HEADER TRANSCRIPTION 18-JAN-17 5MW2 TITLE CRYSTAL STRUCTURE OF BCL-6 BTB-DOMAIN WITH BI-3802 COMPND MOL_ID: 1; COMPND 2 MOLECULE: B-CELL LYMPHOMA 6 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BCL-6,B-CELL LYMPHOMA 5 PROTEIN,BCL-5,PROTEIN LAZ-3,ZINC COMPND 5 FINGER AND BTB DOMAIN-CONTAINING PROTEIN 27,ZINC FINGER PROTEIN 51 SOURCE MOL_ID: 1; SOURCE 2 FRAGMENT: CORRESPONDING TO PDB ID 1R28. OBTAINED FROM EMERALD BI..; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 OTHER_DETAILS: BIND CRYSTAL_ID 1008303 KEYWDS TRANSCRIPTION, INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR G.BADER,G.FLOTZINGER,A.WEISS-PUXBAUM,A.ZOEPHEL REVDAT 1 04-OCT-17 5MW2 0 JRNL AUTH N.KERRES,S.STEURER,S.SCHLAGER,G.BADER,H.BERGER,M.CALIGIURI, JRNL AUTH 2 C.DANK,J.R.ENGEN,P.ETTMAYER,B.FISCHERAUER,G.FLOTZINGER, JRNL AUTH 3 D.GERLACH,T.GERSTBERGER,T.GMASCHITZ,P.GREB,B.HAN,E.HEYES, JRNL AUTH 4 R.E.IACOB,D.KESSLER,H.KOLLE,L.LAMARRE,D.R.LANCIA,S.LUCAS, JRNL AUTH 5 M.MAYER,K.MAYR,N.MISCHERIKOW,K.MUCK,C.PEINSIPP,O.PETERMANN, JRNL AUTH 6 U.REISER,D.RUDOLPH,K.RUMPEL,C.SALOMON,D.SCHARN,R.SCHNITZER, JRNL AUTH 7 A.SCHRENK,N.SCHWEIFER,D.THOMPSON,E.TRAXLER,R.VARECKA,T.VOSS, JRNL AUTH 8 A.WEISS-PUXBAUM,S.WINKLER,X.ZHENG,A.ZOEPHEL,N.KRAUT, JRNL AUTH 9 D.MCCONNELL,M.PEARSON,M.KOEGL JRNL TITL CHEMICALLY INDUCED DEGRADATION OF THE ONCOGENIC JRNL TITL 2 TRANSCRIPTION FACTOR BCL6. JRNL REF CELL REP V. 20 2860 2017 JRNL REFN ESSN 2211-1247 JRNL PMID 28930682 JRNL DOI 10.1016/J.CELREP.2017.08.081 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.6 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) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 4786 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) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.180 REMARK 3 FREE R VALUE TEST SET COUNT : 296 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.000 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.63 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.12 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1346 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2420 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1263 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE : 0.2610 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.17 REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 985 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 14 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 59.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.07700 REMARK 3 B22 (A**2) : 0.66660 REMARK 3 B33 (A**2) : -4.74360 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.46250 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.420 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.660 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.302 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.736 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.312 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 : 0.906 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1036 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1400 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 385 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 25 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 147 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1036 ; 20.000 ; HARMONIC 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 : 136 ; 5.000 ; SEMIHARMONIC 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 : 1164 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 0.91 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 1.88 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.51 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 2.1471 19.6019 16.1916 REMARK 3 T TENSOR REMARK 3 T11: -0.0740 T22: -0.0732 REMARK 3 T33: -0.1798 T12: -0.0441 REMARK 3 T13: 0.0326 T23: 0.0115 REMARK 3 L TENSOR REMARK 3 L11: 1.7955 L22: 1.9773 REMARK 3 L33: 4.7031 L12: 0.5412 REMARK 3 L13: 1.1901 L23: -0.0161 REMARK 3 S TENSOR REMARK 3 S11: -0.0520 S12: 0.0045 S13: 0.0818 REMARK 3 S21: -0.1849 S22: 0.0492 S23: 0.0321 REMARK 3 S31: 0.0638 S32: -0.1498 S33: 0.0028 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5MW2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1200003104. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 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) : 1.000 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 : AUTOPROC, XDS (VERSION MARCH 1 REMARK 200 DATA SCALING SOFTWARE : AUTOPROC (VERSION 1.1.6), REMARK 200 AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4788 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 52.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22.5 % PEG 3350 2 % ISOPROPANOL 0.1 M REMARK 280 CALCIUM CLORIDE 0.1 M HEPES, PH 8, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 15.68350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.32850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 15.68350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.32850 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: 4010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 16.35894 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 52.79111 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 4 REMARK 465 ALA A 5 REMARK 465 ASP A 6 REMARK 465 GLU A 129 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 39 -80.81 58.79 REMARK 500 MET A 114 76.85 -113.40 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 U52 A 201 DBREF 5MW2 A 5 129 UNP P41182 BCL6_HUMAN 5 129 SEQADV 5MW2 SER A 4 UNP P41182 EXPRESSION TAG SEQADV 5MW2 GLN A 8 UNP P41182 CYS 8 CONFLICT SEQADV 5MW2 ARG A 67 UNP P41182 CYS 67 CONFLICT SEQADV 5MW2 ASN A 84 UNP P41182 CYS 84 CONFLICT SEQRES 1 A 126 SER ALA ASP SER GLN ILE GLN PHE THR ARG HIS ALA SER SEQRES 2 A 126 ASP VAL LEU LEU ASN LEU ASN ARG LEU ARG SER ARG ASP SEQRES 3 A 126 ILE LEU THR ASP VAL VAL ILE VAL VAL SER ARG GLU GLN SEQRES 4 A 126 PHE ARG ALA HIS LYS THR VAL LEU MET ALA CYS SER GLY SEQRES 5 A 126 LEU PHE TYR SER ILE PHE THR ASP GLN LEU LYS ARG ASN SEQRES 6 A 126 LEU SER VAL ILE ASN LEU ASP PRO GLU ILE ASN PRO GLU SEQRES 7 A 126 GLY PHE ASN ILE LEU LEU ASP PHE MET TYR THR SER ARG SEQRES 8 A 126 LEU ASN LEU ARG GLU GLY ASN ILE MET ALA VAL MET ALA SEQRES 9 A 126 THR ALA MET TYR LEU GLN MET GLU HIS VAL VAL ASP THR SEQRES 10 A 126 CYS ARG LYS PHE ILE LYS ALA SER GLU HET U52 A 201 34 HETNAM U52 2-[6-[[5-CHLORANYL-2-[(3~{S},5~{R})-3,5- HETNAM 2 U52 DIMETHYLPIPERIDIN-1-YL]PYRIMIDIN-4-YL]AMINO]-1-METHYL- HETNAM 3 U52 2-OXIDANYLIDENE-QUINOLIN-3-YL]OXY-~{N}-METHYL- HETNAM 4 U52 ETHANAMIDE FORMUL 2 U52 C24 H29 CL N6 O3 FORMUL 3 HOH *14(H2 O) HELIX 1 AA1 ARG A 13 ARG A 28 1 16 HELIX 2 AA2 HIS A 46 SER A 54 1 9 HELIX 3 AA3 SER A 54 ASP A 63 1 10 HELIX 4 AA4 ASN A 79 SER A 93 1 15 HELIX 5 AA5 ASN A 101 LEU A 112 1 12 HELIX 6 AA6 MET A 114 SER A 128 1 15 SHEET 1 AA1 3 GLU A 41 ALA A 45 0 SHEET 2 AA1 3 VAL A 34 VAL A 38 -1 N ILE A 36 O PHE A 43 SHEET 3 AA1 3 VAL A 71 ASN A 73 1 O ILE A 72 N VAL A 35 SITE 1 AC1 15 ASN A 21 ARG A 24 MET A 51 ALA A 52 SITE 2 AC1 15 CYS A 53 GLY A 55 TYR A 58 GLU A 81 SITE 3 AC1 15 ASN A 84 PHE A 89 GLN A 113 MET A 114 SITE 4 AC1 15 GLU A 115 HIS A 116 VAL A 117 CRYST1 31.367 72.657 54.883 90.00 105.87 90.00 C 1 2 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 0.031881 0.000000 0.009063 0.00000 SCALE2 0.000000 0.013763 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018943 0.00000