HEADER TRANSCRIPTION 11-DEC-19 6TOI TITLE CRYSTAL STRUCTURE OF HUMAN BCL6 BTB DOMAIN IN COMPLEX WITH COMPOUND TITLE 2 11F 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; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ALA-TRP-VAL-ILE-PRO-ALA; COMPND 9 CHAIN: B; COMPND 10 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: BCL6, BCL5, LAZ3, ZBTB27, ZNF51; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: AI; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET48B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS CANCER, LYMPHOMA, INHIBITOR, DEGRADER, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR G.W.COLLIE,M.J.RODRIGUES,Y.-V.LE BIHAN,R.L.M.VAN MONTFORT REVDAT 3 24-JAN-24 6TOI 1 REMARK REVDAT 2 06-MAY-20 6TOI 1 JRNL REVDAT 1 22-APR-20 6TOI 0 JRNL AUTH B.R.BELLENIE,K.J.CHEUNG,A.VARELA,O.A.PIERRAT,G.W.COLLIE, JRNL AUTH 2 G.M.BOX,M.D.BRIGHT,S.GOWAN,A.HAYES,M.J.RODRIGUES,K.N.SHETTY, JRNL AUTH 3 M.CARTER,O.A.DAVIS,A.T.HENLEY,P.INNOCENTI,L.D.JOHNSON,M.LIU, JRNL AUTH 4 S.DE KLERK,Y.V.LE BIHAN,M.G.LLOYD,P.C.MCANDREW,E.SHEHU, JRNL AUTH 5 R.TALBOT,H.L.WOODWARD,R.BURKE,V.KIRKIN,R.L.M.VAN MONTFORT, JRNL AUTH 6 F.I.RAYNAUD,O.W.ROSSANESE,S.HOELDER JRNL TITL ACHIEVINGIN VIVOTARGET DEPLETION THROUGH THE DISCOVERY AND JRNL TITL 2 OPTIMIZATION OF BENZIMIDAZOLONE BCL6 DEGRADERS. JRNL REF J.MED.CHEM. V. 63 4047 2020 JRNL REFN ISSN 0022-2623 JRNL PMID 32275432 JRNL DOI 10.1021/ACS.JMEDCHEM.9B02076 REMARK 2 REMARK 2 RESOLUTION. 1.58 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 31707 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) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 1539 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 : 50 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.58 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.58 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 635 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2682 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 602 REMARK 3 BIN R VALUE (WORKING SET) : 0.2674 REMARK 3 BIN FREE R VALUE : 0.2815 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 33 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 : 1014 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 156 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.10470 REMARK 3 B22 (A**2) : 1.10470 REMARK 3 B33 (A**2) : -2.20930 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) : 0.200 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.063 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.064 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.058 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.059 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 : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1197 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1626 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 419 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 224 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1197 ; 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 : 160 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : 18 ; 1.000 ; HARMONIC 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 : 1610 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.03 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.70 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 14.08 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: {A|5 - 27} REMARK 3 ORIGIN FOR THE GROUP (A): 28.3700 -27.8057 11.6368 REMARK 3 T TENSOR REMARK 3 T11: -0.0287 T22: -0.0149 REMARK 3 T33: -0.1158 T12: -0.0196 REMARK 3 T13: 0.0078 T23: -0.0198 REMARK 3 L TENSOR REMARK 3 L11: 3.9618 L22: 1.6776 REMARK 3 L33: 5.7241 L12: 0.4816 REMARK 3 L13: 2.6737 L23: 1.1898 REMARK 3 S TENSOR REMARK 3 S11: 0.0493 S12: 0.0070 S13: -0.1069 REMARK 3 S21: 0.1623 S22: -0.0574 S23: 0.0191 REMARK 3 S31: 0.2705 S32: -0.3300 S33: 0.0081 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: {A|28 - 40} REMARK 3 ORIGIN FOR THE GROUP (A): 41.1968 -15.2835 27.8614 REMARK 3 T TENSOR REMARK 3 T11: 0.2048 T22: 0.2271 REMARK 3 T33: 0.1184 T12: -0.0342 REMARK 3 T13: -0.0487 T23: -0.0407 REMARK 3 L TENSOR REMARK 3 L11: 0.5125 L22: 3.9069 REMARK 3 L33: 2.8865 L12: 0.1467 REMARK 3 L13: 0.9435 L23: 0.4318 REMARK 3 S TENSOR REMARK 3 S11: 0.1449 S12: -0.0385 S13: 0.0711 REMARK 3 S21: 0.2788 S22: 0.0749 S23: -0.4096 REMARK 3 S31: -0.1867 S32: 0.1906 S33: -0.2198 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: {A|41 - 46} REMARK 3 ORIGIN FOR THE GROUP (A): 39.6643 -15.9809 28.5244 REMARK 3 T TENSOR REMARK 3 T11: -0.1511 T22: -0.1939 REMARK 3 T33: -0.3040 T12: -0.0096 REMARK 3 T13: -0.0478 T23: -0.0272 REMARK 3 L TENSOR REMARK 3 L11: 0.8165 L22: 0.7998 REMARK 3 L33: 1.4599 L12: 0.2994 REMARK 3 L13: 1.3679 L23: 0.7565 REMARK 3 S TENSOR REMARK 3 S11: -0.0738 S12: -0.1694 S13: 0.0128 REMARK 3 S21: 0.4237 S22: 0.0848 S23: -0.0511 REMARK 3 S31: -0.1514 S32: 0.1913 S33: -0.0110 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: {A|47 - 92} REMARK 3 ORIGIN FOR THE GROUP (A): 33.2622 -10.4784 24.1227 REMARK 3 T TENSOR REMARK 3 T11: 0.0269 T22: -0.0328 REMARK 3 T33: -0.0810 T12: -0.0283 REMARK 3 T13: 0.0187 T23: -0.0127 REMARK 3 L TENSOR REMARK 3 L11: 1.2871 L22: 2.9471 REMARK 3 L33: 2.0752 L12: 1.2558 REMARK 3 L13: -0.1275 L23: 0.9454 REMARK 3 S TENSOR REMARK 3 S11: 0.1027 S12: -0.0029 S13: 0.0826 REMARK 3 S21: 0.1130 S22: 0.0008 S23: -0.0624 REMARK 3 S31: -0.1997 S32: 0.0629 S33: -0.1035 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: {A|93 - 101} REMARK 3 ORIGIN FOR THE GROUP (A): 22.3282 -22.7554 32.5993 REMARK 3 T TENSOR REMARK 3 T11: 0.1550 T22: 0.0657 REMARK 3 T33: -0.0605 T12: -0.0929 REMARK 3 T13: 0.0524 T23: -0.0107 REMARK 3 L TENSOR REMARK 3 L11: 1.9535 L22: 1.6664 REMARK 3 L33: 1.4735 L12: 1.2632 REMARK 3 L13: -0.5541 L23: -1.4450 REMARK 3 S TENSOR REMARK 3 S11: 0.1012 S12: -0.2956 S13: -0.0095 REMARK 3 S21: 0.3356 S22: -0.2160 S23: 0.1884 REMARK 3 S31: 0.0279 S32: 0.1842 S33: 0.1147 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: {A|102 - 114} REMARK 3 ORIGIN FOR THE GROUP (A): 23.4197 -10.5158 31.0151 REMARK 3 T TENSOR REMARK 3 T11: 0.0123 T22: -0.0601 REMARK 3 T33: -0.0879 T12: -0.0325 REMARK 3 T13: 0.0657 T23: -0.0552 REMARK 3 L TENSOR REMARK 3 L11: 3.7405 L22: 6.4669 REMARK 3 L33: 5.4883 L12: 3.4597 REMARK 3 L13: -0.9914 L23: -0.8866 REMARK 3 S TENSOR REMARK 3 