HEADER TRANSCRIPTION 11-DEC-19 6TON
TITLE CRYSTAL STRUCTURE OF HUMAN BCL6 BTB DOMAIN IN COMPLEX WITH COMPOUND
TITLE 2 25B
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 M.J.RODRIGUES,Y.-V.LE BIHAN,R.L.M.VAN MONTFORT
REVDAT 3 24-JAN-24 6TON 1 REMARK
REVDAT 2 06-MAY-20 6TON 1 JRNL
REVDAT 1 22-APR-20 6TON 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. 2.36 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) : 2.36
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.70
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 3 NUMBER OF REFLECTIONS : 10063
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) : 0.197
REMARK 3 R VALUE (WORKING SET) : 0.195
REMARK 3 FREE R VALUE : 0.232
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.220
REMARK 3 FREE R VALUE TEST SET COUNT : 525
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 : 26
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.36
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.39
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.02
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 388
REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2470
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 370
REMARK 3 BIN R VALUE (WORKING SET) : 0.2458
REMARK 3 BIN FREE R VALUE : 0.2729
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.64
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 18
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 : 996
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 43
REMARK 3 SOLVENT ATOMS : 86
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 46.20
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.66
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 1.80940
REMARK 3 B22 (A**2) : 1.80940
REMARK 3 B33 (A**2) : -3.61880
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) : 0.300
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.244
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.197
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.212
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.185
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 : 0.942
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 1099 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 1499 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 377 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL
REMARK 3 GENERAL PLANES : 203 ; 5.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 1099 ; 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 : 146 ; 5.000 ; SEMIHARMONIC
REMARK 3 SUM OF OCCUPANCIES : 3 ; 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 : 1333 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.010
REMARK 3 BOND ANGLES (DEGREES) : 1.11
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.92
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.93
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 7
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: {A|5 - 40}
REMARK 3 ORIGIN FOR THE GROUP (A): 31.8211 -24.5021 16.0946
REMARK 3 T TENSOR
REMARK 3 T11: 0.0123 T22: -0.0433
REMARK 3 T33: -0.0021 T12: 0.0378
REMARK 3 T13: -0.0278 T23: -0.0573
REMARK 3 L TENSOR
REMARK 3 L11: 4.0549 L22: 4.9907
REMARK 3 L33: 6.9383 L12: 0.6943
REMARK 3 L13: -0.4126 L23: 3.1224
REMARK 3 S TENSOR
REMARK 3 S11: 0.1913 S12: -0.0555 S13: -0.1207
REMARK 3 S21: 0.5678 S22: -0.0099 S23: -0.2540
REMARK 3 S31: 0.3222 S32: -0.2507 S33: -0.1814
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: {A|41 - 46}
REMARK 3 ORIGIN FOR THE GROUP (A): 38.9679 -17.1773 27.5666
REMARK 3 T TENSOR
REMARK 3 T11: 0.0144 T22: -0.1574
