HEADER TRANSCRIPTION 11-DEC-19 6TOJ TITLE CRYSTAL STRUCTURE OF HUMAN BCL6 BTB DOMAIN IN COMPLEX WITH COMPOUND TITLE 2 17A 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 6TOJ 1 REMARK REVDAT 2 06-MAY-20 6TOJ 1 JRNL REVDAT 1 22-APR-20 6TOJ 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. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 19739 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 987 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 : 49 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 403 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2264 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 383 REMARK 3 BIN R VALUE (WORKING SET) : 0.2247 REMARK 3 BIN FREE R VALUE : 0.2552 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.96 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 20 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 : 1029 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 107 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.24340 REMARK 3 B22 (A**2) : 2.24340 REMARK 3 B33 (A**2) : -4.48680 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) : 0.110 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.102 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.100 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.096 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 : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1183 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1605 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 428 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 230 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1183 ; 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 : 153 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : 11 ; 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 : 1494 ; 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) : 3.49 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.81 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): 7.3195 86.2503 176.1610 REMARK 3 T TENSOR REMARK 3 T11: -0.0704 T22: -0.0278 REMARK 3 T33: -0.0887 T12: -0.0260 REMARK 3 T13: -0.0289 T23: 0.0499 REMARK 3 L TENSOR REMARK 3 L11: 3.3747 L22: 2.1471 REMARK 3 L33: 6.4051 L12: 0.8114 REMARK 3 L13: -2.7146 L23: -1.1188 REMARK 3 S TENSOR REMARK 3 S11: 0.0516 S12: 0.0052 S13: 0.3918 REMARK 3 S21: 0.1288 S22: 0.0465 S23: -0.0297 REMARK 3 S31: -0.2198 S32: 0.4769 S33: -0.0981 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: {A|28 - 46} REMARK 3 ORIGIN FOR THE GROUP (A): -7.3856 73.5115 194.3780 REMARK 3 T TENSOR REMARK 3 T11: 0.0168 T22: 0.0595 REMARK 3 T33: -0.0463 T12: -0.0403 REMARK 3 T13: 0.0433 T23: 0.0570 REMARK 3 L TENSOR REMARK 3 L11: 2.9455 L22: 4.2543 REMARK 3 L33: 5.6362 L12: -0.7102 REMARK 3 L13: -1.5692 L23: -1.3097 REMARK 3 S TENSOR REMARK 3 S11: 0.1014 S12: -0.3441 S13: -0.1508 REMARK 3 S21: 0.4831 S22: 0.1954 S23: 0.4496 REMARK 3 S31: 0.0527 S32: -0.3034 S33: -0.2969 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: {A|47 - 92} REMARK 3 ORIGIN FOR THE GROUP (A): -0.0959 67.8192 190.7880 REMARK 3 T TENSOR REMARK 3 T11: 0.0243 T22: -0.0628 REMARK 3 T33: -0.0425 T12: -0.0432 REMARK 3 T13: -0.0255 T23: 0.0297 REMARK 3 L TENSOR REMARK 3 L11: 1.9980 L22: 4.0691 REMARK 3 L33: 2.5994 L12: 1.5730 REMARK 3 L13: 0.1080 L23: -0.8761 REMARK 3 S TENSOR REMARK 3 S11: 0.1084 S12: -0.0905 S13: -0.1386 REMARK 3 S21: 0.1898 S22: 0.0111 S23: 0.1176 REMARK 3 S31: 0.2815 S32: -0.1787 S33: -0.1195 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: {A|93 - 101} REMARK 3 ORIGIN FOR THE GROUP (A): 11.1061 80.2001 198.8410 REMARK 3 T TENSOR REMARK 3 T11: 0.1136 T22: -0.0011 REMARK 3 T33: -0.0617 T12: -0.0976 REMARK 3 T13: -0.0676 T23: 0.0024 REMARK 3 L TENSOR REMARK 3 L11: 4.3338 L22: 3.6150 REMARK 3 L33: 0.0000 L12: 0.8010 REMARK 3 L13: -0.1144 L23: 0.8145 REMARK 3 S TENSOR REMARK 3 S11: 0.1547 S12: -0.2538 S13: 0.1327 REMARK 3 S21: 0.2536 S22: -0.2322 S23: -0.2221 REMARK 3 S31: -0.1009 S32: -0.0580 S33: 0.0775 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: {A|102 - 114} REMARK 3 ORIGIN FOR THE GROUP (A): 9.8618 67.6909 197.5550 REMARK 3 T TENSOR REMARK 3 T11: 0.0528 T22: -0.0967 REMARK 3 T33: -0.0432 T12: -0.0441 REMARK 3 T13: -0.0911 T23: 0.0786 REMARK 3 L TENSOR REMARK 3 L11: 2.5655 L22: 3.1839 REMARK 3 L33: 4.0441 L12: -0.3165 REMARK 3 L13: -0.0657 L23: -2.0641 REMARK 3 S TENSOR REMARK 3 S11: 0.1204 S12: -0.2422 S13: -0.3555 REMARK 3 S21: 0.4870 S22: -0.2037 S23: -0.4728 REMARK 3 S31: 0.2326 S32: 0.2275 S33: 0.0832 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: {A|115 - 129} REMARK 3 ORIGIN FOR THE GROUP (A): 19.5455 71.4857 196.6980 REMARK 3 T TENSOR REMARK 3 T11: 0.0053 T22: -0.0067 REMARK 3 T33: 0.0915 T12: -0.0234 REMARK 3 T13: -0.1191 T23: 0.0981 REMARK 3 L TENSOR REMARK 3 L11: 5.4261 L22: 4.9333 REMARK 3 L33: 0.0038 L12: -0.6167 REMARK 3 L13: 1.3987 L23: -1.0077 REMARK 3 S TENSOR REMARK 3 S11: 0.0915 S12: 0.1133 S13: -0.0934 REMARK 3 S21: 0.1352 S22: -0.3186 S23: -0.6665 REMARK 3 S31: -0.0515 S32: 0.2349 S33: 0.2271 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6TOJ 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_1292104966. 