HEADER TRANSCRIPTION 04-NOV-19 6TBT TITLE CRYSTAL STRUCTURE OF THE BCL6 BTB DOMAIN IN COMPLEX WITH AN APT48 TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: B-CELL LYMPHOMA 6 PROTEIN; COMPND 3 CHAIN: A, B; 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 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: APT48 PEPTIDE; COMPND 10 CHAIN: C, D; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: SYNTHETIC PEPTIDE 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(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21* (PLYSS); SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS BCL6, APT48, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR T.ZACHARCHENKO,S.C.WRIGHT REVDAT 3 24-JAN-24 6TBT 1 REMARK REVDAT 2 24-NOV-21 6TBT 1 JRNL REMARK REVDAT 1 13-OCT-21 6TBT 0 JRNL AUTH T.ZACHARCHENKO,A.P.KALVERDA,S.C.WRIGHT JRNL TITL STRUCTURAL BASIS OF APT48 INHIBITION OF THE BCL6 BTB DOMAIN. JRNL REF STRUCTURE 2021 JRNL REFN ISSN 0969-2126 JRNL PMID 34774129 JRNL DOI 10.1016/J.STR.2021.10.010 REMARK 2 REMARK 2 RESOLUTION. 1.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 47080 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) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2515 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.63 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3390 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.3910 REMARK 3 BIN FREE R VALUE SET COUNT : 188 REMARK 3 BIN FREE R VALUE : 0.4000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2090 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 298 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.30000 REMARK 3 B22 (A**2) : 4.30000 REMARK 3 B33 (A**2) : -8.60000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.014 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.014 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.028 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.485 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.969 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2164 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2130 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2922 ; 1.331 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4861 ; 0.935 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 264 ; 5.479 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 107 ;30.393 ;23.084 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 402 ;12.331 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;13.206 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 341 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2424 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 538 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 2 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.558 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : -H,-K,L REMARK 3 TWIN FRACTION : 0.442 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 7 A 129 REMARK 3 ORIGIN FOR THE GROUP (A): 39.0162 19.9967 2.5522 REMARK 3 T TENSOR REMARK 3 T11: 0.0234 T22: 0.0412 REMARK 3 T33: 0.0600 T12: 0.0101 REMARK 3 T13: 0.0192 T23: -0.0108 REMARK 3 L TENSOR REMARK 3 L11: 0.2368 L22: 0.0918 REMARK 3 L33: 0.3061 L12: 0.1110 REMARK 3 L13: -0.1770 L23: -0.0050 REMARK 3 S TENSOR REMARK 3 S11: -0.0101 S12: 0.0510 S13: 0.0149 REMARK 3 S21: 0.0156 S22: 0.0566 S23: 0.0066 REMARK 3 S31: 0.0332 S32: 0.0341 S33: -0.0464 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 7 B 129 REMARK 3 ORIGIN FOR THE GROUP (A): 26.9522 19.5018 23.5353 REMARK 3 T TENSOR REMARK 3 T11: 0.0354 T22: 0.0278 REMARK 3 T33: 0.0634 T12: 0.0171 REMARK 3 T13: 0.0266 T23: 0.0152 REMARK 3 L TENSOR REMARK 3 L11: 0.3292 L22: 0.1581 REMARK 3 L33: 0.4410 L12: -0.1372 REMARK 3 L13: -0.3197 L23: 0.0186 REMARK 3 S TENSOR REMARK 3 S11: -0.0273 S12: -0.0588 S13: -0.0011 REMARK 3 S21: 0.0106 S22: 0.0604 S23: 0.0319 