HEADER TRANSCRIPTION 24-OCT-18 6IN2 TITLE CRYSTAL STRUCTURE OF BRD1 IN COMPLEX WITH 18-CROWN-6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BR140-LIKE PROTEIN,BROMODOMAIN AND PHD FINGER-CONTAINING COMPND 5 PROTEIN 2; 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: BRD1, BRL, BRPF2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BROMODOMAIN, ACETYL-LYSINE, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR T.YOKOYAMA,Y.KOSAKA,K.MATSUMOTO,R.KITAKAMI,Y.NABESHIMA,M.MIZUGUCHI REVDAT 2 27-MAR-24 6IN2 1 REMARK REVDAT 1 30-OCT-19 6IN2 0 JRNL AUTH T.YOKOYAMA,Y.KOSAKA,K.MATSUMOTO,R.KITAKAMI,Y.NABESHIMA, JRNL AUTH 2 M.MIZUGUCHI JRNL TITL CROWN ETHERS AS TRANSTHYRETIN AMYLOIDOGENESIS INHIBITOR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1-2155_1069: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 11345 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 567 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 29.7618 - 2.7766 1.00 2734 144 0.1805 0.2038 REMARK 3 2 2.7766 - 2.2041 1.00 2719 143 0.2089 0.2714 REMARK 3 3 2.2041 - 1.9255 1.00 2685 140 0.2345 0.3014 REMARK 3 4 1.9255 - 1.7495 0.98 2640 140 0.3224 0.3845 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 39.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 1078 REMARK 3 ANGLE : 0.630 1453 REMARK 3 CHIRALITY : 0.060 154 REMARK 3 PLANARITY : 0.005 193 REMARK 3 DIHEDRAL : 19.155 426 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: NOT RESNAME HOH REMARK 3 ORIGIN FOR THE GROUP (A): 8.6041 -1.2047 6.2815 REMARK 3 T TENSOR REMARK 3 T11: 0.2897 T22: 0.2626 REMARK 3 T33: 0.3589 T12: 0.0049 REMARK 3 T13: 0.0669 T23: -0.0175 REMARK 3 L TENSOR REMARK 3 L11: 0.0594 L22: 0.2447 REMARK 3 L33: 0.4499 L12: -0.0412 REMARK 3 L13: -0.0867 L23: -0.0913 REMARK 3 S TENSOR REMARK 3 S11: -0.0699 S12: -0.0991 S13: -0.0518 REMARK 3 S21: 0.0199 S22: 0.0660 S23: 0.0469 REMARK 3 S31: 0.0749 S32: 0.0207 S33: -0.0001 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 6IN2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1300009394. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-16 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11371 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 29.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17% PEG4000, 0.1 M SODIUM ACETATE PH REMARK 280 4.4, 0.2 M AMMONIUM ACETATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 29.82050 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 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 HIS A 562 REMARK 465 ARG A 563 REMARK 465 LEU A 564 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue O4B A 702 DBREF 6IN2 A 563 680 UNP O95696 BRD1_HUMAN 563 680 SEQADV 6IN2 HIS A 562 UNP O95696 EXPRESSION TAG SEQADV 6IN2 LEU A 681 UNP O95696 EXPRESSION TAG SEQADV 6IN2 GLU A 682 UNP O95696 EXPRESSION TAG SEQADV 6IN2 HIS A 683 UNP O95696 EXPRESSION TAG SEQADV 6IN2 HIS A 684 UNP O95696 EXPRESSION TAG SEQADV 6IN2 HIS A 685 UNP O95696 EXPRESSION TAG SEQADV 6IN2 HIS A 686 UNP O95696 EXPRESSION TAG SEQADV 6IN2 HIS A 687 UNP O95696 EXPRESSION TAG SEQADV 6IN2 HIS A 688 UNP O95696 EXPRESSION TAG SEQRES 1 A 127 HIS ARG LEU THR PRO LEU THR VAL LEU LEU ARG SER VAL SEQRES 2 A 127 LEU ASP GLN LEU GLN ASP LYS ASP PRO ALA ARG ILE PHE SEQRES 3 A 127 ALA GLN PRO VAL SER LEU LYS GLU VAL PRO ASP TYR LEU SEQRES 4 A 127 ASP HIS ILE LYS HIS PRO MET ASP PHE ALA THR MET ARG SEQRES 5 A 127 LYS ARG LEU GLU ALA GLN GLY TYR LYS ASN LEU HIS GLU SEQRES 6 A 127 PHE GLU GLU ASP PHE ASP LEU ILE ILE ASP ASN CYS MET SEQRES 7 A 127 LYS TYR ASN ALA ARG ASP THR VAL PHE TYR ARG ALA ALA SEQRES 8 A 127 VAL ARG LEU ARG ASP GLN GLY GLY VAL VAL LEU ARG GLN SEQRES 9 A 127 ALA ARG ARG GLU VAL ASP SER ILE GLY LEU GLU GLU ALA SEQRES 10 A 127 SER GLY LEU GLU HIS HIS HIS HIS HIS HIS HET ACT A 701 4 HET O4B A 702 18 HETNAM ACT ACETATE ION HETNAM O4B 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 O4B C12 H24 O6 FORMUL 4 HOH *73(H2 O) HELIX 1 AA1 THR A 565 LYS A 581 1 17 HELIX 2 AA2 ASP A 598 ILE A 603 1 6 HELIX 3 AA3 ASP A 608 ALA A 618 1 11 HELIX 4 AA4 ASN A 623 ASN A 642 1 20 HELIX 5 AA5 THR A 646 GLY A 674 1 29 HELIX 6 AA6 GLY A 674 HIS A 684 1 11 SITE 1 AC1 5 VAL A 591 ASN A 642 PHE A 648 HOH A 807 SITE 2 AC1 5 HOH A 812 SITE 1 AC2 6 GLN A 577 ASP A 580 LYS A 581 GLN A 658 SITE 2 AC2 6 VAL A 662 HIS A 688 CRYST1 27.926 59.641 35.831 90.00 106.60 90.00 P 1 21 1 2 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 0.035809 0.000000 0.010678 0.00000 SCALE2 0.000000 0.016767 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029123 0.00000