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 : 19812 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 47.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 24.80 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 25.50 REMARK 200 R MERGE FOR SHELL (I) : 3.51100 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 (%): 62.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.27 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 55.57667 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 111.15333 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 83.36500 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 138.94167 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 27.78833 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 55.57667 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 111.15333 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 138.94167 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 83.36500 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 27.78833 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: 5270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 -66.99900 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 116.04567 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 361.24833 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 330 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 407 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 LEU A 0 CD2 REMARK 470 ARG A 13 NE CZ NH1 NH2 REMARK 470 GLN A 64 NE2 REMARK 470 ARG A 98 NE CZ NH1 NH2 REMARK 470 LYS A 126 CD CE NZ REMARK 470 GLU A 129 C O CB CG CD OE1 OE2 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 ASP A 6 -145.77 -87.81 REMARK 500 CYS A 8 159.39 -47.24 REMARK 500 SER A 39 -121.16 57.96 REMARK 500 SER A 39 -120.16 57.96 REMARK 500 SER A 93 -1.52 77.67 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 NQQ 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 DBREF 6TOJ A 5 129 UNP P41182 BCL6_HUMAN 5 129 SEQADV 6TOJ GLY A -14 UNP P41182 EXPRESSION TAG SEQADV 6TOJ PRO A -13 UNP P41182 EXPRESSION TAG SEQADV 6TOJ GLY A -12 UNP P41182 EXPRESSION TAG SEQADV 6TOJ LEU A -11 UNP P41182 EXPRESSION TAG SEQADV 6TOJ ASP A -10 UNP P41182 EXPRESSION TAG SEQADV 6TOJ TYR A -9 UNP P41182 EXPRESSION TAG SEQADV 6TOJ LYS A -8 UNP P41182 EXPRESSION TAG SEQADV 6TOJ ASP A -7 UNP P41182 EXPRESSION TAG SEQADV 6TOJ ASP A -6 UNP P41182 EXPRESSION TAG SEQADV 6TOJ ASP A -5 UNP P41182 EXPRESSION TAG SEQADV 6TOJ ASP A -4 UNP P41182 EXPRESSION TAG SEQADV 6TOJ LYS A -3 UNP P41182 EXPRESSION TAG SEQADV 6TOJ GLU A -2 UNP P41182 EXPRESSION TAG SEQADV 6TOJ ASN A -1 UNP P41182 EXPRESSION TAG SEQADV 6TOJ LEU A 0 UNP P41182 EXPRESSION TAG SEQADV 6TOJ TYR A 1 UNP P41182 EXPRESSION TAG SEQADV 6TOJ PHE A 2 UNP P41182 EXPRESSION TAG SEQADV 6TOJ GLN A 3 UNP P41182 EXPRESSION TAG SEQADV 6TOJ 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 NQQ A 201 27 HET EDO A 202 4 HET EDO A 203 4 HET EDO A 204 4 HET EDO A 205 4 HETNAM NQQ 2-CHLORANYL-4-[[1-METHYL-3-(3-METHYL-3-OXIDANYL-BUTYL)- HETNAM 2 NQQ 2-OXIDANYLIDENE-BENZIMIDAZOL-5-YL]AMINO]PYRIDINE-3- HETNAM 3 NQQ CARBONITRILE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 NQQ C19 H20 CL N5 O2 FORMUL 3 EDO 4(C2 H6 O2) FORMUL 7 HOH *107(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 ALA A 127 1 14 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 ARG A 24 LEU A 25 SITE 2 AC1 17 MET A 51 ALA A 52 CYS A 53 GLY A 55 SITE 3 AC1 17 TYR A 58 GLN A 113 MET A 114 GLU A 115 SITE 4 AC1 17 EDO A 203 HOH A 303 HOH A 305 HOH A 339 SITE 5 AC1 17 HOH A 353 SITE 1 AC2 3 GLN A 3 ILE A 72 ASN A 73 SITE 1 AC3 4 ASN A 21 ARG A 24 NQQ A 201 HOH A 364 SITE 1 AC4 2 GLU A 41 HOH A 324 SITE 1 AC5 4 ALA A 5 ILE A 78 HOH A 313 HOH A 332 CRYST1 66.999 66.999 166.730 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 0.014926 0.008617 0.000000 0.00000 SCALE2 0.000000 0.017235 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005998 0.00000