REMARK 3 T33: -0.1647 T12: -0.0318
REMARK 3 T13: -0.0745 T23: -0.1750
REMARK 3 L TENSOR
REMARK 3 L11: 2.5648 L22: -2.5057
REMARK 3 L33: 0.2041 L12: -1.4296
REMARK 3 L13: -0.2387 L23: 2.6894
REMARK 3 S TENSOR
REMARK 3 S11: -0.0006 S12: -0.0400 S13: 0.2778
REMARK 3 S21: 0.2490 S22: 0.0103 S23: -0.1103
REMARK 3 S31: -0.1106 S32: 0.0850 S33: -0.0096
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: {A|47 - 79}
REMARK 3 ORIGIN FOR THE GROUP (A): 33.8125 -7.9380 23.0415
REMARK 3 T TENSOR
REMARK 3 T11: 0.0644 T22: -0.1632
REMARK 3 T33: 0.0545 T12: -0.0840
REMARK 3 T13: 0.1962 T23: -0.0622
REMARK 3 L TENSOR
REMARK 3 L11: 3.1101 L22: 8.1187
REMARK 3 L33: 5.4074 L12: 1.4833
REMARK 3 L13: 0.8713 L23: 3.7472
REMARK 3 S TENSOR
REMARK 3 S11: 0.1820 S12: -0.1178 S13: 0.7394
REMARK 3 S21: 0.1099 S22: 0.1834 S23: -0.1923
REMARK 3 S31: -0.7086 S32: 0.2107 S33: -0.3654
REMARK 3
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: {A|80 - 101}
REMARK 3 ORIGIN FOR THE GROUP (A): 25.9810 -21.6789 30.1769
REMARK 3 T TENSOR
REMARK 3 T11: 0.2204 T22: -0.0609
REMARK 3 T33: -0.0745 T12: -0.0604
REMARK 3 T13: 0.0689 T23: 0.0093
REMARK 3 L TENSOR
REMARK 3 L11: 5.2458 L22: 9.1511
REMARK 3 L33: 3.9769 L12: 2.4172
REMARK 3 L13: -3.5222 L23: 0.6527
REMARK 3 S TENSOR
REMARK 3 S11: 0.0789 S12: -0.3086 S13: -0.1430
REMARK 3 S21: 0.7799 S22: -0.1932 S23: 0.0943
REMARK 3 S31: 0.1529 S32: -0.1645 S33: 0.1143
REMARK 3
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: {A|102 - 114}
REMARK 3 ORIGIN FOR THE GROUP (A): 22.7075 -11.5688 31.8453
REMARK 3 T TENSOR
REMARK 3 T11: -0.0160 T22: -0.2112
REMARK 3 T33: -0.1453 T12: -0.1349
REMARK 3 T13: 0.1887 T23: -0.0665
REMARK 3 L TENSOR
REMARK 3 L11: -1.2303 L22: 6.2898
REMARK 3 L33: 5.2287 L12: -0.6918
REMARK 3 L13: -2.4281 L23: 1.9588
REMARK 3 S TENSOR
REMARK 3 S11: 0.2386 S12: -0.3773 S13: 0.5022
REMARK 3 S21: 0.3803 S22: -0.1411 S23: 0.2187
REMARK 3 S31: 0.2412 S32: -0.4892 S33: -0.0975
REMARK 3
REMARK 3 TLS GROUP : 6
REMARK 3 SELECTION: {A|115 - 129}
REMARK 3 ORIGIN FOR THE GROUP (A): 12.9165 -15.8659 31.7669
REMARK 3 T TENSOR
REMARK 3 T11: 0.1581 T22: 0.0058
REMARK 3 T33: 0.0966 T12: -0.1721
REMARK 3 T13: 0.2076 T23: -0.0556
REMARK 3 L TENSOR
REMARK 3 L11: 5.8538 L22: 7.6189
REMARK 3 L33: 0.0000 L12: -1.3139
REMARK 3 L13: -3.5848 L23: 1.2910
REMARK 3 S TENSOR
REMARK 3 S11: -0.1174 S12: 0.2938 S13: 0.2330
REMARK 3 S21: 0.2828 S22: -0.2071 S23: 0.4364
REMARK 3 S31: 0.0811 S32: -0.2322 S33: 0.3245
REMARK 3
REMARK 3 TLS GROUP : 7
REMARK 3 SELECTION: {B|0 - 5}
REMARK 3 ORIGIN FOR THE GROUP (A): 17.8872 -32.5471 2.2551
REMARK 3 T TENSOR
REMARK 3 T11: -0.2109 T22: 0.1749
REMARK 3 T33: 0.0717 T12: -0.0301
REMARK 3 T13: -0.0556 T23: -0.2076
REMARK 3 L TENSOR
REMARK 3 L11: 2.6995 L22: -2.1065
REMARK 3 L33: 0.0016 L12: -1.0450
REMARK 3 L13: 0.3036 L23: 1.2840
REMARK 3 S TENSOR
REMARK 3 S11: 0.1094 S12: -0.0115 S13: -0.0364
REMARK 3 S21: -0.0317 S22: -0.0986 S23: -0.0126
REMARK 3 S31: 0.0885 S32: 0.0755 S33: -0.0108
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 6TON 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_1292104977.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 17-MAR-18
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 : NULL
REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10122
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.360
REMARK 200 RESOLUTION RANGE LOW (A) : 48.170
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 14.50
REMARK 200 R MERGE (I) : 0.30000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.6000
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) : 2.45
