HEADER TRANSFERASE 30-OCT-17 6BHD TITLE CRYSTAL STRUCTURE OF SETDB1 WITH A MODIFIED H3 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE SETDB1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 190-410; COMPND 5 SYNONYM: ERG-ASSOCIATED PROTEIN WITH SET DOMAIN, ESET, HISTONE H3-K9 COMPND 6 METHYLTRANSFERASE 4, H3-K9-HMTASE 4, LYSINE N-METHYLTRANSFERASE 1E, COMPND 7 SET DOMAIN BIFURCATED 1; COMPND 8 EC: 2.1.1.43; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: HISTONE H3.1; COMPND 12 CHAIN: B; COMPND 13 SYNONYM: HISTONE H3/A, HISTONE H3/B, HISTONE H3/C, HISTONE H3/D, COMPND 14 HISTONE H3/F, HISTONE H3/H, HISTONE H3/I, HISTONE H3/J, HISTONE H3/K, COMPND 15 HISTONE H3/L; COMPND 16 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: SETDB1, KIAA0067, KMT1E; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-V2R-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28-MHL; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS STRUCTURAL GENOMICS, EPIGENETICS, HISTONE MODIFICATION, STRUCTURAL KEYWDS 2 GENOMICS CONSORTIUM, SGC, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.QIN,W.TEMPEL,C.BOUNTRA,C.H.ARROWSMITH,A.M.EDWARDS,J.MIN,STRUCTURAL AUTHOR 2 GENOMICS CONSORTIUM (SGC) REVDAT 3 03-APR-24 6BHD 1 REMARK REVDAT 2 03-JAN-18 6BHD 1 JRNL REVDAT 1 06-DEC-17 6BHD 0 JRNL AUTH R.Z.JURKOWSKA,S.QIN,G.KUNGULOVSKI,W.TEMPEL,Y.LIU, JRNL AUTH 2 P.BASHTRYKOV,J.STIEFELMAIER,T.P.JURKOWSKI,S.KUDITHIPUDI, JRNL AUTH 3 S.WEIRICH,R.TAMAS,H.WU,L.DOMBROVSKI,P.LOPPNAU,R.REINHARDT, JRNL AUTH 4 J.MIN,A.JELTSCH JRNL TITL H3K14AC IS LINKED TO METHYLATION OF H3K9 BY THE TRIPLE TUDOR JRNL TITL 2 DOMAIN OF SETDB1. JRNL REF NAT COMMUN V. 8 2057 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 29234025 JRNL DOI 10.1038/S41467-017-02259-9 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 70524 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3722 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) : 1.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5177 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE SET COUNT : 294 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1805 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 203 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.17000 REMARK 3 B22 (A**2) : 0.32000 REMARK 3 B33 (A**2) : -0.10000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.06000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.039 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.041 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.028 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.471 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1997 ; 0.019 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1911 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2734 ; 1.937 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4441 ; 1.106 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 266 ; 6.949 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 78 ;28.886 ;22.949 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 355 ;12.186 