REMARK 3 S31: 0.0326 S32: 0.0197 S33: -0.0331 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 6 REMARK 3 ORIGIN FOR THE GROUP (A): 36.6636 2.1811 1.7802 REMARK 3 T TENSOR REMARK 3 T11: 0.0536 T22: 0.0031 REMARK 3 T33: 0.0377 T12: 0.0061 REMARK 3 T13: 0.0238 T23: -0.0038 REMARK 3 L TENSOR REMARK 3 L11: 2.5665 L22: 5.6379 REMARK 3 L33: 2.4768 L12: 0.5803 REMARK 3 L13: 2.4256 L23: 1.5557 REMARK 3 S TENSOR REMARK 3 S11: -0.0382 S12: 0.0524 S13: -0.0619 REMARK 3 S21: 0.3538 S22: 0.1115 S23: -0.1099 REMARK 3 S31: 0.0310 S32: 0.0676 S33: -0.0733 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 6 REMARK 3 ORIGIN FOR THE GROUP (A): 29.4241 1.7269 23.8382 REMARK 3 T TENSOR REMARK 3 T11: 0.0516 T22: 0.0279 REMARK 3 T33: 0.0907 T12: 0.0313 REMARK 3 T13: 0.0217 T23: 0.0311 REMARK 3 L TENSOR REMARK 3 L11: 0.0965 L22: 6.1954 REMARK 3 L33: 0.0013 L12: -0.7712 REMARK 3 L13: -0.0079 L23: 0.0632 REMARK 3 S TENSOR REMARK 3 S11: 0.0071 S12: -0.0076 S13: 0.0041 REMARK 3 S21: -0.2269 S22: 0.0175 S23: -0.0460 REMARK 3 S31: -0.0027 S32: -0.0014 S33: -0.0246 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6TBT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1292105111. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-17 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 : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96861 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49659 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 78.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.39 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 19.98 REMARK 200 R MERGE FOR SHELL (I) : 1.77000 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: 1R2B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4 M NACL, 0.1 M TRIS PH 7, 0.2 M REMARK 280 MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 52.13333 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 104.26667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 104.26667 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 52.13333 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -118.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 4 REMARK 465 PRO A 5 REMARK 465 ASP A 6 REMARK 465 GLY B 4 REMARK 465 PRO B 5 REMARK 465 ASP B 6 REMARK 465 GLY C -5 REMARK 465 PRO C -4 REMARK 465 HIS C -3 REMARK 465 GLY C -2 REMARK 465 PRO C -1 REMARK 465 ARG C 0 REMARK 465 GLY C 7 REMARK 465 PRO C 8 REMARK 465 GLY D -5 REMARK 465 PRO D -4 REMARK 465 HIS D -3 REMARK 465 GLY D -2 REMARK 465 PRO D -1 REMARK 465 ARG D 0 REMARK 465 GLY D 7 REMARK 465 PRO D 8 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 -106.00 55.76 REMARK 500 SER A 93 -3.60 73.87 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 445 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A 446 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH A 447 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A 448 DISTANCE = 7.51 ANGSTROMS REMARK 525 HOH B 439 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH B 440 DISTANCE = 7.03 ANGSTROMS REMARK 525 HOH B 441 DISTANCE = 7.74 ANGSTROMS REMARK 525 HOH B 442 DISTANCE = 8.66 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 205 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 68 O REMARK 620 2 SER B 70 OG 106.2 REMARK 620 3 HOH B 351 O 105.9 104.7 REMARK 620 4 HOH B 363 O 74.0 84.3 170.4 REMARK 620 5 HOH B 387 O 158.2 77.9 93.3 85.4 REMARK 620 6 HOH B 397 O 73.3 176.4 78.8 92.1 101.