HEADER TRANSCRIPTION 11-DEC-19 6TOL
TITLE CRYSTAL STRUCTURE OF HUMAN BCL6 BTB DOMAIN IN COMPLEX WITH COMPOUND
TITLE 2 25A
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
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
KEYWDS CANCER, LYMPHOMA, INHIBITOR, DEGRADER, TRANSCRIPTION
EXPDTA X-RAY DIFFRACTION
AUTHOR M.J.RODRIGUES,Y.-V.LE BIHAN,R.L.M.VAN MONTFORT
REVDAT 3 24-JAN-24 6TOL 1 REMARK
REVDAT 2 06-MAY-20 6TOL 1 JRNL
REVDAT 1 22-APR-20 6TOL 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. 1.64 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) : 1.64
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.13
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 28228
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) : 0.182
REMARK 3 R VALUE (WORKING SET) : 0.181
REMARK 3 FREE R VALUE : 0.205
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030
REMARK 3 FREE R VALUE TEST SET COUNT : 1421
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) : 1.64
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.65
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.82
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 565
REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2233
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 535
REMARK 3 BIN R VALUE (WORKING SET) : 0.2215
REMARK 3 BIN FREE R VALUE : 0.2519
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.31
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 30
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 : 1032
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 69
REMARK 3 SOLVENT ATOMS : 161
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 33.85
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.11
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -1.76920
REMARK 3 B22 (A**2) : -1.76920
REMARK 3 B33 (A**2) : 3.53830
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) : 0.210
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.079
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.079
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.071
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.073
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 : 0.964
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 1173 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 1580 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 421 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL
REMARK 3 GENERAL PLANES : 220 ; 5.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 1173 ; 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 : 151 ; 5.000 ; SEMIHARMONIC
REMARK 3 SUM OF OCCUPANCIES : 21 ; 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 : 1570 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.010
REMARK 3 BOND ANGLES (DEGREES) : 0.99
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.73
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 14.56
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 6
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: {A|-1 - 27}
REMARK 3 ORIGIN FOR THE GROUP (A): -26.2739 28.5109 10.1219
REMARK 3 T TENSOR
REMARK 3 T11: -0.0326 T22: -0.0087
REMARK 3 T33: -0.0371 T12: -0.0232
