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- PDB-5e9m: Crystal Structure of BAZ2B bromodomain in complex with N-methyltr... -

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Basic information

Entry
Database: PDB / ID: 5e9m
TitleCrystal Structure of BAZ2B bromodomain in complex with N-methyltrimethylacetamide
ComponentsBromodomain adjacent to zinc finger domain protein 2B
KeywordsTRANSCRIPTION / four helical bundle
Function / homology
Function and homology information


chromatin remodeling / regulation of transcription by RNA polymerase II / chromatin / DNA binding / zinc ion binding / nucleus
Similarity search - Function
BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain ...BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / PHD-finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
N-methyltrimethylacetamide / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.778 Å
AuthorsLolli, G. / Caflisch, A.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: High-Throughput Fragment Docking into the BAZ2B Bromodomain: Efficient in Silico Screening for X-Ray Crystallography.
Authors: Lolli, G. / Caflisch, A.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain adjacent to zinc finger domain protein 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6472
Polymers13,5321
Non-polymers1151
Water2,918162
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.370, 96.111, 57.811
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2182-

HOH

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Components

#1: Protein Bromodomain adjacent to zinc finger domain protein 2B / hWALp4


Mass: 13531.574 Da / Num. of mol.: 1 / Fragment: Bromodomain (residues 2054-2168)
Source method: isolated from a genetically manipulated source
Details: First two residues SM derive from the expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2B, KIAA1476 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UIF8
#2: Chemical ChemComp-BAE / N-methyltrimethylacetamide / N,2,2-trimethylpropanamide


Mass: 115.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 4.18 Å3/Da / Density % sol: 70.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG500MME (20%), PEG1000 (2%), PEG3350 (2%), PEG20000 (10%), MPD (2%)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.778→48.056 Å / Num. all: 22139 / Num. obs: 22139 / % possible obs: 99.7 % / Redundancy: 6.4 % / Rpim(I) all: 0.015 / Rrim(I) all: 0.038 / Rsym value: 0.031 / Net I/av σ(I): 17.574 / Net I/σ(I): 28.8 / Num. measured all: 141369
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.778-1.876.50.4551.72042931640.210.455499
1.87-1.9960.3012.51804830290.1540.3016.499.7
1.99-2.126.40.1495.11811928340.0740.14911.299.8
2.12-2.296.70.098.51755826290.0430.0917.199.5
2.29-2.516.80.05812.91684424890.0260.05823.5100
2.51-2.816.10.03819.51343022010.0190.03833.499.9
2.81-3.256.70.02626.11320119850.0120.02650100
3.25-3.986.30.02129.61070416930.010.02172.299.9
3.98-5.6260.01639803313320.0080.01680.699.9
5.62-48.0566.40.01242.850037830.0060.01285.799.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IR5

4ir5


Resolution: 1.778→48.056 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 24.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.198 2073 5.01 %
Rwork0.174 39327 -
obs0.1752 22139 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.73 Å2 / Biso mean: 39.0841 Å2 / Biso min: 20.01 Å2
Refinement stepCycle: final / Resolution: 1.778→48.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 8 162 1117
Biso mean--31.34 45.84 -
Num. residues----116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006990
X-RAY DIFFRACTIONf_angle_d1.0541335
X-RAY DIFFRACTIONf_chiral_restr0.036144
X-RAY DIFFRACTIONf_plane_restr0.005169
X-RAY DIFFRACTIONf_dihedral_angle_d15.163385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7777-1.8190.25571340.2942583X-RAY DIFFRACTION96
1.819-1.86450.27791420.2592657X-RAY DIFFRACTION99
1.8645-1.91490.32511350.29612563X-RAY DIFFRACTION96
1.9149-1.97130.2921310.27082521X-RAY DIFFRACTION94
1.9713-2.03490.26251440.21222696X-RAY DIFFRACTION100
2.0349-2.10770.23371320.22022512X-RAY DIFFRACTION95
2.1077-2.1920.21331410.17722672X-RAY DIFFRACTION100
2.192-2.29180.20231300.17652550X-RAY DIFFRACTION97
2.2918-2.41260.18491390.17072689X-RAY DIFFRACTION100
2.4126-2.56380.18041470.16642653X-RAY DIFFRACTION100
2.5638-2.76170.2151330.16822633X-RAY DIFFRACTION98
2.7617-3.03960.19741410.17632666X-RAY DIFFRACTION100
3.0396-3.47930.18261360.18182644X-RAY DIFFRACTION99
3.4793-4.38310.17181430.14442630X-RAY DIFFRACTION99
4.3831-48.0560.17951450.14652658X-RAY DIFFRACTION99
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)
15.61820.2019-2.52250.041-0.04421.1561-0.5561-0.8326-1.1266-0.0497-0.12720.005-0.20050.370.75920.4313-0.0380.0130.50650.110.50831.3447-34.4201-9.8133
23.2365-1.7092-1.11972.74180.75692.3592-0.2131-0.0816-0.55350.32130.09520.38160.2678-0.09840.06930.30310.01280.00580.25530.01850.3221-23.3092-25.46060.2337
31.13991.2435-0.47679.11060.33231.15350.04360.02320.54690.15490.04740.3708-0.4474-0.15590.03680.33420.0632-0.01920.26950.02770.3809-28.9044-7.1173-6.064
41.35670.9091-0.398.75170.13531.32260.15440.18570.1986-0.5950.0653-0.5022-0.29990.1294-0.19080.4537-0.01660.03540.21490.03210.2677-19.6139-6.6085-6.4086
52.7535-0.9596-0.00672.8774-0.1612.99590.05380.0787-0.0157-0.0172-0.0374-0.0615-0.21910.2121-0.00710.2741-0.0054-0.02060.21120.00730.1937-17.5443-17.5802-3.4417
63.7137-2.1052-0.51695.97960.89613.8701-0.5459-0.436-0.23260.97630.3275-0.08650.46540.47720.12110.4250.0719-0.01520.33250.04790.248-16.9651-22.47496.7139
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1856 through 1868 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1869 through 1889 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1890 through 1900 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1901 through 1910 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1911 through 1948 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1949 through 1971 )A0

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