HEADER TRANSFERASE 24-DEC-19 6VDB TITLE SETD2 IN COMPLEX WITH A H3-VARIANT SUPER-SUBSTRATE PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE SETD2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HIF-1,HUNTINGTIN YEAST PARTNER B,HUNTINGTIN-INTERACTING COMPND 5 PROTEIN 1,HIP-1,HUNTINGTIN-INTERACTING PROTEIN B,LYSINE N- COMPND 6 METHYLTRANSFERASE 3A,PROTEIN-LYSINE N-METHYLTRANSFERASE SETD2,SET COMPND 7 DOMAIN-CONTAINING PROTEIN 2,HSET2,P231HBP; COMPND 8 EC: 2.1.1.-; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: ALA-PRO-ARG-PHE-GLY-GLY-VAL-MET-ARG-PRO-ASN-ARG; COMPND 12 CHAIN: H; COMPND 13 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: SETD2, HIF1, HYPB, KIAA1732, KMT3A, SET2, HSPC069; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: CODON PLUS RIL (STRATAGEN); 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 KEYWDS TRANSFERASE, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC EXPDTA X-RAY DIFFRACTION AUTHOR S.BELDAR,W.TEMPEL,C.H.ARROWSMITH,C.BOUNTRA,A.M.EDWARDS,A.JELTSCH, AUTHOR 2 J.MIN,STRUCTURAL GENOMICS CONSORTIUM,STRUCTURAL GENOMICS CONSORTIUM AUTHOR 3 (SGC) REVDAT 4 11-OCT-23 6VDB 1 REMARK REVDAT 3 11-NOV-20 6VDB 1 TITLE REVDAT 2 30-SEP-20 6VDB 1 JRNL REVDAT 1 29-JAN-20 6VDB 0 JRNL AUTH M.K.SCHUHMACHER,S.BELDAR,M.S.KHELLA,A.BROHM,J.LUDWIG, JRNL AUTH 2 W.TEMPEL,S.WEIRICH,J.MIN,A.JELTSCH JRNL TITL SEQUENCE SPECIFICITY ANALYSIS OF THE SETD2 PROTEIN LYSINE JRNL TITL 2 METHYLTRANSFERASE AND DISCOVERY OF A SETD2 SUPER-SUBSTRATE. JRNL REF COMMUN BIOL V. 3 511 2020 JRNL REFN ESSN 2399-3642 JRNL PMID 32939018 JRNL DOI 10.1038/S42003-020-01223-6 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 16545 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) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 735 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.32 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.55 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2289 REMARK 3 BIN FREE R VALUE : 0.1987 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 14 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1912 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 24 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -19.92160 REMARK 3 B22 (A**2) : 10.38020 REMARK 3 B33 (A**2) : 9.54130 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) : 0.330 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.239 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.209 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.236 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.210 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 : 0.909 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.854 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : NULL ; NULL ; NULL REMARK 3 BOND ANGLES : NULL ; NULL ; NULL REMARK 3 TORSION ANGLES : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS : NULL ; NULL ; NULL 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 : NULL ; NULL ; NULL 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 : NULL ; NULL ; NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : NULL REMARK 3 OTHER TORSION ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 LATEST REFINEMENT ROUNDS WERE AGAINST THE EARLIER COLLECTED "IN- REMARK 3 HOUSE" COPPER ANODE DATA, OUT OF CONCERN ABOUT RADIATION-INDUCED REMARK 3 CRYSTAL DAMAGE. REMARK 3 CYS1471 APPEARS TO BE COVALENTLY MODIFIED. DENSITY SUPPORT IS WEAK REMARK 3 AND/OR AMBIGUOUS FOR SIGNIFICANT MODEL FEATURES, FOR EXAMPLE SETD2 REMARK 3 GLN1676, LIGAND PEPTIDE R31, R37. TWO CONFORMATIONS OF THE R37 REMARK 3 SIDE CHAIN WERE MODELED TO DENOTE UNCERTAINTY IN THE ACTUAL REMARK 3 CONFORMATION, RATHER THAN OBSERVATION OF THOSE SPECIFIC REMARK 3 CONFORMATIONS, AS WE FAILED TO FIT A FAVORED ROTAMER TO THE WEAK REMARK 3 DENSITY. REMARK 4 REMARK 4 6VDB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1000245990. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-19; 21-OCT-19 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; N REMARK 200 RADIATION SOURCE : APS; ROTATING ANODE REMARK 200 BEAMLINE : 24-ID-E; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; RIGAKU FR-E REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918; 1.5418 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL; CCD REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M; RIGAKU REMARK 200 SATURN A200 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16627 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 47.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.14200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 8.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 47.65 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.04800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 5JLB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M KSCN, 0.1 M TRIS-HCL PH 8.5, AND REMARK 280 26% PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 30.18500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.80500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.26000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.80500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.18500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.26000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H 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 MET A 1417 REMARK 465 HIS A 1418 REMARK 465 HIS A 1419 REMARK 465 HIS A 1420 REMARK 465 HIS A 1421 REMARK 465 HIS A 1422 REMARK 465 HIS A 1423 REMARK 465 SER A 1424 REMARK 465 SER A 1425 REMARK 465 GLY A 1426 REMARK 465 ARG A 1427 REMARK 465 GLU A 1428 REMARK 465 ASN A 1429 REMARK 465 LEU A 1430 REMARK 465 TYR A 1431 REMARK 465 PHE A 1432 REMARK 465 GLN A 1433 REMARK 465 GLY A 1434 REMARK 465 GLU A 1435 REMARK 465 THR A 1436 REMARK 465 SER A 1437 REMARK 465 VAL A 1438 REMARK 465 PRO A 1439 REMARK 465 PRO A 1440 REMARK 465 GLY A 1441 