REMARK 3 T13: -0.0203 T23: 0.0303
REMARK 3 L TENSOR
REMARK 3 L11: 3.9431 L22: 1.8609
REMARK 3 L33: 5.0204 L12: 0.2968
REMARK 3 L13: -2.5716 L23: -0.9113
REMARK 3 S TENSOR
REMARK 3 S11: 0.0806 S12: 0.1046 S13: 0.2793
REMARK 3 S21: 0.1004 S22: -0.0072 S23: -0.0611
REMARK 3 S31: -0.2635 S32: 0.3006 S33: -0.0734
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: {A|28 - 46}
REMARK 3 ORIGIN FOR THE GROUP (A): -40.8665 16.2057 26.3095
REMARK 3 T TENSOR
REMARK 3 T11: -0.0352 T22: -0.0149
REMARK 3 T33: -0.0412 T12: -0.0309
REMARK 3 T13: 0.0540 T23: 0.0498
REMARK 3 L TENSOR
REMARK 3 L11: 2.3554 L22: 4.2721
REMARK 3 L33: 2.3868 L12: -0.1879
REMARK 3 L13: -0.9234 L23: -0.9150
REMARK 3 S TENSOR
REMARK 3 S11: 0.1539 S12: -0.2167 S13: -0.0620
REMARK 3 S21: 0.3651 S22: 0.0997 S23: 0.4668
REMARK 3 S31: -0.0186 S32: -0.3012 S33: -0.2536
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: {A|47 - 92}
REMARK 3 ORIGIN FOR THE GROUP (A): -33.3746 10.2304 24.1626
REMARK 3 T TENSOR
REMARK 3 T11: 0.0075 T22: -0.0750
REMARK 3 T33: -0.0266 T12: -0.0355
REMARK 3 T13: -0.0138 T23: 0.0253
REMARK 3 L TENSOR
REMARK 3 L11: 1.6334 L22: 3.3962
REMARK 3 L33: 1.8193 L12: 1.4923
REMARK 3 L13: 0.1348 L23: -0.7402
REMARK 3 S TENSOR
REMARK 3 S11: 0.0994 S12: -0.0728 S13: -0.1246
REMARK 3 S21: 0.1693 S22: -0.0189 S23: 0.0862
REMARK 3 S31: 0.2419 S32: -0.1109 S33: -0.0804
REMARK 3
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: {A|93 - 101}
REMARK 3 ORIGIN FOR THE GROUP (A): -21.9448 22.3373 33.3910
REMARK 3 T TENSOR
REMARK 3 T11: 0.1409 T22: -0.0173
REMARK 3 T33: -0.0672 T12: -0.1012
REMARK 3 T13: -0.0610 T23: 0.0211
REMARK 3 L TENSOR
REMARK 3 L11: 2.6242 L22: 0.4501
REMARK 3 L33: 0.4032 L12: 0.4909
REMARK 3 L13: 2.1502 L23: 0.9434
REMARK 3 S TENSOR
REMARK 3 S11: 0.0935 S12: -0.2745 S13: 0.0139
REMARK 3 S21: 0.4048 S22: -0.1881 S23: -0.2218
REMARK 3 S31: -0.1506 S32: -0.0777 S33: 0.0946
REMARK 3
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: {A|102 - 114}
REMARK 3 ORIGIN FOR THE GROUP (A): -23.5077 10.1696 31.0411
REMARK 3 T TENSOR
REMARK 3 T11: 0.0294 T22: -0.0752
REMARK 3 T33: -0.0311 T12: -0.0351
REMARK 3 T13: -0.0700 T23: 0.0729
REMARK 3 L TENSOR
REMARK 3 L11: 2.1171 L22: 4.4287
REMARK 3 L33: 4.5683 L12: 1.3802
REMARK 3 L13: 0.0466 L23: -0.1894
REMARK 3 S TENSOR
REMARK 3 S11: 0.2367 S12: -0.2777 S13: -0.3183
REMARK 3 S21: 0.4425 S22: -0.2557 S23: -0.3528
REMARK 3 S31: 0.1883 S32: 0.2457 S33: 0.0190
REMARK 3
REMARK 3 TLS GROUP : 6
REMARK 3 SELECTION: {A|115 - 129}
REMARK 3 ORIGIN FOR THE GROUP (A): -13.5706 14.2118 30.4977
REMARK 3 T TENSOR
REMARK 3 T11: 0.0029 T22: -0.0265
REMARK 3 T33: 0.0796 T12: -0.0227
REMARK 3 T13: -0.0975 T23: 0.0888
REMARK 3 L TENSOR
REMARK 3 L11: 9.0474 L22: 5.5342
REMARK 3 L33: 0.1210 L12: 0.1690
REMARK 3 L13: 3.4497 L23: -0.9976
REMARK 3 S TENSOR
REMARK 3 S11: -0.0108 S12: 0.0835 S13: -0.0462
REMARK 3 S21: 0.2770 S22: -0.1903 S23: -0.6419
REMARK 3 S31: -0.1614 S32: 0.1824 S33: 0.2011
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 6TOL 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_1292104975.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-JUL-19
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 : 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) : 0.9159
