HEADER TRANSCRIPTION 23-JAN-22 7TO8 TITLE BRD3-BD1 IN COMPLEX WITH RAPID LINEAR PEPTIDE 2XACK.1 (DIACK.1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: BD1 (UNP RESIDUES 25-147); COMPND 5 SYNONYM: RING3-LIKE PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 2XACK.1 (DIACK.1); COMPND 9 CHAIN: C; 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: BRD3, KIAA0043, RING3L; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS BET, BROMODOMAIN, RAPID, BRD3, ACETYLATED, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR K.PATEL,J.K.K.LOW,J.P.MACKAY REVDAT 4 07-FEB-24 7TO8 1 JRNL REVDAT 3 15-NOV-23 7TO8 1 REMARK REVDAT 2 25-OCT-23 7TO8 1 REMARK REVDAT 1 25-JAN-23 7TO8 0 JRNL AUTH J.K.K.LOW,K.PATEL,N.JONES,P.SOLOMON,A.NORMAN,J.W.C.MAXWELL, JRNL AUTH 2 P.PACHL,J.M.MATTHEWS,R.J.PAYNE,T.PASSIOURA,H.SUGA, JRNL AUTH 3 L.J.WALPORT,J.P.MACKAY JRNL TITL MRNA DISPLAY REVEALS A CLASS OF HIGH-AFFINITY JRNL TITL 2 BROMODOMAIN-BINDING MOTIFS THAT ARE NOT FOUND IN THE HUMAN JRNL TITL 3 PROTEOME. JRNL REF J.BIOL.CHEM. V. 299 05482 2023 JRNL REFN ESSN 1083-351X JRNL PMID 37992806 JRNL DOI 10.1016/J.JBC.2023.105482 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 43884 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2190 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 41.0500 - 3.7800 0.99 2655 147 0.1703 0.1814 REMARK 3 2 3.7800 - 3.0000 1.00 2628 166 0.1635 0.1875 REMARK 3 3 3.0000 - 2.6200 1.00 2638 127 0.1779 0.2117 REMARK 3 4 2.6200 - 2.3800 0.99 2629 126 0.1792 0.1924 REMARK 3 5 2.3800 - 2.2100 0.99 2574 168 0.1837 0.2073 REMARK 3 6 2.2100 - 2.0800 1.00 2618 139 0.1768 0.2127 REMARK 3 7 2.0800 - 1.9800 1.00 2620 131 0.1842 0.2178 REMARK 3 8 1.9800 - 1.8900 0.99 2625 124 0.1867 0.2235 REMARK 3 9 1.8900 - 1.8200 0.99 2616 120 0.1828 0.2047 REMARK 3 10 1.8200 - 1.7500 0.99 2611 129 0.1835 0.2347 REMARK 3 11 1.7500 - 1.7000 1.00 2603 114 0.1828 0.1877 REMARK 3 12 1.7000 - 1.6500 0.99 2623 124 0.1779 0.2164 REMARK 3 13 1.6500 - 1.6100 0.99 2579 152 0.1791 0.2062 REMARK 3 14 1.6100 - 1.5700 0.99 2546 149 0.1895 0.2057 REMARK 3 15 1.5700 - 1.5300 0.98 2563 139 0.2016 0.2163 REMARK 3 16 1.5300 - 1.5000 0.98 2566 135 0.2176 0.2653 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.128 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.523 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.85 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 2265 REMARK 3 ANGLE : 0.833 3061 REMARK 3 CHIRALITY : 0.046 323 REMARK 3 PLANARITY : 0.005 386 REMARK 3 DIHEDRAL : 12.591 308 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7TO8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1000262657. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-19 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 : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.953732 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43909 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 41.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.37300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.600 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: PDB ENTRY 3S91 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MMT, PH 6.0, 25% W/V PEG1500, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 32.21700 REMARK 290 SMTRY3 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 -40.84200 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 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 GLN A 20 REMARK 465 PRO A 21 REMARK 465 LEU A 22 REMARK 465 GLY A 23 REMARK 465 SER A 24 REMARK 465 GLU A 25 REMARK 465 VAL A 26 REMARK 465 SER A 27 REMARK 465 ASN A 28 REMARK 465 PRO A 29 REMARK 465 SER A 30 REMARK 465 LYS A 31 REMARK 465 GLN B 20 REMARK 465 PRO B 21 REMARK 465 LEU B 22 REMARK 465 GLY B 23 REMARK 465 SER B 24 REMARK 465 