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8
REMARK 200 DATA REDUNDANCY IN SHELL : 15.50
REMARK 200 R MERGE FOR SHELL (I) : 3.28300
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 (%): 67.05
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.73
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 56.68433
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 113.36867
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 85.02650
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 141.71083
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 28.34217
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 56.68433
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 113.36867
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 141.71083
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 85.02650
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 28.34217
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: 5260 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 13490 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 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 33.75150
REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -58.45931
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 28.34217
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B
REMARK 350 BIOMT1 3 0.500000 -0.866025 0.000000 0.00000
REMARK 350 BIOMT2 3 0.866025 0.500000 0.000000 0.00000
REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 28.34217
REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 33.75150
REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 -58.45931
REMARK 350 BIOMT3 4 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 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 ARG A 40 CG CD NE CZ NH1 NH2
REMARK 470 GLU A 41 CD OE1 OE2
REMARK 470 GLN A 64 CD OE1 NE2
REMARK 470 GLU A 77 CD OE1 OE2
REMARK 470 GLU A 81 OE1 OE2
REMARK 470 ARG A 98 NE CZ NH1 NH2
REMARK 470 GLU A 99 CG CD OE1 OE2
REMARK 470 ARG A 122 CZ NH1 NH2
REMARK 470 LYS A 123 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 17.24 59.52
REMARK 500 SER A 39 -120.35 52.64
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 382 DISTANCE = 7.43 ANGSTROMS
REMARK 525 HOH A 383 DISTANCE = 8.07 ANGSTROMS
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NR5 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 B 101
DBREF 6TON A 5 129 UNP P41182 BCL6_HUMAN 5 129
DBREF 6TON B 0 5 PDB 6TON 6TON 0 5
SEQADV 6TON GLY A 2 UNP P41182 EXPRESSION TAG
SEQADV 6TON PRO A 3 UNP P41182 EXPRESSION TAG
SEQADV 6TON 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 NR5 A 201 35
HET EDO A 202 4
HET EDO B 101 4
HETNAM NR5 5-[[5-CHLORANYL-2-(2,2,6,6-TETRAMETHYLMORPHOLIN-4-YL)
HETNAM 2 NR5 PYRIMIDIN-4-YL]AMINO]-1-METHYL-3-(3-METHYL-3-OXIDANYL-
HETNAM 3 NR5 BUTYL)BENZIMIDAZOL-2-ONE
HETNAM EDO 1,2-ETHANEDIOL
HETSYN EDO ETHYLENE GLYCOL
FORMUL 3 NR5 C25 H35 CL N6 O3
FORMUL 4 EDO 2(C2 H6 O2)
FORMUL 6 HOH *86(H2 O)
HELIX 1 AA1 ARG A 13 ASP A 29 1 17
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 LEU A 112 1 12
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 15 ASP A 17 ASN A 21 LEU A 25 ARG A 28
SITE 2 AC1 15 MET A 51 ALA A 52 CYS A 53 TYR A 58
SITE 3 AC1 15 GLN A 113 MET A 114 GLU A 115 HOH A 308
SITE 4 AC1 15 HOH A 313 HOH A 322 HOH A 334
SITE 1 AC2 3 GLU A 99 ILE A 125 SER A 128
SITE 1 AC3 4 ILE A 9 ASN A 73 PHE A 124 TRP B 1
CRYST1 67.503 67.503 170.053 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 0.014814 0.008553 0.000000 0.00000
SCALE2 0.000000 0.017106 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005881 0.00000