HEADER TRANSFERASE 06-JUN-16 5KCO TITLE SETDB1 IN COMPLEX WITH AN EARLY STAGE, LOW AFFINITY FRAGMENT CANDIDATE TITLE 2 MODELLED AT REDUCED OCCUPANCY COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE SETDB1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 196-403; 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,SET COMPND 7 DOMAIN BIFURCATED 1; COMPND 8 EC: 2.1.1.43; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SETDB1, KIAA0067, KMT1E; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) CODON PLUS; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28-MHL KEYWDS FRAGMENT SCREENING, DIAMOND I04-1 XCHEM, PANDDA, STRUCTURAL GENOMICS, KEYWDS 2 STRUCTURAL GENOMICS CONSORTIUM, SGC, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR W.TEMPEL,R.J.HARDING,P.MADER,E.DOBROVETSKY,J.R.WALKER,P.J.BROWN, AUTHOR 2 M.SCHAPIRA,P.COLLINS,N.PEARCE,J.BRANDAO-NETO,A.DOUANGAMATH,F.VON AUTHOR 3 DELFT,C.BOUNTRA,C.H.ARROWSMITH,A.M.EDWARDS,V.SANTHAKUMAR,STRUCTURAL AUTHOR 4 GENOMICS CONSORTIUM (SGC) REVDAT 2 27-SEP-23 5KCO 1 REMARK REVDAT 1 27-JUL-16 5KCO 0 JRNL AUTH W.TEMPEL,R.J.HARDING,P.MADER,E.DOBROVETSKY,J.R.WALKER, JRNL AUTH 2 P.J.BROWN,M.SCHAPIRA,C.H.ARROWSMITH,A.M.EDWARDS, JRNL AUTH 3 S.SANTHAKUMAR,STRUCTURAL GENOMICS CONSORTIUM (SGC) JRNL TITL SETDB1 IN COMPLEX WITH AN EARLY STAGE, LOW AFFINITY FRAGMENT JRNL TITL 2 CANDIDATE MODELLED AT REDUCED OCCUPANCY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0151 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) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 41091 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2204 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) : 1.47 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.51 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2907 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.18 REMARK 3 BIN R VALUE (WORKING SET) : 0.2980 REMARK 3 BIN FREE R VALUE SET COUNT : 156 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1711 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 81 REMARK 3 SOLVENT ATOMS : 143 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.90000 REMARK 3 B22 (A**2) : -0.86000 REMARK 3 B33 (A**2) : -0.04000 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): 0.068 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.071 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.052 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.422 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1882 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1780 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2568 ; 1.761 ; 1.956 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4094 ; 1.008 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 234 ; 6.744 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 83 ;28.206 ;22.530 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 326 ;10.409 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;16.620 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 278 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2135 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 454 ; 0.001 ; 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): 880 ; 2.347 ; 1.865 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 881 ; 2.346 ; 1.865 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1110 ; 3.305 ; 2.790 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: USERS OF THIS CRYSTAL STRUCTURE: VERIFY REMARK 3 OUR INTEPRETION OF THE ELECTRON DENSITY. AMPLITUDES AND UNMERGED REMARK 3 INTENSITIES ARE INCLUDED WITH THIS DEPOSITION. DIFFRACTION REMARK 3 IMAGES WILL BE DEPOSITED IN A PUBLIC REPOSITORY. GEOMETRY REMARK 3 RESTRAINTS FOR THE FRAGMENT CANDIDATE WERE PREPARED WITH GRADE. REMARK 3 SOME OCCUPANCIES WERE REFINED WITH PHENIX SOFTWARE. AMBIGUOUS REMARK 3 DIFFERENCE DENSITY SUGGESTS MORE THAN ONE MAIN CHAIN REMARK 3 CONFORMATION FOR RESIDUES 235..239. REMARK 4 REMARK 4 5KCO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000222007. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-15 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 : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92819 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.26 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43355 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 REMARK 200 RESOLUTION RANGE LOW (A) : 47.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 1.44500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 3DLM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG-3350, 0.2M LITHIUM SULFATE, REMARK 280 0.1M BIS-TRIS. TRYPSIN HAD BEEN ADDED TO THE PROTEIN STOCK REMARK 280 SOLUTION., PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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 27.88600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.26100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.88050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.26100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.88600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.88050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 179 REMARK 465 HIS A 180 REMARK 465 HIS A 181 REMARK 465 HIS A 182 REMARK 465 HIS A 183 REMARK 465 HIS A 184 REMARK 465 HIS A 185 REMARK 465 SER A 186 REMARK 465 SER A 187 REMARK 465 GLY A 188 REMARK 465 ARG A 189 REMARK 465 LYS A 402 REMARK 465 THR A 403 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 215 CD CE NZ REMARK 470 LYS A 233 NZ REMARK 470 ASN A 236 CG OD1 ND2 REMARK 470 LYS A 237 CG CD CE NZ REMARK 470 LYS A 239 NZ REMARK 470 LYS A 257 CG CD CE NZ REMARK 470 LYS A 267 CD CE NZ REMARK 470 LYS A 269 CD CE NZ REMARK 470 LYS A 288 CE NZ REMARK 470 LYS A 355 CE NZ REMARK 470 ASP A 381 CG OD1 OD2 REMARK 470 MET A 401 C O CB CG SD CE REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 283 CD GLU A 283 OE1 0.067 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 315 NE - CZ - NH1 ANGL. DEV. = 3.2 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 -8.81 90.33 REMARK 500 SER A 201 -10.98 92.66 REMARK 500 ASN A 236 51.31 -116.12 REMARK 500 LYS A 237 -171.44 -175.48 REMARK 500 ASP A 250 51.83 -95.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6RO A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 551 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 552 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 553 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5KCH RELATED DB: PDB DBREF 5KCO A 196 403 UNP Q15047 SETB1_HUMAN 196 403 SEQADV 5KCO MET A 179 UNP Q15047 INITIATING METHIONINE SEQADV 5KCO HIS A 180 UNP Q15047 EXPRESSION TAG SEQADV 5KCO HIS A 181 UNP Q15047 EXPRESSION TAG SEQADV 5KCO HIS A 182 UNP Q15047 EXPRESSION TAG SEQADV 5KCO HIS A 183 UNP Q15047 EXPRESSION TAG SEQADV 5KCO HIS A 184 UNP Q15047 EXPRESSION TAG SEQADV 5KCO HIS A 185 UNP Q15047 EXPRESSION TAG SEQADV 5KCO SER A 186 UNP Q15047 EXPRESSION TAG SEQADV 5KCO SER A 187 UNP Q15047 EXPRESSION TAG SEQADV 5KCO GLY A 188 UNP Q15047 EXPRESSION TAG SEQADV 5KCO ARG A 189 UNP Q15047 EXPRESSION TAG SEQADV 5KCO GLU A 190 UNP Q15047 EXPRESSION TAG SEQADV 5KCO ASN A 191 UNP Q15047 EXPRESSION TAG SEQADV 5KCO LEU A 192 UNP Q15047 EXPRESSION TAG SEQADV 5KCO