GLU B 25 REMARK 465 VAL B 26 REMARK 465 SER B 27 REMARK 465 ASN B 28 REMARK 465 PRO B 29 REMARK 465 SER B 30 REMARK 465 LYS B 31 REMARK 465 ALA C 1 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 48 CE NZ REMARK 480 LYS A 67 CE NZ REMARK 480 LYS A 88 CG CD CE NZ REMARK 480 LYS B 35 CD CE NZ REMARK 480 LYS B 67 CD CE NZ REMARK 480 GLN B 103 CD OE1 NE2 REMARK 480 GLN B 142 CD OE1 NE2 REMARK 480 GLU B 143 CG CD OE1 OE2 DBREF 7TO8 A 25 147 UNP Q15059 BRD3_HUMAN 25 147 DBREF 7TO8 B 25 147 UNP Q15059 BRD3_HUMAN 25 147 DBREF 7TO8 C 1 14 PDB 7TO8 7TO8 1 14 SEQADV 7TO8 GLN A 20 UNP Q15059 EXPRESSION TAG SEQADV 7TO8 PRO A 21 UNP Q15059 EXPRESSION TAG SEQADV 7TO8 LEU A 22 UNP Q15059 EXPRESSION TAG SEQADV 7TO8 GLY A 23 UNP Q15059 EXPRESSION TAG SEQADV 7TO8 SER A 24 UNP Q15059 EXPRESSION TAG SEQADV 7TO8 GLN B 20 UNP Q15059 EXPRESSION TAG SEQADV 7TO8 PRO B 21 UNP Q15059 EXPRESSION TAG SEQADV 7TO8 LEU B 22 UNP Q15059 EXPRESSION TAG SEQADV 7TO8 GLY B 23 UNP Q15059 EXPRESSION TAG SEQADV 7TO8 SER B 24 UNP Q15059 EXPRESSION TAG SEQRES 1 A 128 GLN PRO LEU GLY SER GLU VAL SER ASN PRO SER LYS PRO SEQRES 2 A 128 GLY ARG LYS THR ASN GLN LEU GLN TYR MET GLN ASN VAL SEQRES 3 A 128 VAL VAL LYS THR LEU TRP LYS HIS GLN PHE ALA TRP PRO SEQRES 4 A 128 PHE TYR GLN PRO VAL ASP ALA ILE LYS LEU ASN LEU PRO SEQRES 5 A 128 ASP TYR HIS LYS ILE ILE LYS ASN PRO MET ASP MET GLY SEQRES 6 A 128 THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR TRP SER SEQRES 7 A 128 ALA SER GLU CYS MET GLN ASP PHE ASN THR MET PHE THR SEQRES 8 A 128 ASN CYS TYR ILE TYR ASN LYS PRO THR ASP ASP ILE VAL SEQRES 9 A 128 LEU MET ALA GLN ALA LEU GLU LYS ILE PHE LEU GLN LYS SEQRES 10 A 128 VAL ALA GLN MET PRO GLN GLU GLU VAL GLU LEU SEQRES 1 B 128 GLN PRO LEU GLY SER GLU VAL SER ASN PRO SER LYS PRO SEQRES 2 B 128 GLY ARG LYS THR ASN GLN LEU GLN TYR MET GLN ASN VAL SEQRES 3 B 128 VAL VAL LYS THR LEU TRP LYS HIS GLN PHE ALA TRP PRO SEQRES 4 B 128 PHE TYR GLN PRO VAL ASP ALA ILE LYS LEU ASN LEU PRO SEQRES 5 B 128 ASP TYR HIS LYS ILE ILE LYS ASN PRO MET ASP MET GLY SEQRES 6 B 128 THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR TRP SER SEQRES 7 B 128 ALA SER GLU CYS MET GLN ASP PHE ASN THR MET PHE THR SEQRES 8 B 128 ASN CYS TYR ILE TYR ASN LYS PRO THR ASP ASP ILE VAL SEQRES 9 B 128 LEU MET ALA GLN ALA LEU GLU LYS ILE PHE LEU GLN LYS SEQRES 10 B 128 VAL ALA GLN MET PRO GLN GLU GLU VAL GLU LEU SEQRES 1 C 14 ALA GLN ARG SER LEU ALY LEU LEU ALY HIS LEU TYR HIS SEQRES 2 C 14 GLY HET ALY C 6 24 HET ALY C 9 24 HET GOL A 201 6 HET GOL B 201 6 HETNAM ALY N(6)-ACETYLLYSINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ALY 2(C8 H16 N2 O3) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 6 HOH *231(H2 O) HELIX 1 AA1 THR A 36 VAL A 45 1 10 HELIX 2 AA2 VAL A 45 LYS A 52 1 8 HELIX 3 AA3 ALA A 56 TYR A 60 5 5 HELIX 4 AA4 ASP A 72 ILE A 77 1 6 HELIX 5 AA5 ASP A 82 ASN A 92 1 11 HELIX 6 AA6 SER A 97 ASN A 116 1 20 HELIX 7 AA7 ASP A 120 GLN A 139 1 20 HELIX 8 AA8 THR B 36 VAL B 45 1 10 HELIX 9 AA9 VAL B 45 LYS B 52 1 8 HELIX 10 AB1 ALA B 56 TYR B 60 5 5 HELIX 11 AB2 ASP B 72 ILE B 77 1 6 HELIX 12 AB3 ASP B 82 ASN B 92 1 11 HELIX 13 AB4 SER B 97 ASN B 116 1 20 HELIX 14 AB5 ASP B 120 GLN B 139 1 20 HELIX 15 AB6 SER C 4 GLY C 14 1 11 LINK C ALEU C 5 N AALY C 6 1555 1555 1.33 LINK C BLEU C 5 N BALY C 6 1555 1555 1.33 LINK C AALY C 6 N ALEU C 7 1555 1555 1.33 LINK C BALY C 6 N BLEU C 7 1555 1555 1.33 LINK C ALEU C 8 N AALY C 9 1555 1555 1.33 LINK C BLEU C 8 N BALY C 9 1555 1555 1.33 LINK C AALY C 9 N AHIS C 10 1555 1555 1.33 LINK C BALY C 9 N BHIS C 10 1555 1555 1.33 CRYST1 40.842 64.434 53.473 90.00 95.04 90.00 P 1 21 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 0.024485 0.000000 0.002157 0.00000 SCALE2 0.000000 0.015520 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018773 0.00000