REMARK 465 SER A 1442 REMARK 465 ALA A 1443 REMARK 465 LEU A 1444 REMARK 465 VAL A 1445 REMARK 465 GLY A 1446 REMARK 465 PRO A 1447 REMARK 465 SER A 1448 REMARK 465 LYS A 1486 REMARK 465 LYS A 1487 REMARK 465 ASN A 1488 REMARK 465 LYS A 1489 REMARK 465 SER A 1490 REMARK 465 HIS A 1491 REMARK 465 ARG A 1492 REMARK 465 ASP A 1493 REMARK 465 ILE A 1494 REMARK 465 LYS A 1495 REMARK 465 ARG A 1496 REMARK 465 MET A 1704 REMARK 465 LYS A 1705 REMARK 465 LYS A 1706 REMARK 465 GLU A 1707 REMARK 465 ARG A 1708 REMARK 465 SER A 1709 REMARK 465 ARG A 1710 REMARK 465 LYS A 1711 REMARK 465 TYR H 41 REMARK 465 ARG H 42 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 VAL A1450 CG1 CG2 REMARK 470 ASP A1452 CG OD1 OD2 REMARK 470 ARG A1455 CG CD NE CZ NH1 NH2 REMARK 470 GLN A1458 CG CD OE1 NE2 REMARK 470 ARG A1459 CG CD NE CZ NH1 NH2 REMARK 470 LYS A1461 CG CD CE NZ REMARK 470 GLU A1462 CG CD OE1 OE2 REMARK 470 LYS A1465 CD CE NZ REMARK 470 GLN A1466 CG CD OE1 NE2 REMARK 470 LYS A1468 CG CD CE NZ REMARK 470 GLU A1477 OE1 OE2 REMARK 470 GLU A1484 CG CD OE1 OE2 REMARK 470 MET A1497 CG SD CE REMARK 470 GLN A1498 CG CD OE1 NE2 REMARK 470 LYS A1506 CG CD CE NZ REMARK 470 ASP A1507 CG OD1 OD2 REMARK 470 ARG A1509 NE CZ NH1 NH2 REMARK 470 GLU A1518 CG CD OE1 OE2 REMARK 470 LEU A1521 CD1 CD2 REMARK 470 ARG A1532 NH1 NH2 REMARK 470 TYR A1538 CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A1547 CE NZ REMARK 470 HIS A1549 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A1553 OE1 OE2 REMARK 470 GLU A1558 CD OE1 OE2 REMARK 470 LYS A1568 CG CD CE NZ REMARK 470 ASN A1573 OD1 ND2 REMARK 470 LYS A1587 CG CD CE NZ REMARK 470 ARG A1598 CG CD NE CZ NH1 NH2 REMARK 470 LYS A1600 CE NZ REMARK 470 LYS A1610 CD CE NZ REMARK 470 ASN A1611 CG OD1 ND2 REMARK 470 ASP A1612 CG OD1 OD2 REMARK 470 GLU A1613 OE1 OE2 REMARK 470 GLU A1632 CG CD OE1 OE2 REMARK 470 LYS A1639 NZ REMARK 470 GLN A1645 OE1 NE2 REMARK 470 LEU A1655 CD1 CD2 REMARK 470 LYS A1673 CD CE NZ REMARK 470 ASN A1684 CG OD1 ND2 REMARK 470 GLU A1692 CG CD OE1 OE2 REMARK 470 LYS A1703 CD CE NZ REMARK 470 ASN H 39 CG OD1 ND2 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 ASN A1541 42.97 -109.41 REMARK 500 LYS A1559 11.07 -140.97 REMARK 500 VAL A1576 -69.96 -99.07 REMARK 500 LEU A1609 -65.69 -106.46 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 A1921 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1499 SG REMARK 620 2 CYS A1501 SG 110.2 REMARK 620 3 CYS A1516 SG 104.4 109.1 REMARK 620 4 CYS A1520 SG 117.5 107.3 108.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1922 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1516 SG REMARK 620 2 CYS A1529 SG 117.7 REMARK 620 3 CYS A1533 SG 97.1 113.9 REMARK 620 4 CYS A1539 SG 111.1 101.3 116.