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- PDB-2oo1: Crystal structure of the Bromo domain 2 of human Bromodomain cont... -

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Basic information

Entry
Database: PDB / ID: 2oo1
TitleCrystal structure of the Bromo domain 2 of human Bromodomain containing protein 3 (BRD3)
ComponentsBromodomain-containing protein 3
KeywordsSIGNALING PROTEIN / BRD3 / bromodomain containing protein 3 / ORFX / RING3 like gene / RING3L / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H3K27cr reader activity / histone H3K18cr reader activity / histone H3K9cr reader activity / histone H3K9me2/3 reader activity / lncRNA binding / endodermal cell differentiation / protein localization to chromatin / : / molecular condensate scaffold activity / histone binding ...histone H3K27cr reader activity / histone H3K18cr reader activity / histone H3K9cr reader activity / histone H3K9me2/3 reader activity / lncRNA binding / endodermal cell differentiation / protein localization to chromatin / : / molecular condensate scaffold activity / histone binding / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-7PE / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFilippakopoulos, P. / Bullock, A. / Papagrigoriou, E. / Keates, T. / Cooper, C. / Smee, C. / Ugochukwu, E. / Debreczeni, J. / von Delft, F. / Arrowsmith, C. ...Filippakopoulos, P. / Bullock, A. / Papagrigoriou, E. / Keates, T. / Cooper, C. / Smee, C. / Ugochukwu, E. / Debreczeni, J. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Histone recognition and large-scale structural analysis of the human bromodomain family.
Authors: Filippakopoulos, P. / Picaud, S. / Mangos, M. / Keates, T. / Lambert, J.P. / Barsyte-Lovejoy, D. / Felletar, I. / Volkmer, R. / Muller, S. / Pawson, T. / Gingras, A.C. / Arrowsmith, C.H. / Knapp, S.
History
DepositionJan 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 11, 2012Group: Database references
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 3
B: Bromodomain-containing protein 3
C: Bromodomain-containing protein 3
D: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,14516
Polymers53,2304
Non-polymers91512
Water8,557475
1
A: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5175
Polymers13,3071
Non-polymers2094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4944
Polymers13,3071
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6182
Polymers13,3071
Non-polymers3101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5175
Polymers13,3071
Non-polymers2094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.837, 64.678, 91.827
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Bromodomain-containing protein 3 / RING3-like protein


Mass: 13307.399 Da / Num. of mol.: 4 / Fragment: Bromo 2 Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-R3 / References: UniProt: Q15059
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT


Mass: 310.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M NaF, 0.1M BTProp, 20% PEG3350, 10% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 26, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 4.9 % / Av σ(I) over netI: 6.6 / Number: 335488 / Rmerge(I) obs: 0.094 / Χ2: 1.06 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 69114 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.665097.810.0561.0634.6
2.913.6699.710.0791.0986.9
2.542.9199.710.0961.1974.7
2.312.5499.910.1281.1154.8
2.142.3110010.1741.1314.8
2.022.1410010.2621.0884.7
1.912.0210010.4611.0194.7
1.831.9110010.7930.9744.7
1.761.8310010.9424.5
1.71.7610010.9294.1
ReflectionResolution: 1.7→50 Å / Num. all: 69322 / Num. obs: 69114 / % possible obs: 99.7 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Χ2: 1.061 / Net I/σ(I): 6.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.1 % / Num. unique all: 6853 / Χ2: 0.929 / % possible all: 100

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å45.26 Å
Translation2.5 Å45.26 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1X0J

1x0j


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.943 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The molecule 7PE should be a polyethylene glycol 3350. Only the fragment has been built due to electron density that was incomplete for full assignment.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 3417 5 %RANDOM
Rwork0.186 ---
all0.187 ---
obs0.187 69114 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.332 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å20 Å2
2---0.81 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3573 0 48 475 4096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0213728
X-RAY DIFFRACTIONr_bond_other_d0.0020.022627
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.965016
X-RAY DIFFRACTIONr_angle_other_deg1.0136346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8745440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5222.712177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80215629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4821526
X-RAY DIFFRACTIONr_chiral_restr0.1070.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024082
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02796
X-RAY DIFFRACTIONr_nbd_refined0.2280.2911
X-RAY DIFFRACTIONr_nbd_other0.2060.22779
X-RAY DIFFRACTIONr_nbtor_refined0.1930.21888
X-RAY DIFFRACTIONr_nbtor_other0.0920.21744
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2345
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.218
X-RAY DIFFRACTIONr_mcbond_it1.1591.52225
X-RAY DIFFRACTIONr_mcbond_other0.3571.5858
X-RAY DIFFRACTIONr_mcangle_it2.03223576
X-RAY DIFFRACTIONr_scbond_it3.05331546
X-RAY DIFFRACTIONr_scangle_it4.774.51438
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 265 -
Rwork0.251 4726 -
obs-4991 100 %

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