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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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