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1923 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1631 SG REMARK 620 2 CYS A1678 SG 114.5 REMARK 620 3 CYS A1680 SG 113.3 102.4 REMARK 620 4 CYS A1685 SG 114.7 104.6 106.1 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 SAH A 1901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1921 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1922 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1923 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SCN H 101 DBREF 6VDB A 1433 1711 UNP Q9BYW2 SETD2_HUMAN 1433 1711 DBREF 6VDB H 29 42 PDB 6VDB 6VDB 29 42 SEQADV 6VDB MET A 1417 UNP Q9BYW2 INITIATING METHIONINE SEQADV 6VDB HIS A 1418 UNP Q9BYW2 EXPRESSION TAG SEQADV 6VDB HIS A 1419 UNP Q9BYW2 EXPRESSION TAG SEQADV 6VDB HIS A 1420 UNP Q9BYW2 EXPRESSION TAG SEQADV 6VDB HIS A 1421 UNP Q9BYW2 EXPRESSION TAG SEQADV 6VDB HIS A 1422 UNP Q9BYW2 EXPRESSION TAG SEQADV 6VDB HIS A 1423 UNP Q9BYW2 EXPRESSION TAG SEQADV 6VDB SER A 1424 UNP Q9BYW2 EXPRESSION TAG SEQADV 6VDB SER A 1425 UNP Q9BYW2 EXPRESSION TAG SEQADV 6VDB GLY A 1426 UNP Q9BYW2 EXPRESSION TAG SEQADV 6VDB ARG A 1427 UNP Q9BYW2 EXPRESSION TAG SEQADV 6VDB GLU A 1428 UNP Q9BYW2 EXPRESSION TAG SEQADV 6VDB ASN A 1429 UNP Q9BYW2 EXPRESSION TAG SEQADV 6VDB LEU A 1430 UNP Q9BYW2 EXPRESSION TAG SEQADV 6VDB TYR A 1431 UNP Q9BYW2 EXPRESSION TAG SEQADV 6VDB PHE A 1432 UNP Q9BYW2 EXPRESSION TAG SEQRES 1 A 295 MET HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU ASN SEQRES 2 A 295 LEU TYR PHE GLN GLY GLU THR SER VAL PRO PRO GLY SER SEQRES 3 A 295 ALA LEU VAL GLY PRO SER CYS VAL MET ASP ASP PHE ARG SEQRES 4 A 295 ASP PRO GLN ARG TRP LYS GLU CYS ALA LYS GLN GLY LYS SEQRES 5 A 295 MET PRO CYS TYR PHE ASP LEU ILE GLU GLU ASN VAL TYR SEQRES 6 A 295 LEU THR GLU ARG LYS LYS ASN LYS SER HIS ARG ASP ILE SEQRES 7 A 295 LYS ARG MET GLN CYS GLU CYS THR PRO LEU SER LYS ASP SEQRES 8 A 295 GLU ARG ALA GLN GLY GLU ILE ALA CYS GLY GLU ASP CYS SEQRES 9 A 295 LEU ASN ARG LEU LEU MET ILE GLU CYS SER SER ARG CYS SEQRES 10 A 295 PRO ASN GLY ASP TYR CYS SER ASN ARG ARG PHE GLN ARG SEQRES 11 A 295 LYS GLN HIS ALA ASP VAL GLU VAL ILE LEU THR GLU LYS SEQRES 12 A 295 LYS GLY TRP GLY LEU ARG ALA ALA LYS ASP LEU PRO SER SEQRES 13 A 295 ASN THR PHE VAL LEU GLU TYR CYS GLY GLU VAL LEU ASP SEQRES 14 A 295 HIS LYS GLU PHE LYS ALA ARG VAL LYS GLU TYR ALA ARG SEQRES 15 A 295 ASN LYS ASN ILE HIS TYR TYR PHE MET ALA LEU LYS ASN SEQRES 16 A 295 ASP GLU ILE ILE ASP ALA THR GLN LYS GLY ASN CYS SER SEQRES 17 A 295 ARG PHE MET ASN HIS SER CYS GLU PRO ASN CYS GLU THR SEQRES 18 A 295 GLN LYS TRP THR VAL ASN GLY GLN LEU ARG VAL GLY PHE SEQRES 19 A 295 PHE THR THR LYS LEU VAL PRO SER GLY SER GLU LEU THR SEQRES 20 A 295 PHE ASP TYR GLN PHE GLN ARG TYR GLY LYS GLU ALA GLN SEQRES 21 A 295 LYS CYS PHE CYS GLY SER ALA ASN CYS ARG GLY TYR LEU SEQRES 22 A 295 GLY GLY GLU ASN ARG VAL SER ILE ARG ALA ALA GLY GLY SEQRES 23 A 295 LYS MET LYS LYS GLU ARG SER ARG LYS SEQRES 1 H 14 ALA PRO ARG PHE GLY GLY VAL MET ARG PRO ASN ARG TYR SEQRES 2 H 14 ARG HET SAH A1901 26 HET UNX A1902 1 HET UNX A1903 1 HET UNX A1904 1 HET UNX A1905 1 HET UNX A1906 1 HET UNX