HEADER TRANSCRIPTION 23-JAN-22 7TOA TITLE BRD3-BD1 IN COMPLEX WITH RAPID LINEAR PEPTIDE 3XACK.1 (TRIACK.1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 3; COMPND 3 CHAIN: B, A; COMPND 4 FRAGMENT: BD1 (UNP RESIDUES 32-147); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 3XACK.1 (TRIACK.1); COMPND 8 CHAIN: D; COMPND 9 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, E2F1, BRD3, ACETYLATED, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR K.PATEL,J.K.K.LOW,J.P.MACKAY REVDAT 4 07-FEB-24 7TOA 1 JRNL REVDAT 3 15-NOV-23 7TOA 1 REMARK REVDAT 2 25-OCT-23 7TOA 1 REMARK REVDAT 1 25-JAN-23 7TOA 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. 1.41 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) : 1.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 52700 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 2594 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 41.0200 - 3.7600 1.00 2710 148 0.1596 0.1770 REMARK 3 2 3.7600 - 2.9800 1.00 2679 140 0.1579 0.2078 REMARK 3 3 2.9800 - 2.6100 0.98 2617 137 0.1627 0.1671 REMARK 3 4 2.6100 - 2.3700 1.00 2669 125 0.1604 0.1908 REMARK 3 5 2.3700 - 2.2000 1.00 2644 150 0.1528 0.1809 REMARK 3 6 2.2000 - 2.0700 1.00 2656 112 0.1453 0.1583 REMARK 3 7 2.0700 - 1.9700 1.00 2663 147 0.1449 0.2062 REMARK 3 8 1.9700 - 1.8800 1.00 2634 141 0.1487 0.2007 REMARK 3 9 1.8800 - 1.8100 1.00 2678 121 0.1567 0.1959 REMARK 3 10 1.8100 - 1.7500 1.00 2600 160 0.1629 0.2099 REMARK 3 11 1.7500 - 1.6900 1.00 2640 132 0.1705 0.2121 REMARK 3 12 1.6900 - 1.6400 1.00 2635 142 0.1654 0.2156 REMARK 3 13 1.6400 - 1.6000 0.98 2619 131 0.1718 0.2345 REMARK 3 14 1.6000 - 1.5600 0.97 2564 124 0.1915 0.2412 REMARK 3 15 1.5600 - 1.5300 0.99 2618 125 0.2054 0.2354 REMARK 3 16 1.5300 - 1.4900 0.99 2632 133 0.2188 0.2801 REMARK 3 17 1.4900 - 1.4600 1.00 2634 148 0.2394 0.2695 REMARK 3 18 1.4600 - 1.4400 1.00 2649 142 0.2667 0.2951 REMARK 3 19 1.4400 - 1.4100 0.98 2565 136 0.3028 0.3353 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) : 0.159 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.840 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.28 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.30 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 : 0.005 2233 REMARK 3 ANGLE : 0.873 3014 REMARK 3 CHIRALITY : 0.068 320 REMARK 3 PLANARITY : 0.004 379 REMARK 3 DIHEDRAL : 14.676 310 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 7TOA 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_1000262660. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-NOV-21 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 : MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.953722 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 : 52733 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.410 REMARK 200 RESOLUTION RANGE LOW (A) : 41.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.41 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 1.49700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 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 (%): 48.