S11: 0.2516 S12: -0.2058 S13: 0.3293 REMARK 3 S21: 0.4967 S22: -0.2748 S23: 0.4081 REMARK 3 S31: -0.2620 S32: -0.3266 S33: 0.0232 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: {A|115 - 129} REMARK 3 ORIGIN FOR THE GROUP (A): 13.6496 -15.0230 31.2656 REMARK 3 T TENSOR REMARK 3 T11: 0.0261 T22: 0.0595 REMARK 3 T33: 0.0230 T12: -0.0579 REMARK 3 T13: 0.0956 T23: -0.1026 REMARK 3 L TENSOR REMARK 3 L11: 7.7775 L22: 8.6056 REMARK 3 L33: 0.0164 L12: 0.2929 REMARK 3 L13: -1.8542 L23: 0.2583 REMARK 3 S TENSOR REMARK 3 S11: -0.0693 S12: 0.0839 S13: 0.2077 REMARK 3 S21: 0.4382 S22: -0.1820 S23: 0.7287 REMARK 3 S31: 0.1889 S32: -0.4140 S33: 0.2512 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: {B|0 - 5} REMARK 3 ORIGIN FOR THE GROUP (A): 19.2167 -32.5148 2.1249 REMARK 3 T TENSOR REMARK 3 T11: -0.0596 T22: 0.1280 REMARK 3 T33: -0.0659 T12: -0.0519 REMARK 3 T13: -0.0132 T23: -0.0315 REMARK 3 L TENSOR REMARK 3 L11: 2.6402 L22: 0.6717 REMARK 3 L33: 1.1591 L12: 0.9467 REMARK 3 L13: 1.1387 L23: 3.6942 REMARK 3 S TENSOR REMARK 3 S11: 0.0967 S12: -0.0500 S13: -0.0477 REMARK 3 S21: -0.0990 S22: 0.0572 S23: 0.0750 REMARK 3 S31: 0.0747 S32: -0.0494 S33: -0.1539 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6TOI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1292104952. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-AUG-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9660 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31728 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 55.278 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 11.90 REMARK 200 R MERGE FOR SHELL (I) : 0.76900 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3BIM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 MICROLITER OF THE BCL6-BTB/WVIP REMARK 280 COMPLEX AT 4 MG/ML PLUS 1 MICROLITER OF A CRYSTALLISATION REMARK 280 SOLUTION CONSISTING OF 1 M K2HPO4, 0.7 M NAH2PO4, 75 MM SODIUM REMARK 280 ACETATE BUFFER PH 4.5 AND 2 % DMSO, AGAINST 350 MICROLITER OF REMARK 280 CRYSTALLISATION SOLUTION., PH 7, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.54667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 111.09333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 83.32000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 138.86667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 27.77333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 55.54667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 111.09333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 138.86667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 83.32000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 27.77333 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 BIOMT1 2 0.500000 0.866025 0.000000 33.83000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -58.59528 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 27.77333 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 310 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 372 LIES ON A SPECIAL POSITION. 