HEADER TRANSFERASE 06-FEB-17 5N1Z TITLE CRYSTAL STRUCTURE OF THE BCL6 BTB DOMAIN IN COMPLEX WITH PYRAZOLO- TITLE 2 PYRIMIDINE MACROCYCLIC LIGAND 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: KOMAGATAELLA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.ROBB,A.FERGUSON,D.HARGREAVES REVDAT 3 08-MAY-24 5N1Z 1 REMARK ATOM REVDAT 2 07-JUN-17 5N1Z 1 JRNL REVDAT 1 17-MAY-17 5N1Z 0 JRNL AUTH W.MCCOULL,R.D.ABRAMS,E.ANDERSON,K.BLADES,P.BARTON,M.BOX, JRNL AUTH 2 J.BURGESS,K.BYTH,Q.CAO,C.CHUAQUI,R.J.CARBAJO,T.CHEUNG, JRNL AUTH 3 E.CODE,A.D.FERGUSON,S.FILLERY,N.O.FULLER,E.GANGL,N.GAO, JRNL AUTH 4 M.GRIST,D.HARGREAVES,M.R.HOWARD,J.HU,P.D.KEMMITT,J.E.NELSON, JRNL AUTH 5 N.O'CONNELL,D.B.PRINCE,P.RAUBO,P.B.RAWLINS,G.R.ROBB,J.SHI, JRNL AUTH 6 M.J.WARING,D.WHITTAKER,M.WYLOT,X.ZHU JRNL TITL DISCOVERY OF PYRAZOLO[1,5-A]PYRIMIDINE B-CELL LYMPHOMA 6 JRNL TITL 2 (BCL6) BINDERS AND OPTIMIZATION TO HIGH AFFINITY MACROCYCLIC JRNL TITL 3 INHIBITORS. JRNL REF J. MED. CHEM. V. 60 4386 2017 JRNL REFN ISSN 1520-4804 JRNL PMID 28485934 JRNL DOI 10.1021/ACS.JMEDCHEM.7B00359 REMARK 2 REMARK 2 RESOLUTION. 1.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.5 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) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 10507 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) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 536 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 : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.01 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.95 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2960 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2038 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2823 REMARK 3 BIN R VALUE (WORKING SET) : 0.2016 REMARK 3 BIN FREE R VALUE : 0.2493 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.63 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 137 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 993 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 39 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -9.34320 REMARK 3 B22 (A**2) : 4.80010 REMARK 3 B33 (A**2) : 4.54310 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.29380 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.253 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.158 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.141 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.161 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.144 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 : 0.902 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.847 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1048 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1417 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 392 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 26 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 148 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1048 ; 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 : 137 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL 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 : 1281 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.06 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.18 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.34 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): -5.6344 -1.9492 -10.2257 REMARK 3 T TENSOR REMARK 3 T11: -0.1147 T22: -0.0287 REMARK 3 T33: -0.0146 T12: -0.0404 REMARK 3 T13: 0.0115 T23: 0.0030 REMARK 3 L TENSOR REMARK 3 L11: 0.4661 L22: 1.1168 REMARK 3 L33: 2.7940 L12: 0.2521 REMARK 3 L13: 0.0267 L23: -0.4844 REMARK 3 S TENSOR REMARK 3 S11: -0.0996 S12: 0.0934 S13: 0.0425 REMARK 3 S21: -0.2458 S22: 0.0596 S23: 0.0523 REMARK 3 S31: 0.3099 S32: -0.1863 S33: 0.0399 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5N1Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1200003427. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10507 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 35.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.28700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: UNKNOWN, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 15.44500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.94500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 15.44500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.94500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 4550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 308 LIES ON A SPECIAL POSITION. 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 -120.38 56.86 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 CL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8GQ A 202 DBREF 5N1Z A 6 128 UNP P41182 BCL6_HUMAN 6 128 SEQADV 5N1Z GLN A 8 UNP P41182 CYS 8 ENGINEERED MUTATION SEQADV 5N1Z ARG A 67 UNP P41182 CYS 67 ENGINEERED MUTATION SEQADV 5N1Z ASN A 84 UNP P41182 CYS 84 ENGINEERED MUTATION SEQRES 1 A 123 ASP SER GLN ILE GLN PHE THR ARG HIS ALA SER ASP VAL SEQRES 2 A 123 LEU LEU ASN LEU ASN ARG LEU ARG SER ARG ASP ILE LEU SEQRES 3 A 123 THR ASP VAL VAL ILE VAL VAL SER ARG GLU GLN PHE ARG SEQRES 4 A 123 ALA HIS LYS THR VAL LEU MET ALA CYS SER GLY LEU PHE SEQRES 5 A 123 TYR SER ILE PHE THR ASP GLN LEU LYS ARG ASN LEU SER SEQRES 6 A 123 VAL ILE ASN LEU ASP PRO GLU ILE ASN PRO GLU GLY PHE SEQRES 7 A 123 ASN ILE LEU LEU ASP PHE MET TYR THR SER ARG LEU ASN SEQRES 8 A 123 LEU ARG GLU GLY ASN ILE MET ALA VAL MET ALA THR ALA SEQRES 9 A 123 MET TYR LEU GLN MET GLU HIS VAL VAL ASP THR CYS ARG SEQRES 10 A 123 LYS PHE ILE LYS ALA SER HET CL A 201 1 HET 8GQ A 202 36 HETNAM CL CHLORIDE ION HETNAM 8GQ PYRAZOLO-PYRIMIDINE MACROCYCLE FORMUL 2 CL CL 1- FORMUL 3 8GQ C25 H25 N7 O4 FORMUL 4 HOH *39(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 ALA A 127 1 14 SHEET 1 AA1 3 GLU A 41 ALA A 45 0 SHEET 2 AA1 3 VAL A 34 VAL A 38 -1 N ILE A 36 O PHE A 43 SHEET 3 AA1 3 VAL A 71 ASN A 73 1 O ILE A 72 N VAL A 37 SITE 1 AC1 5 MET A 114 GLU A 115 HIS A 116 VAL A 117 SITE 2 AC1 5 8GQ A 202 SITE 1 AC2 15 ASN A 21 ARG A 24 LEU A 25 ARG A 28 SITE 2 AC2 15 MET A 51 ALA A 52 GLY A 55 TYR A 58 SITE 3 AC2 15 GLU A 81 ASN A 84 GLN A 113 MET A 114 SITE 4 AC2 15 GLU A 115 CL A 201 HOH A 320 CRYST1 30.890 71.890 54.950 90.00 105.92 90.00 C 1 2 1 4 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 0.032373 0.000000 0.009234 0.00000 SCALE2 0.000000 0.013910 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018924 0.00000