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS, PH 5.5, 25% W/V REMARK 280 PEG3350, 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 32.23300 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: 3080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 40.72600 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 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 B 35 CG CD CE NZ REMARK 480 LYS B 52 CD CE NZ REMARK 480 LYS B 67 CD CE NZ REMARK 480 LYS B 87 NZ REMARK 480 GLN B 103 CG CD OE1 NE2 REMARK 480 GLU B 143 CG CD OE1 OE2 REMARK 480 LYS A 67 CE NZ REMARK 480 LYS A 88 CG CD CE NZ REMARK 480 LYS A 117 CE NZ REMARK 480 GLN A 142 CG CD OE1 NE2 REMARK 480 GLU A 143 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 372 O HOH A 315 1556 2.16 REMARK 500 REMARK 500 REMARK: NULL DBREF 7TOA B 32 147 UNP Q15059 BRD3_HUMAN 32 147 DBREF 7TOA A 32 147 UNP Q15059 BRD3_HUMAN 32 147 DBREF 7TOA D 3 13 PDB 7TOA 7TOA 3 13 SEQRES 1 B 116 PRO GLY ARG LYS THR ASN GLN LEU GLN TYR MET GLN ASN SEQRES 2 B 116 VAL VAL VAL LYS THR LEU TRP LYS HIS GLN PHE ALA TRP SEQRES 3 B 116 PRO PHE TYR GLN PRO VAL ASP ALA ILE LYS LEU ASN LEU SEQRES 4 B 116 PRO ASP TYR HIS LYS ILE ILE LYS ASN PRO MET ASP MET SEQRES 5 B 116 GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR TRP SEQRES 6 B 116 SER ALA SER GLU CYS MET GLN ASP PHE ASN THR MET PHE SEQRES 7 B 116 THR ASN CYS TYR ILE TYR ASN LYS PRO THR ASP ASP ILE SEQRES 8 B 116 VAL LEU MET ALA GLN ALA LEU GLU LYS ILE PHE LEU GLN SEQRES 9 B 116 LYS VAL ALA GLN MET PRO GLN GLU GLU VAL GLU LEU SEQRES 1 A 116 PRO GLY ARG LYS THR ASN GLN LEU GLN TYR MET GLN ASN SEQRES 2 A 116 VAL VAL VAL LYS THR LEU TRP LYS HIS GLN PHE ALA TRP SEQRES 3 A 116 PRO PHE TYR GLN PRO VAL ASP ALA ILE LYS LEU ASN LEU SEQRES 4 A 116 PRO ASP TYR HIS LYS ILE ILE LYS ASN PRO MET ASP MET SEQRES 5 A 116 GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR TRP SEQRES 6 A 116 SER ALA SER GLU CYS MET GLN ASP PHE ASN THR MET PHE SEQRES 7 A 116 THR ASN CYS TYR ILE TYR ASN LYS PRO THR ASP ASP ILE SEQRES 8 A 116 VAL LEU MET ALA GLN ALA LEU GLU LYS ILE PHE LEU GLN SEQRES 9 A 116 LYS VAL ALA GLN MET PRO GLN GLU GLU VAL GLU LEU SEQRES 1 D 11 ARG SER LEU ALY LEU LEU ALY HIS LEU ALY HIS HET ALY D 6 24 HET ALY D 9 24 HET ALY D 12 24 HET GOL B 201 6 HET GOL A 201 6 HETNAM ALY N(6)-ACETYLLYSINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ALY 3(C8 H16 N2 O3) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 6 HOH *196(H2 O) HELIX 1 AA1 THR B 36 VAL B 45 1 10 HELIX 2 AA2 VAL B 45 HIS B 53 1 9 HELIX 3 AA3 ALA B 56 TYR B 60 5 5 HELIX 4 AA4 ASP B 72 ILE B 77 1 6 HELIX 5 AA5 ASP B 82 ASN B 92 1 11 HELIX 6 AA6 SER B 97 ASN B 116 1 20 HELIX 7 AA7 ASP B 120 GLN B 139 1 20 HELIX 8 AA8 THR A 36 VAL A 45 1 10 HELIX 9 AA9 VAL A 45 LYS A 52 1 8 HELIX 10 AB1 ALA A 56 TYR A 60 5 5 HELIX 11 AB2 ASP A 72 ILE A 77 1 6 HELIX 12 AB3 ASP A 82 ASN A 92 1 11 HELIX 13 AB4 SER A 97 ASN A 116 1 20 HELIX 14 AB5 ASP A 120 GLN A 139 1 20 HELIX 15 AB6 SER D 4 HIS D 13 1 10 LINK C ALEU D 5 N AALY D 6 1555 1555 1.33 LINK C BLEU D 5 N BALY D 6 1555 1555 1.33 LINK C AALY D 6 N ALEU D 7 1555 1555 1.33 LINK C BALY D 6 N BLEU D 7 1555 1555 1.33 LINK C ALEU D 8 N AALY D 9 1555 1555 1.33 LINK C BLEU D 8 N BALY D 9 1555 1555 1.33 LINK C AALY D 9 N AHIS D 10 1555 1555 1.33 LINK C BALY D 9 N BHIS D 10 1555 1555 1.33 LINK C ALEU D 11 N AALY D 12 1555 1555 1.33 LINK C BLEU D 11 N BALY D 12 1555 1555 1.33 LINK C AALY D 12 N AHIS D 13 1555 1555 1.33 LINK C BALY D 12 N BHIS D 13 1555 1555 1.33 CRYST1 40.726 64.466 53.415 90.00 95.47 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 0.024554 0.000000 0.002350 0.00000 SCALE2 0.000000 0.015512 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018807 0.00000