9 N SER F 10 1555 1555 1.33 LINK SG CYS A1324 ZN ZN A1501 1555 1555 2.34 LINK SG CYS A1327 ZN ZN A1501 1555 1555 2.30 LINK SG CYS A1336 ZN ZN A1502 1555 1555 2.28 LINK SG CYS A1341 ZN ZN A1502 1555 1555 2.30 LINK ND1 HIS A1346 ZN ZN A1501 1555 1555 2.02 LINK SG CYS A1349 ZN ZN A1501 1555 1555 2.23 LINK SG CYS A1362 ZN ZN A1502 1555 1555 2.36 LINK NE2 HIS A1365 ZN ZN A1502 1555 1555 2.08 LINK SG CYS A1367 ZN ZN A1504 1555 1555 2.34 LINK SG CYS A1370 ZN ZN A1504 1555 1555 2.30 LINK SG CYS A1378 ZN ZN A1503 1555 1555 2.30 LINK SG CYS A1381 ZN ZN A1503 1555 1555 2.30 LINK SG CYS A1386 ZN ZN A1504 1555 1555 2.12 LINK ND1 HIS A1389 ZN ZN A1504 1555 1555 2.15 LINK SG CYS A1405 ZN ZN A1503 1555 1555 2.32 LINK NE2 HIS A1408 ZN ZN A1503 1555 1555 2.10 LINK SG CYS D1324 ZN ZN D1501 1555 1555 2.32 LINK SG CYS D1327 ZN ZN D1501 1555 1555 2.27 LINK SG CYS D1336 ZN ZN D1502 1555 1555 2.32 LINK SG CYS D1341 ZN ZN D1502 1555 1555 2.28 LINK ND1 HIS D1346 ZN ZN D1501 1555 1555 2.11 LINK SG CYS D1349 ZN ZN D1501 1555 1555 2.30 LINK SG CYS D1362 ZN ZN D1502 1555 1555 2.30 LINK NE2 HIS D1365 ZN ZN D1502 1555 1555 2.03 LINK SG CYS D1367 ZN ZN D1504 1555 1555 2.30 LINK SG CYS D1370 ZN ZN D1504 1555 1555 2.30 LINK SG CYS D1378 ZN ZN D1503 1555 1555 2.30 LINK SG CYS D1381 ZN ZN D1503 1555 1555 2.29 LINK SG CYS D1386 ZN ZN D1504 1555 1555 2.30 LINK ND1 HIS D1389 ZN ZN D1504 1555 1555 2.12 LINK SG CYS D1405 ZN ZN D1503 1555 1555 2.36 LINK NE2 HIS D1408 ZN ZN D1503 1555 1555 2.07 SITE 1 AC1 4 CYS A1324 CYS A1327 HIS A1346 CYS A1349 SITE 1 AC2 4 CYS A1336 CYS A1341 CYS A1362 HIS A1365 SITE 1 AC3 4 CYS A1378 CYS A1381 CYS A1405 HIS A1408 SITE 1 AC4 4 CYS A1367 CYS A1370 CYS A1386 HIS A1389 SITE 1 AC5 5 TRP A1364 PHE A1377 GLU A1379 HOH A1651 SITE 2 AC5 5 HOH A1661 SITE 1 AC6 4 CYS A1327 HIS A1346 CYS A1349 ARG B 8 SITE 1 AC7 3 TRP D1364 PHE D1377 GLU D1379 SITE 1 AC8 4 CYS D1324 CYS D1327 HIS D1346 CYS D1349 SITE 1 AC9 4 CYS D1336 CYS D1341 CYS D1362 HIS D1365 SITE 1 BC1 4 CYS D1378 CYS D1381 CYS D1405 HIS D1408 SITE 1 BC2 4 CYS D1367 CYS D1370 CYS D1386 HIS D1389 CRYST1 56.200 59.960 95.230 90.00 90.00 90.00 P 21 21 21 8 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 0.017794 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016678 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010501 0.00000