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;17.305 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 309 ; 0.127 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2209 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 423 ; 0.003 ; 0.020 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): 976 ; 3.228 ; 1.410 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 975 ; 3.224 ; 1.407 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1228 ; 4.028 ; 2.118 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): 3907 ; 2.955 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 140 ;19.119 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3944 ; 8.964 ; 5.000 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: ELECTRON DENSITY SUGGESTS THAT A HEPES REMARK 3 BUFFER MOLECULE MAY BIND IN THE AROMATIC CAGE OF TD2. COOT WAS REMARK 3 USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS REMARK 3 EVALUATED WITH MOLPROBITY. REMARK 4 REMARK 4 6BHD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1000230842. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-AUG-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9686 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74273 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 41.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 1.01800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: SIMILAR, NEARLY ISOMORPHOUS CRYSTAL STRUCTURE, TO REMARK 200 BE PUBLISHED REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.2 M SODIUM CHLORIDE, REMARK 280 0.1 M HEPES, 5% GLYCEROL, PH 7.5, VAPOR DIFFUSION, TEMPERATURE REMARK 280 291K 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 36.22400 REMARK 290 SMTRY3 2 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: 1890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 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 172 REMARK 465 HIS A 173 REMARK 465 HIS A 174 REMARK 465 HIS A 175 REMARK 465 HIS A 176 REMARK 465 HIS A 177 REMARK 465 HIS A 178 REMARK 465 SER A 179 REMARK 465 SER A 180 REMARK 465 GLY A 181 REMARK 465 ARG A 182 REMARK 465 GLU A 183 REMARK 465 ASN A 184 REMARK 465 LEU A 185 REMARK 465 TYR A 186 REMARK 465 PHE A 187 REMARK 465 GLN A 188 REMARK 465 ASN A 272 REMARK 465 SER A 407 REMARK 465 ALA A 408 REMARK 465 LEU A 409 REMARK 465 GLU A 410 REMARK 465 ACE B 3 REMARK 465 LYS B 4 REMARK 465 GLN B 5 REMARK 465 THR B 6 REMARK 465 GLN B 19 REMARK 465 NH2 B 20 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 LYS A 194 CE NZ REMARK 470 ARG A 209 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 233 CD CE NZ REMARK 470 ASN A 236 CG OD1 ND2 REMARK 470 LYS A 237 CG CD CE NZ REMARK 470 LYS A 257 CE NZ REMARK 470 ASP A 270 CG OD1 OD2 REMARK 470 GLN A 273 CG CD OE1 NE2 REMARK 470 TRP A 275 CZ3 CH2 REMARK 470 LYS A 288 NZ REMARK 470 LYS A 290 CE NZ REMARK 470 GLN A 307 CD OE1 NE2 REMARK 470 LYS A 349 NZ REMARK 470 LYS A 364 CE NZ REMARK 470 LYS A 402 CE NZ REMARK 470 SER A 405 OG REMARK 470 ARG B 17 NE CZ NH1 NH2 REMARK 470 LYS B 18 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 ASN A 286 CB - CA - C ANGL. DEV. = 16.5 DEGREES REMARK 500 ARG A 292 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 315 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 315 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 390 NE - CZ - NH1 ANGL. DEV. = 3.4 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 SER A 201 -13.45 101.34 REMARK 500 ASP A 250 54.10 -92.31 REMARK 500 ASP A 256 6.57 82.