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 205 DBREF 6TBT A 6 129 UNP P41182 BCL6_HUMAN 6 129 DBREF 6TBT B 6 129 UNP P41182 BCL6_HUMAN 6 129 DBREF 6TBT C -5 8 PDB 6TBT 6TBT -5 8 DBREF 6TBT D -5 8 PDB 6TBT 6TBT -5 8 SEQADV 6TBT GLY A 4 UNP P41182 EXPRESSION TAG SEQADV 6TBT PRO A 5 UNP P41182 EXPRESSION TAG SEQADV 6TBT GLN A 8 UNP P41182 CYS 8 ENGINEERED MUTATION SEQADV 6TBT ARG A 67 UNP P41182 CYS 67 ENGINEERED MUTATION SEQADV 6TBT ASN A 84 UNP P41182 CYS 84 ENGINEERED MUTATION SEQADV 6TBT GLY B 4 UNP P41182 EXPRESSION TAG SEQADV 6TBT PRO B 5 UNP P41182 EXPRESSION TAG SEQADV 6TBT GLN B 8 UNP P41182 CYS 8 ENGINEERED MUTATION SEQADV 6TBT ARG B 67 UNP P41182 CYS 67 ENGINEERED MUTATION SEQADV 6TBT ASN B 84 UNP P41182 CYS 84 ENGINEERED MUTATION SEQRES 1 A 126 GLY PRO ASP SER GLN ILE GLN PHE THR ARG HIS ALA SER SEQRES 2 A 126 ASP VAL LEU LEU ASN LEU ASN ARG LEU ARG SER ARG ASP SEQRES 3 A 126 ILE LEU THR ASP VAL VAL ILE VAL VAL SER ARG GLU GLN SEQRES 4 A 126 PHE ARG ALA HIS LYS THR VAL LEU MET ALA CYS SER GLY SEQRES 5 A 126 LEU PHE TYR SER ILE PHE THR ASP GLN LEU LYS ARG ASN SEQRES 6 A 126 LEU SER VAL ILE ASN LEU ASP PRO GLU ILE ASN PRO GLU SEQRES 7 A 126 GLY PHE ASN ILE LEU LEU ASP PHE MET TYR THR SER ARG SEQRES 8 A 126 LEU ASN LEU ARG GLU GLY ASN ILE MET ALA VAL MET ALA SEQRES 9 A 126 THR ALA MET TYR LEU GLN MET GLU HIS VAL VAL ASP THR SEQRES 10 A 126 CYS ARG LYS PHE ILE LYS ALA SER GLU SEQRES 1 B 126 GLY PRO ASP SER GLN ILE GLN PHE THR ARG HIS ALA SER SEQRES 2 B 126 ASP VAL LEU LEU ASN LEU ASN ARG LEU ARG SER ARG ASP SEQRES 3 B 126 ILE LEU THR ASP VAL VAL ILE VAL VAL SER ARG GLU GLN SEQRES 4 B 126 PHE ARG ALA HIS LYS THR VAL LEU MET ALA CYS SER GLY SEQRES 5 B 126 LEU PHE TYR SER ILE PHE THR ASP GLN LEU LYS ARG ASN SEQRES 6 B 126 LEU SER VAL ILE ASN LEU ASP PRO GLU ILE ASN PRO GLU SEQRES 7 B 126 GLY PHE ASN ILE LEU LEU ASP PHE MET TYR THR SER ARG SEQRES 8 B 126 LEU ASN LEU ARG GLU GLY ASN ILE MET ALA VAL MET ALA SEQRES 9 B 126 THR ALA MET TYR LEU GLN MET GLU HIS VAL VAL ASP THR SEQRES 10 B 126 CYS ARG LYS PHE ILE LYS ALA SER GLU SEQRES 1 C 14 GLY PRO HIS GLY PRO ARG ASP TRP CYS LEU PHE GLY GLY SEQRES 2 C 14 PRO SEQRES 1 D 14 GLY PRO HIS GLY PRO ARG ASP TRP CYS LEU PHE GLY GLY SEQRES 2 D 14 PRO HET CL A 201 1 HET CL A 202 1 HET CL A 203 1 HET CL A 204 1 HET CL B 201 1 HET MG B 202 1 HET MG B 203 1 HET GOL B 204 6 HET NA B 205 1 HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 CL 5(CL 1-) FORMUL 10 MG 2(MG 2+) FORMUL 12 GOL C3 H8 O3 FORMUL 13 NA NA 1+ FORMUL 14 HOH *298(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 ASP A 63 ASN A 68 1 6 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 HELIX 8 AA8 ARG B 13 ASP B 29 1 17 HELIX 9 AA9 HIS B 46 SER B 54 1 9 HELIX 10 AB1 SER B 54 ASP B 63 1 10 HELIX 11 AB2 ASP B 63 ASN B 68 1 6 HELIX 12 AB3 ASN B 79 SER B 93 1 15 HELIX 13 AB4 ASN B 101 GLN B 113 1 13 HELIX 14 AB5 MET B 114 SER B 128 1 15 SHEET 1 AA1 3 ARG B 94 LEU B 95 0 SHEET 2 AA1 3 ILE A 9 PHE A 11 -1 N ILE A 9 O LEU B 95 SHEET 3 AA1 3 TRP D 2 LEU D 4 -1 O CYS D 3 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 LEU A 74 1 O LEU A 74 N VAL A 37 SHEET 1 AA3 3 ARG A 94 LEU A 95 0 SHEET 2 AA3 3 ILE B 9 GLN B 10 -1 O ILE B 9 N LEU A 95 SHEET 3 AA3 3 CYS C 3 LEU C 4 -1 O CYS C 3 N GLN B 10 SHEET 1 AA4 3 GLU B 41 ALA B 45 0 SHEET 2 AA4 3 VAL B 34 VAL B 38 -1 N ILE B 36 O PHE B 43 SHEET 3 AA4 3 VAL B 71 ASN B 73 1 O ILE B 72 N VAL B 37 LINK O ASN B 68 NA NA B 205 1555 1555 2.57 LINK OG SER B 70 NA NA B 205 1555 1555 2.61 LINK NA NA B 205 O HOH B 351 1555 1555 2.35 LINK NA NA B 205 O HOH B 363 1555 1555 2.40 LINK NA NA B 205 O HOH B 387 1555 1555 2.34 LINK NA NA B 205 O HOH B 397 1555 1555 2.81 SITE 1 AC1 3 MET A 114 HIS A 116 VAL A 117 SITE 1 AC2 2 ARG A 67 LEU B 31 SITE 1 AC3 2 ARG A 40 ASN B 79 SITE 1 AC4 3 ARG A 98 GLY A 100 HOH A 349 SITE 1 AC5 3 MET B 114 HIS B 116 VAL B 117 SITE 1 AC6 1 ASP B 33 SITE 1 AC7 2 GLY B 100 ALA B 104 SITE 1 AC8 6 LEU A 31 THR A 48 HOH A 330 ASP B 33 SITE 2 AC8 6 LYS B 47 THR B 48 SITE 1 AC9 6 ASN B 68 SER B 70 HOH B 351 HOH B 363 SITE 2 AC9 6 HOH B 387 HOH B 397 CRYST1 65.630 65.630 156.400 90.00 90.00 120.00 P 31 2 1 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 0.015237 0.008797 0.000000 0.00000 SCALE2 0.000000 0.017594 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006394 0.00000