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- PDB-3q2e: Crystal structure of the second bromodomain of human bromodomain ... -

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Basic information

Entry
Database: PDB / ID: 3q2e
TitleCrystal structure of the second bromodomain of human bromodomain and WD repeat-containing protein 1 isoform A (WDR9)
ComponentsBromodomain and WD repeat-containing protein 1
KeywordsSIGNALING PROTEIN / Structural Genomics Consortium / SGC / Bromodomain / cell cycle progression / signal transduction / apoptosis / gene regulation / Down syndrome region-2 on chromosome 21
Function / homology
Function and homology information


interleukin-7-mediated signaling pathway / Chromatin modifying enzymes / cytoskeleton organization / Interleukin-7 signaling / chromatin organization / regulation of cell shape / nucleolus / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily ...: / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Bromodomain and WD repeat-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.74 Å
AuthorsFilippakopoulos, P. / Felletar, I. / Picaud, S. / Keates, T. / Krojer, T. / Muniz, J. / Gileadi, O. / Von Delft, F. / Arrowsmith, C.H. / Edwards, A. ...Filippakopoulos, P. / Felletar, I. / Picaud, S. / Keates, T. / Krojer, T. / Muniz, J. / Gileadi, O. / Von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Bountra, C. / 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
DepositionDec 20, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Nov 1, 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 and WD repeat-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5062
Polymers14,4471
Non-polymers591
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.660, 51.660, 151.360
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-90-

HOH

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Components

#1: Protein Bromodomain and WD repeat-containing protein 1 / WD repeat-containing protein 9


Mass: 14447.411 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1310-1430
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRWD1, C21orf107, WDR9 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q9NSI6
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.02 Å3/Da / Density % sol: 39.04 % / Mosaicity: 0.28 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M (NH4)COOCH3, 0.1M BisTris, 25% PEG 3350 , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionRedundancy: 6.7 % / Av σ(I) over netI: 5.6 / Number: 87081 / Rsym value: 0.088 / D res high: 1.74 Å / D res low: 28.892 Å / Num. obs: 12968 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.528.8997.910.0390.0395.6
3.895.510010.050.056
3.183.8910010.0670.0676.5
2.753.1810010.0610.0616.7
2.462.7510010.0810.0816.9
2.252.4699.810.1290.1297
2.082.2599.810.1850.1857
1.952.0899.610.3390.3397.1
1.831.9599.510.5410.5417.1
1.741.839810.870.876.1
ReflectionResolution: 1.74→28.892 Å / Num. all: 13033 / Num. obs: 12968 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 12.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.74-1.836.10.9510.870.91097317970.3750.9510.87298
1.83-1.957.10.5830.5411.41229017230.2160.5830.5413.899.5
1.95-2.087.10.3660.3392.21171216510.1360.3660.3395.899.6
2.08-2.2570.20.1854.11091315500.0750.20.1859.899.8
2.25-2.4670.1390.1295.7994214240.0520.1390.12913.299.8
2.46-2.756.90.0870.0818.9897713060.0330.0870.08117.5100
2.75-3.186.70.0660.06110.6789311710.0250.0660.06122100
3.18-3.896.50.0730.0677.9665810270.0290.0730.06726.4100
3.89-5.560.0540.0511.249418240.0220.0540.0528.9100
5.5-28.8925.60.0430.03914.127824950.0180.0430.0392997.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 49.93 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å25.46 Å
Translation2.5 Å25.46 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
DNAdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MB3, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY

3mb3

2oss

2ouo

2grc

2oo1

3dai

3d7c

3dwy


Resolution: 1.74→28.89 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.2165 / WRfactor Rwork: 0.1822 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8744 / SU B: 4.247 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1125 / SU Rfree: 0.1098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2191 634 4.9 %RANDOM
Rwork0.1852 ---
all0.1867 13042 --
obs0.1867 12942 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 89.96 Å2 / Biso mean: 29.4449 Å2 / Biso min: 11.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.1 Å20 Å2
2--0.2 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.74→28.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms862 0 4 105 971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022898
X-RAY DIFFRACTIONr_bond_other_d0.0020.02620
X-RAY DIFFRACTIONr_angle_refined_deg1.451.9691217
X-RAY DIFFRACTIONr_angle_other_deg0.93431510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9155110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63524.56546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36315156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.969156
X-RAY DIFFRACTIONr_chiral_restr0.0920.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02186
X-RAY DIFFRACTIONr_mcbond_it2.9883547
X-RAY DIFFRACTIONr_mcbond_other0.9093211
X-RAY DIFFRACTIONr_mcangle_it4.6755887
X-RAY DIFFRACTIONr_scbond_it7.5938351
X-RAY DIFFRACTIONr_scangle_it10.53511328
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 47 -
Rwork0.348 845 -
all-892 -
obs--96.22 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-4.54094.7643-5.668234.0038-1.003328.22970.0429-0.3715-0.2751-1.0918-0.2983-1.3835-0.3311.960.25540.04030.02430.07640.25430.05780.2233-5.509331.43310.7041
21.8641-1.21510.29470.8529-0.23850.70370.00910.0805-0.0695-0.0263-0.0475-0.0060.0107-0.03110.03840.1040.0118-0.00490.0503-0.0090.0545-26.217828.64463.9642
33.6206-0.6946-1.62740.6151-0.23121.27230.06160.06460.1289-0.0814-0.1019-0.1546-0.0553-0.05380.04040.13520.01720.01330.05040.02160.0744-19.469935.22693.326
43.5764-0.5475-0.54470.15690.02851.6515-0.1027-0.03710.19780.17080.1027-0.0884-0.22360.092400.150.0061-0.04090.0491-0.03420.0689-17.017532.681814.0421
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1317 - 1323
2X-RAY DIFFRACTION2A1324 - 1362
3X-RAY DIFFRACTION3A1363 - 1395
4X-RAY DIFFRACTION4A1396 - 1423

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