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 789 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH A 790 DISTANCE = 6.27 ANGSTROMS 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 NA A 535 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 338 O REMARK 620 2 HOH A 668 O 99.8 REMARK 620 3 HOH A 734 O 82.2 89.2 REMARK 620 4 HOH A 746 O 91.1 87.9 172.2 REMARK 620 5 HOH A 783 O 170.9 74.6 90.5 95.8 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 535 DBREF 6BHD A 190 410 UNP Q15047 SETB1_HUMAN 190 410 DBREF 6BHD B 4 19 UNP P68431 H31_HUMAN 5 20 SEQADV 6BHD MET A 172 UNP Q15047 EXPRESSION TAG SEQADV 6BHD HIS A 173 UNP Q15047 EXPRESSION TAG SEQADV 6BHD HIS A 174 UNP Q15047 EXPRESSION TAG SEQADV 6BHD HIS A 175 UNP Q15047 EXPRESSION TAG SEQADV 6BHD HIS A 176 UNP Q15047 EXPRESSION TAG SEQADV 6BHD HIS A 177 UNP Q15047 EXPRESSION TAG SEQADV 6BHD HIS A 178 UNP Q15047 EXPRESSION TAG SEQADV 6BHD SER A 179 UNP Q15047 EXPRESSION TAG SEQADV 6BHD SER A 180 UNP Q15047 EXPRESSION TAG SEQADV 6BHD GLY A 181 UNP Q15047 EXPRESSION TAG SEQADV 6BHD ARG A 182 UNP Q15047 EXPRESSION TAG SEQADV 6BHD GLU A 183 UNP Q15047 EXPRESSION TAG SEQADV 6BHD ASN A 184 UNP Q15047 EXPRESSION TAG SEQADV 6BHD LEU A 185 UNP Q15047 EXPRESSION TAG SEQADV 6BHD TYR A 186 UNP Q15047 EXPRESSION TAG SEQADV 6BHD PHE A 187 UNP Q15047 EXPRESSION TAG SEQADV 6BHD GLN A 188 UNP Q15047 EXPRESSION TAG SEQADV 6BHD GLY A 189 UNP Q15047 EXPRESSION TAG SEQADV 6BHD ACE B 3 UNP P68431 ACETYLATION SEQADV 6BHD NH2 B 20 UNP P68431 AMIDATION SEQRES 1 A 239 MET HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU ASN SEQRES 2 A 239 LEU TYR PHE GLN GLY GLY GLU LEU SER LYS ASP GLY ASP SEQRES 3 A 239 LEU ILE VAL SER MET ARG ILE LEU GLY LYS LYS ARG THR SEQRES 4 A 239 LYS THR TRP HIS LYS GLY THR LEU ILE ALA ILE GLN THR SEQRES 5 A 239 VAL GLY PRO GLY LYS LYS TYR LYS VAL LYS PHE ASP ASN SEQRES 6 A 239 LYS GLY LYS SER LEU LEU SER GLY ASN HIS ILE ALA TYR SEQRES 7 A 239 ASP TYR HIS PRO PRO ALA ASP LYS LEU TYR VAL GLY SER SEQRES 8 A 239 ARG VAL VAL ALA LYS TYR LYS ASP GLY ASN GLN VAL TRP SEQRES 9 A 239 LEU TYR ALA GLY ILE VAL ALA GLU THR PRO ASN VAL LYS SEQRES 10 A 239 ASN LYS LEU ARG PHE LEU ILE PHE PHE ASP ASP GLY TYR SEQRES 11 A 239 ALA SER TYR VAL THR GLN SER GLU LEU TYR PRO ILE CYS SEQRES 12 A 239 ARG PRO LEU LYS LYS THR TRP GLU ASP ILE GLU ASP ILE SEQRES 13 A 239 SER CYS ARG ASP PHE ILE GLU GLU TYR VAL THR ALA TYR SEQRES 14 A 239 PRO ASN ARG PRO MET VAL LEU LEU LYS SER GLY GLN LEU SEQRES 15 A 239 ILE LYS THR GLU TRP GLU GLY THR TRP TRP LYS SER ARG SEQRES 16 A 239 VAL GLU GLU VAL ASP GLY SER LEU VAL ARG ILE LEU PHE SEQRES 17 A 239 LEU ASP ASP LYS ARG CYS GLU TRP ILE TYR ARG GLY