TYR A 193 UNP Q15047 EXPRESSION TAG SEQADV 5KCO PHE A 194 UNP Q15047 EXPRESSION TAG SEQADV 5KCO GLN A 195 UNP Q15047 EXPRESSION TAG SEQRES 1 A 225 MET HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU ASN SEQRES 2 A 225 LEU TYR PHE GLN GLY ASP LEU ILE VAL SER MET ARG ILE SEQRES 3 A 225 LEU GLY LYS LYS ARG THR LYS THR TRP HIS LYS GLY THR SEQRES 4 A 225 LEU ILE ALA ILE GLN THR VAL GLY PRO GLY LYS LYS TYR SEQRES 5 A 225 LYS VAL LYS PHE ASP ASN LYS GLY LYS SER LEU LEU SER SEQRES 6 A 225 GLY ASN HIS ILE ALA TYR ASP TYR HIS PRO PRO ALA ASP SEQRES 7 A 225 LYS LEU TYR VAL GLY SER ARG VAL VAL ALA LYS TYR LYS SEQRES 8 A 225 ASP GLY ASN GLN VAL TRP LEU TYR ALA GLY ILE VAL ALA SEQRES 9 A 225 GLU THR PRO ASN VAL LYS ASN LYS LEU ARG PHE LEU ILE SEQRES 10 A 225 PHE PHE ASP ASP GLY TYR ALA SER TYR VAL THR GLN SER SEQRES 11 A 225 GLU LEU TYR PRO ILE CYS ARG PRO LEU LYS LYS THR TRP SEQRES 12 A 225 GLU ASP ILE GLU ASP ILE SER CYS ARG ASP PHE ILE GLU SEQRES 13 A 225 GLU TYR VAL THR ALA TYR PRO ASN ARG PRO MET VAL LEU SEQRES 14 A 225 LEU LYS SER GLY GLN LEU ILE LYS THR GLU TRP GLU GLY SEQRES 15 A 225 THR TRP TRP LYS SER ARG VAL GLU GLU VAL ASP GLY SER SEQRES 16 A 225 LEU VAL ARG ILE LEU PHE LEU ASP ASP LYS ARG CYS GLU SEQRES 17 A 225 TRP ILE TYR ARG GLY SER THR ARG LEU GLU PRO MET PHE SEQRES 18 A 225 SER MET LYS THR HET SO4 A 501 5 HET SO4 A 502 5 HET 6RO A 503 12 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 UNX A 535 1 HET UNX A 536 1 HET UNX A 537 1 HET UNX A 538 1 HET UNX A 539 1 HET UNX A 540 1 HET UNX A 541 1 HET UNX A 542 1 HET UNX A 543 1 HET UNX A 544 1 HET UNX A 545 1 HET UNX A 546 1 HET UNX A 547 1 HET UNX A 548 1 HET UNX A 549 1 HET UNX A 550 1 HET DMS A 551 4 HET DMS A 552 4 HET DMS A 553 4 HETNAM SO4 SULFATE ION HETNAM 6RO ~{N}-(4-CHLOROPHENYL)METHANESULFONAMIDE HETNAM UNX UNKNOWN ATOM OR ION HETNAM DMS DIMETHYL SULFOXIDE FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 6RO C7 H8 CL N O2 S FORMUL 5 UNX 47(X) FORMUL 52 DMS 3(C2 H6 O S) FORMUL 55 HOH *143(H2 O) HELIX 1 AA1 SER A 243 ASN A 245 5 3 HELIX 2 AA2 PRO A 254 LEU A 258 5 5 HELIX 3 AA3 THR A 306 SER A 308 5 3 HELIX 4 AA4 LYS A 319 ILE A 324 5 6 HELIX 5 AA5 ASP A 326 TYR A 340 1 15 HELIX 6 AA6 LEU A 395 MET A 401 1 7 SHEET 1 AA1 4 ASN 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 229 N GLN A 222 SHEET 4 AA1 4 LYS A 239 LEU A 242 -1 O SER A 240 N VAL A 232 SHEET 1 AA2 4 ASN 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 GLY A 206 O HIS A 214 SHEET 4 AA2 4 ILE A 247 TYR A 249 -1 O ALA A 248 N LEU A 205 SHEET 1 AA3 2 PHE A 194 GLN A 195 0 SHEET 2 AA3 2 LEU A 198 ILE A 199 -1 O LEU A 198 N GLN 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 GLN A 273 GLU A 283 -1 N ALA A 282 O LEU A 294 SHEET 4 AA4 5 ARG A 263 ASP A 270 -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 THR A 361 N TRP A 358 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 ILE A 388 N VAL A 375 CISPEP 1 TYR A 340 PRO A 341 0 13.20 SITE 1 AC1 5 HIS A 214 LYS A 215 HOH A 612 HOH A 634 SITE 2 AC1 5 HOH A 639 SITE 1 AC2 5 ARG A 209 TRP A 363 LYS A 364 ASP A 381 SITE 2 AC2 5 HOH A 614 SITE 1 AC3 8 PHE A 296 GLY A 300 ALA A 302 SER A 328 SITE 2 AC3 8 PHE A 332 TYR A 389 SER A 392 HOH A 655 SITE 1 AC4 4 LYS A 207 LYS A 208 LYS A 211 HOH A 652 SITE 1 AC5 7 TRP A 358 TRP A 363 PHE A 379 ASP A 382 SITE 2 AC5 7 ARG A 384 HOH A 609 HOH A 672 SITE 1 AC6 3 GLU A 190 ASN A 191 THR A 223 CRYST1 55.772 63.761 70.522 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 0.017930 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015684 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014180 0.00000