A1907 1 HET UNX A1908 1 HET UNX A1909 1 HET UNX A1910 1 HET UNX A1911 1 HET UNX A1912 1 HET UNX A1913 1 HET UNX A1914 1 HET UNX A1915 1 HET UNX A1916 1 HET UNX A1917 1 HET UNX A1918 1 HET UNX A1919 1 HET UNX A1920 1 HET ZN A1921 1 HET ZN A1922 1 HET ZN A1923 1 HET SCN H 101 3 HET UNX H 102 1 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM UNX UNKNOWN ATOM OR ION HETNAM ZN ZINC ION HETNAM SCN THIOCYANATE ION FORMUL 3 SAH C14 H20 N6 O5 S FORMUL 4 UNX 20(X) FORMUL 23 ZN 3(ZN 2+) FORMUL 26 SCN C N S 1- FORMUL 28 HOH *24(H2 O) HELIX 1 AA1 VAL A 1450 ARG A 1455 5 6 HELIX 2 AA2 ASP A 1456 GLN A 1466 1 11 HELIX 3 AA3 SER A 1505 GLN A 1511 1 7 HELIX 4 AA4 CYS A 1520 LEU A 1525 1 6 HELIX 5 AA5 ASN A 1535 CYS A 1539 5 5 HELIX 6 AA6 ASP A 1585 LYS A 1600 1 16 HELIX 7 AA7 ASN A 1622 MET A 1627 5 6 HELIX 8 AA8 SER A 1696 GLY A 1701 1 6 SHEET 1 AA1 2 ASP A1474 LEU A1475 0 SHEET 2 AA1 2 LYS A1620 GLY A1621 1 O GLY A1621 N ASP A1474 SHEET 1 AA2 4 VAL A1480 TYR A1481 0 SHEET 2 AA2 4 GLU A1582 LEU A1584 1 O VAL A1583 N VAL A1480 SHEET 3 AA2 4 GLU A1613 ASP A1616 -1 O ASP A1616 N GLU A1582 SHEET 4 AA2 4 PHE A1606 LYS A1610 -1 N MET A1607 O ILE A1615 SHEET 1 AA3 2 VAL A1552 LEU A1556 0 SHEET 2 AA3 2 TRP A1562 ALA A1566 -1 O GLY A1563 N ILE A1555 SHEET 1 AA4 3 PHE A1575 GLU A1578 0 SHEET 2 AA4 3 GLN A1645 THR A1652 -1 O PHE A1650 N VAL A1576 SHEET 3 AA4 3 CYS A1635 VAL A1642 -1 N VAL A1642 O GLN A1645 SHEET 1 AA5 2 ASN A1628 HIS A1629 0 SHEET 2 AA5 2 THR A1663 PHE A1664 1 O PHE A1664 N ASN A1628 SHEET 1 AA6 2 GLN A1669 ARG A1670 0 SHEET 2 AA6 2 GLY H 34 VAL H 35 -1 O VAL H 35 N GLN A1669 SHEET 1 AA7 2 GLN A1676 LYS A1677 0 SHEET 2 AA7 2 TYR A1688 LEU A1689 -1 O LEU A1689 N GLN A1676 SSBOND 1 CYS A 1449 CYS A 1463 1555 1555 2.04 LINK SG CYS A1499 ZN ZN A1921 1555 1555 2.29 LINK SG CYS A1501 ZN ZN A1921 1555 1555 2.49 LINK SG CYS A1516 ZN ZN A1921 1555 1555 2.49 LINK SG CYS A1516 ZN ZN A1922 1555 1555 2.25 LINK SG CYS A1520 ZN ZN A1921 1555 1555 2.45 LINK SG CYS A1529 ZN ZN A1922 1555 1555 2.51 LINK SG CYS A1533 ZN ZN A1922 1555 1555 2.35 LINK SG CYS A1539 ZN ZN A1922 1555 1555 2.24 LINK SG CYS A1631 ZN ZN A1923 1555 1555 2.37 LINK SG CYS A1678 ZN ZN A1923 1555 1555 2.41 LINK SG CYS A1680 ZN ZN A1923 1555 1555 2.23 LINK SG CYS A1685 ZN ZN A1923 1555 1555 2.41 SITE 1 AC1 16 LYS A1560 GLY A1561 TRP A1562 HIS A1603 SITE 2 AC1 16 TYR A1604 TYR A1605 ARG A1625 PHE A1626 SITE 3 AC1 16 ASN A1628 HIS A1629 TYR A1666 GLN A1676 SITE 4 AC1 16 LYS A1677 CYS A1678 PHE A1679 LEU A1689 SITE 1 AC2 4 CYS A1499 CYS A1501 CYS A1516 CYS A1520 SITE 1 AC3 4 CYS A1516 CYS A1529 CYS A1533 CYS A1539 SITE 1 AC4 4 CYS A1631 CYS A1678 CYS A1680 CYS A1685 SITE 1 AC5 5 GLN A1638 LYS A1639 PRO H 38 ASN H 39 SITE 2 AC5 5 ARG H 40 CRYST1 60.370 76.520 77.610 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 0.016565 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013068 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012885 0.00000