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- PDB-1x0j: Crystal structure analysis of the N-terminal bromodomain of human Brd2 -

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Basic information

Entry
Database: PDB / ID: 1x0j
TitleCrystal structure analysis of the N-terminal bromodomain of human Brd2
ComponentsBromodomain-containing protein 2BRD2
KeywordsTRANSCRIPTION / alpha-helical domain / bromodomain / binds to acetylated histones / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


chromatin looping / acetylation-dependent protein binding / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...chromatin looping / acetylation-dependent protein binding / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / protein phosphorylation / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsNakamura, Y. / Umehara, T. / Shirouzu, M. / Padmanabhan, B. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structural basis for acetylated histone H4 recognition by the human Brd2 bromodomain
Authors: Nakamura, Y. / Umehara, T. / Shirouzu, M. / Padmanabhan, B. / Yokoyama, S.
History
DepositionMar 23, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
B: Bromodomain-containing protein 2
C: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0587
Polymers44,4003
Non-polymers6584
Water6,341352
1
A: Bromodomain-containing protein 2
B: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9094
Polymers29,6002
Non-polymers3092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-17 kcal/mol
Surface area12320 Å2
MethodPISA
2
C: Bromodomain-containing protein 2
hetero molecules

C: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2996
Polymers29,6002
Non-polymers6994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)114.397, 55.363, 67.584
Angle α, β, γ (deg.)90.00, 94.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Bromodomain-containing protein 2 / BRD2 / Brd2 / RING3 protein / O27.1.1


Mass: 14800.136 Da / Num. of mol.: 3 / Fragment: N-terminal bromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: expressed by cell-free expression method / Plasmid: pCR2.1-TOPO vector / Production host: Escherichia coli (E. coli) / References: UniProt: P25440
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: PEGMME 5K, AS, pH 6.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 36172 / Num. obs: 36172 / % possible obs: 91.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.062
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.46 / % possible all: 48.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: SAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.21 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21273 1806 5 %RANDOM
Rwork0.17785 ---
all0.18 ---
obs0.1797 34340 92.1 %-
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: 30.298 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å2-0.69 Å2
2---0.18 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 0 36 352 3171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222894
X-RAY DIFFRACTIONr_bond_other_d0.0050.022564
X-RAY DIFFRACTIONr_angle_refined_deg2.8481.9463908
X-RAY DIFFRACTIONr_angle_other_deg1.31936017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.265330
X-RAY DIFFRACTIONr_chiral_restr0.1980.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023100
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02566
X-RAY DIFFRACTIONr_nbd_refined0.220.2694
X-RAY DIFFRACTIONr_nbd_other0.2360.22909
X-RAY DIFFRACTIONr_nbtor_other0.1050.21646
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.290.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.216
X-RAY DIFFRACTIONr_mcbond_it1.4691.51675
X-RAY DIFFRACTIONr_mcangle_it2.74822723
X-RAY DIFFRACTIONr_scbond_it4.73231219
X-RAY DIFFRACTIONr_scangle_it7.0024.51185
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.391 75
Rwork0.338 1234
obs-1234

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