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 0.7.4
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28338
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640
REMARK 200 RESOLUTION RANGE LOW (A) : 47.760
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 23.60
REMARK 200 R MERGE (I) : 0.07000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 19.90
REMARK 200 R MERGE FOR SHELL (I) : 3.14900
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 (%): 62.75
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.30
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 MICROLITER OF BCL6-BTB AT 10 MG/ML
REMARK 280 PLUS 1.5 MICROLITER OF A CRYSTALLISATION SOLUTION CONSISTING OF
REMARK 280 0.1 M TRIS PH 7.5 AND 0.80 M NA/K TARTRATE, AGAINST 300
REMARK 280 MICROLITER OF CRYSTALLISATION SOLUTION., VAPOR DIFFUSION,
REMARK 280 HANGING DROP, 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 55.81733
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 111.63467
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 83.72600
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 139.54333
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 27.90867
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 55.81733
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 111.63467
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 139.54333
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 83.72600
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 27.90867
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: 7220 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 13720 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 0.500000 0.866025 0.000000 -33.57150
REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 58.14754
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 27.90867
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 397 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 454 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 -14
REMARK 465 PRO A -13
REMARK 465 GLY A -12
REMARK 465 LEU A -11
REMARK 465 ASP A -10
REMARK 465 TYR A -9
REMARK 465 LYS A -8
REMARK 465 ASP A -7
REMARK 465 ASP A -6
REMARK 465 ASP A -5
REMARK 465 ASP A -4
REMARK 465 LYS A -3
REMARK 465 GLU A -2
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 ASN A -1 N CA CB CG OD1 ND2
REMARK 470 ARG A 13 NE CZ NH1 NH2
REMARK 470 GLN A 64 OE1
REMARK 470 ARG A 98 NH2
REMARK 470 GLU A 99 OE2
REMARK 470 LYS A 123 NZ
REMARK 470 LYS A 126 CE NZ
REMARK 470 GLU A 129 O
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 -128.35 53.62
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 NQW 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 EDO A 206
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 207
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 208
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 209
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 210
DBREF 6TOL A 5 129 UNP P41182 BCL6_HUMAN 5 129
SEQADV 6TOL GLY A -14 UNP P41182 EXPRESSION TAG
SEQADV 6TOL PRO A -13 UNP P41182 EXPRESSION TAG
SEQADV 6TOL GLY A -12 UNP P41182 EXPRESSION TAG
SEQADV 6TOL LEU A -11 UNP P41182 EXPRESSION TAG