SER SEQRES 18 A 239 THR ARG LEU GLU PRO MET PHE SER MET LYS THR SER SER SEQRES 19 A 239 ALA SER ALA LEU GLU SEQRES 1 B 18 ACE LYS GLN THR ALA ARG MLY SER THR GLY GLY ALY ALA SEQRES 2 B 18 PRO ARG LYS GLN NH2 MODRES 6BHD MLY B 9 LYS MODIFIED RESIDUE MODRES 6BHD ALY B 14 LYS MODIFIED RESIDUE HET MLY B 9 11 HET ALY B 14 12 HET UNX A 501 1 HET UNX A 502 1 HET UNX A 503 1 HET UNX A 504 1 HET UNX A 505 1 HET UNX A 506 1 HET UNX A 507 1 HET UNX A 508 1 HET UNX A 509 1 HET UNX A 510 1 HET UNX A 511 1 HET UNX A 512 1 HET UNX A 513 1 HET UNX A 514 1 HET UNX A 515 1 HET UNX A 516 1 HET UNX A 517 1 HET UNX A 518 1 HET UNX A 519 1 HET UNX A 520 1 HET UNX A 521 1 HET UNX A 522 1 HET UNX A 523 1 HET UNX A 524 1 HET UNX A 525 1 HET UNX A 526 1 HET UNX A 527 1 HET UNX A 528 1 HET UNX A 529 1 HET UNX A 530 1 HET UNX A 531 1 HET UNX A 532 1 HET UNX A 533 1 HET UNX A 534 1 HET NA A 535 1 HET UNX B 101 1 HETNAM MLY N-DIMETHYL-LYSINE HETNAM ALY N(6)-ACETYLLYSINE HETNAM UNX UNKNOWN ATOM OR ION HETNAM NA SODIUM ION FORMUL 2 MLY C8 H18 N2 O2 FORMUL 2 ALY C8 H16 N2 O3 FORMUL 3 UNX 35(X) FORMUL 37 NA NA 1+ FORMUL 39 HOH *203(H2 O) HELIX 1 AA1 SER A 243 ASN A 245 5 3 HELIX 2 AA2 THR A 306 SER A 308 5 3 HELIX 3 AA3 LYS A 319 ILE A 324 5 6 HELIX 4 AA4 ASP A 326 TYR A 340 1 15 HELIX 5 AA5 LEU A 395 SER A 404 1 10 SHEET 1 AA1 4 GLU A 191 LEU A 192 0 SHEET 2 AA1 4 TRP A 213 VAL A 224 -1 O ILE A 221 N LEU A 192 SHEET 3 AA1 4 GLY A 227 PHE A 234 -1 O LYS A 231 N ILE A 219 SHEET 4 AA1 4 LYS A 239 LEU A 242 -1 O LEU A 242 N TYR A 230 SHEET 1 AA2 4 GLU A 191 LEU A 192 0 SHEET 2 AA2 4 TRP A 213 VAL A 224 -1 O ILE A 221 N LEU A 192 SHEET 3 AA2 4 ARG A 203 LYS A 207 -1 N ILE A 204 O GLY A 216 SHEET 4 AA2 4 ILE A 247 TYR A 249 -1 O ALA A 248 N LEU A 205 SHEET 1 AA3 2 LYS A 194 ASP A 195 0 SHEET 2 AA3 2 LEU A 198 ILE A 199 -1 O LEU A 198 N ASP A 195 SHEET 1 AA4 5 ALA A 302 VAL A 305 0 SHEET 2 AA4 5 PHE A 293 PHE A 297 -1 N ILE A 295 O SER A 303 SHEET 3 AA4 5 VAL A 274 GLU A 283 -1 N ALA A 282 O LEU A 294 SHEET 4 AA4 5 ARG A 263 LYS A 269 -1 N TYR A 268 O TRP A 275 SHEET 5 AA4 5 LEU A 310 PRO A 312 -1 O TYR A 311 N VAL A 265 SHEET 1 AA5 4 LEU A 353 TRP A 358 0 SHEET 2 AA5 4 THR A 361 ASP A 371 -1 O TRP A 363 N THR A 356 SHEET 3 AA5 4 LEU A 374 PHE A 379 -1 O ARG A 376 N GLU A 368 SHEET 4 AA5 4 ARG A 384 TYR A 389 -1 O GLU A 386 N ILE A 377 LINK C ARG B 8 N MLY B 9 1555 1555 1.30 LINK C MLY B 9 N SER B 10 1555 1555 1.34 LINK C GLY B 13 N ALY B 14 1555 1555 1.32 LINK C ALY B 14 N ALA B 15 1555 1555 1.33 LINK O THR A 338 NA NA A 535 1555 1555 2.41 LINK NA NA A 535 O HOH A 668 1555 1555 2.41 LINK NA NA A 535 O HOH A 734 1555 1555 2.26 LINK NA NA A 535 O HOH A 746 1555 1555 2.50 LINK NA NA A 535 O HOH A 783 1555 1555 2.49 CISPEP 1 TYR A 340 PRO A 341 0 11.73 SITE 1 AC1 5 THR A 338 HOH A 668 HOH A 734 HOH A 746 SITE 2 AC1 5 HOH A 783 CRYST1 37.258 72.448 52.505 90.00 104.84 90.00 P 1 21 1 2 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 0.026840 0.000000 0.007111 0.00000 SCALE2 0.000000 0.013803 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019703 0.00000