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 GLY A 2 REMARK 465 PRO A 3 REMARK 465 GLY A 4 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 ASP A 6 CG OD1 OD2 REMARK 470 ARG A 13 NE CZ NH1 NH2 REMARK 470 GLU A 41 OE1 OE2 REMARK 470 GLU A 77 CD OE1 OE2 REMARK 470 ARG A 94 NH1 REMARK 470 GLU A 99 CD OE1 OE2 REMARK 470 LYS A 123 CD CE NZ REMARK 470 LYS A 126 CD CE NZ REMARK 470 GLU A 129 O REMARK 470 ALA B 0 N CB REMARK 470 ALA B 5 CA C O CB 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 LEU A 31 19.77 59.38 REMARK 500 SER A 39 -127.46 62.00 REMARK 500 SER A 93 -2.13 78.17 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 448 DISTANCE = 6.35 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NQN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 101 DBREF 6TOI A 5 129 UNP P41182 BCL6_HUMAN 5 129 DBREF 6TOI B 0 5 PDB 6TOI 6TOI 0 5 SEQADV 6TOI GLY A 2 UNP P41182 EXPRESSION TAG SEQADV 6TOI PRO A 3 UNP P41182 EXPRESSION TAG SEQADV 6TOI GLY A 4 UNP P41182 EXPRESSION TAG SEQRES 1 A 128 GLY PRO GLY ALA ASP SER CYS ILE GLN PHE THR ARG HIS SEQRES 2 A 128 ALA SER ASP VAL LEU LEU ASN LEU ASN ARG LEU ARG SER SEQRES 3 A 128 ARG ASP ILE LEU THR ASP VAL VAL ILE VAL VAL SER ARG SEQRES 4 A 128 GLU GLN PHE ARG ALA HIS LYS THR VAL LEU MET ALA CYS SEQRES 5 A 128 SER GLY LEU PHE TYR SER ILE PHE THR ASP GLN LEU LYS SEQRES 6 A 128 CYS ASN LEU SER VAL ILE ASN LEU ASP PRO GLU ILE ASN SEQRES 7 A 128 PRO GLU GLY PHE CYS ILE LEU LEU ASP PHE MET TYR THR SEQRES 8 A 128 SER ARG LEU ASN LEU ARG GLU GLY ASN ILE MET ALA VAL SEQRES 9 A 128 MET ALA THR ALA MET TYR LEU GLN MET GLU HIS VAL VAL SEQRES 10 A 128 ASP THR CYS ARG LYS PHE ILE LYS ALA SER GLU SEQRES 1 B 6 ALA TRP VAL ILE PRO ALA HET NQN A 201 26 HET EDO A 202 4 HET EDO A 203 4 HET EDO A 204 4 HET EDO A 205 4 HET DMS A 206 4 HET DMS A 207 4 HET EDO B 101 4 HETNAM NQN 2-CHLORANYL-4-[[1-METHYL-3-[(3~{R})-3-OXIDANYLBUTYL]-2- HETNAM 2 NQN OXIDANYLIDENE-BENZIMIDAZOL-5-YL]AMINO]PYRIDINE-3- HETNAM 3 NQN CARBONITRILE HETNAM EDO 1,2-ETHANEDIOL HETNAM DMS DIMETHYL SULFOXIDE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 NQN C18 H18 CL N5 O2 FORMUL 4 EDO 5(C2 H6 O2) FORMUL 8 DMS 2(C2 H6 O S) FORMUL 11 HOH *156(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 THR A 62 1 9 HELIX 4 AA4 LEU A 65 LEU A 69 5 5 HELIX 5 AA5 ASN A 79 SER A 93 1 15 HELIX 6 AA6 ASN A 101 GLN A 113 1 13 HELIX 7 AA7 MET A 114 SER A 128 1 15 SHEET 1 AA1 2 GLN A 10 PHE A 11 0 SHEET 2 AA1 2 TRP B 1 VAL B 2 -1 O VAL B 2 N GLN A 10 SHEET 1 AA2 3 GLU A 41 ALA A 45 0 SHEET 2 AA2 3 VAL A 34 VAL A 38 -1 N ILE A 36 O PHE A 43 SHEET 3 AA2 3 VAL A 71 ASN A 73 1 O ILE A 72 N VAL A 37 SITE 1 AC1 16 ASP A 17 ASN A 21 ARG A 24 LEU A 25 SITE 2 AC1 16 MET A 51 ALA A 52 CYS A 53 GLY A 55 SITE 3 AC1 16 TYR A 58 GLN A 113 MET A 114 GLU A 115 SITE 4 AC1 16 HIS A 116 HOH A 303 HOH A 350 HOH A 364 SITE 1 AC2 4 ASP A 63 GLN A 64 ARG A 98 GLU A 99 SITE 1 AC3 2 HOH A 359 ALA B 5 SITE 1 AC4 3 LEU A 65 GLU A 99 SER A 128 SITE 1 AC5 2 PRO A 76 HOH A 302 SITE 1 AC6 4 VAL A 37 GLN A 42 VAL A 71 HOH A 321 SITE 1 AC7 5 ILE A 72 ASN A 73 PHE A 124 TRP B 1 SITE 2 AC7 5 HOH B 203 CRYST1 67.660 67.660 166.640 90.00 90.00 120.00 P 61 2 2 12 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 0.014780 0.008533 0.000000 0.00000 SCALE2 0.000000 0.017066 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006001 0.00000