SEQADV 6TOL ASP A -10 UNP P41182 EXPRESSION TAG
SEQADV 6TOL TYR A -9 UNP P41182 EXPRESSION TAG
SEQADV 6TOL LYS A -8 UNP P41182 EXPRESSION TAG
SEQADV 6TOL ASP A -7 UNP P41182 EXPRESSION TAG
SEQADV 6TOL ASP A -6 UNP P41182 EXPRESSION TAG
SEQADV 6TOL ASP A -5 UNP P41182 EXPRESSION TAG
SEQADV 6TOL ASP A -4 UNP P41182 EXPRESSION TAG
SEQADV 6TOL LYS A -3 UNP P41182 EXPRESSION TAG
SEQADV 6TOL GLU A -2 UNP P41182 EXPRESSION TAG
SEQADV 6TOL ASN A -1 UNP P41182 EXPRESSION TAG
SEQADV 6TOL LEU A 0 UNP P41182 EXPRESSION TAG
SEQADV 6TOL TYR A 1 UNP P41182 EXPRESSION TAG
SEQADV 6TOL PHE A 2 UNP P41182 EXPRESSION TAG
SEQADV 6TOL GLN A 3 UNP P41182 EXPRESSION TAG
SEQADV 6TOL GLY A 4 UNP P41182 EXPRESSION TAG
SEQRES 1 A 144 GLY PRO GLY LEU ASP TYR LYS ASP ASP ASP ASP LYS GLU
SEQRES 2 A 144 ASN LEU TYR PHE GLN GLY ALA ASP SER CYS ILE GLN PHE
SEQRES 3 A 144 THR ARG HIS ALA SER ASP VAL LEU LEU ASN LEU ASN ARG
SEQRES 4 A 144 LEU ARG SER ARG ASP ILE LEU THR ASP VAL VAL ILE VAL
SEQRES 5 A 144 VAL SER ARG GLU GLN PHE ARG ALA HIS LYS THR VAL LEU
SEQRES 6 A 144 MET ALA CYS SER GLY LEU PHE TYR SER ILE PHE THR ASP
SEQRES 7 A 144 GLN LEU LYS CYS ASN LEU SER VAL ILE ASN LEU ASP PRO
SEQRES 8 A 144 GLU ILE ASN PRO GLU GLY PHE CYS ILE LEU LEU ASP PHE
SEQRES 9 A 144 MET TYR THR SER ARG LEU ASN LEU ARG GLU GLY ASN ILE
SEQRES 10 A 144 MET ALA VAL MET ALA THR ALA MET TYR LEU GLN MET GLU
SEQRES 11 A 144 HIS VAL VAL ASP THR CYS ARG LYS PHE ILE LYS ALA SER
SEQRES 12 A 144 GLU
HET NQW A 201 33
HET EDO A 202 4
HET EDO A 203 4
HET EDO A 204 4
HET EDO A 205 4
HET EDO A 206 4
HET EDO A 207 8
HET EDO A 208 4
HET EDO A 209 4
HET DMS A 210 4
HETNAM NQW 5-[[5-CHLORANYL-2-[(2~{S},6~{R})-2,6-DIMETHYLMORPHOLIN-
HETNAM 2 NQW 4-YL]PYRIMIDIN-4-YL]AMINO]-1-METHYL-3-(3-METHYL-3-
HETNAM 3 NQW OXIDANYL-BUTYL)BENZIMIDAZOL-2-ONE
HETNAM EDO 1,2-ETHANEDIOL
HETNAM DMS DIMETHYL SULFOXIDE
HETSYN EDO ETHYLENE GLYCOL
FORMUL 2 NQW C23 H31 CL N6 O3
FORMUL 3 EDO 8(C2 H6 O2)
FORMUL 11 DMS C2 H6 O S
FORMUL 12 HOH *161(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 ASN A 79 SER A 93 1 15
HELIX 5 AA5 ASN A 101 GLN A 113 1 13
HELIX 6 AA6 MET A 114 GLU A 129 1 16
SHEET 1 AA1 2 TYR A 1 GLN A 3 0
SHEET 2 AA1 2 ILE A 9 PHE A 11 -1 O GLN A 10 N PHE A 2
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 17 ASP A 17 ASN A 21 LEU A 25 MET A 51
SITE 2 AC1 17 ALA A 52 CYS A 53 GLY A 55 TYR A 58
SITE 3 AC1 17 GLN A 113 MET A 114 GLU A 115 EDO A 204
SITE 4 AC1 17 EDO A 209 HOH A 326 HOH A 339 HOH A 341
SITE 5 AC1 17 HOH A 356
SITE 1 AC2 4 GLN A 3 ILE A 9 ASN A 73 HOH A 337
SITE 1 AC3 1 GLN A 42
SITE 1 AC4 5 GLU A 115 HIS A 116 NQW A 201 EDO A 209
SITE 2 AC4 5 HOH A 346
SITE 1 AC5 7 SER A 39 PRO A 76 GLU A 77 ILE A 78
SITE 2 AC5 7 ASN A 79 HOH A 336 HOH A 414
SITE 1 AC6 2 GLU A 99 SER A 128
SITE 1 AC7 6 ASN A 23 ARG A 24 SER A 27 HOH A 342
SITE 2 AC7 6 HOH A 361 HOH A 364
SITE 1 AC8 3 SER A 16 HOH A 328 HOH A 404
SITE 1 AC9 5 ASN A 21 ARG A 24 NQW A 201 EDO A 204
SITE 2 AC9 5 HOH A 351
SITE 1 AD1 1 HOH A 357
CRYST1 67.143 67.143 167.452 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 0.014894 0.008599 0.000000 0.00000
SCALE2 0.000000 0.017198 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005972 0.00000