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- PDB-4cuq: Crystal structure of human BAZ2B in complex with fragment-2 N09594 -

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Basic information

Entry
Database: PDB / ID: 4cuq
TitleCrystal structure of human BAZ2B in complex with fragment-2 N09594
ComponentsBROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN PROTEIN 2B
KeywordsTRANSCRIPTION
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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
4-[(3S)-3-hydroxy-3-methoxypropyl]phenol / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsBradley, A.R. / Liu, Y. / Krojer, T. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Knapp, S. / von Delft, F.
CitationJournal: To be Published
Title: Crystal Structure of Human Baz2B in Complex with Fragment-2 N09594
Authors: R Bradley, A. / Liu, Y. / Krojer, T. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Knapp, S. / von Delft, F.
History
DepositionMar 21, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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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)13,8012
Polymers13,6191
Non-polymers1821
Water2,288127
1
A: BROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN PROTEIN 2B
hetero molecules

A: BROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN PROTEIN 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6024
Polymers27,2372
Non-polymers3642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area1230 Å2
ΔGint-11.3 kcal/mol
Surface area14790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.760, 96.500, 57.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein BROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN PROTEIN 2B / HWALP4 / BAZ2B


Mass: 13618.652 Da / Num. of mol.: 1 / Fragment: BROMODOMAIN, RESIDUES 1858-1972
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 / References: UniProt: Q9UIF8
#2: Chemical ChemComp-5K3 / 4-[(3S)-3-hydroxy-3-methoxypropyl]phenol


Mass: 182.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 4.45 Å3/Da / Density % sol: 72.39 % / Description: NONE
Crystal growpH: 6.4 / Details: 33% PEG SMEAR LOW, 0.1M MES PH 6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Apr 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.11→28.85 Å / Num. obs: 13598 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 35.88 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.2
Reflection shellResolution: 2.11→2.16 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.8 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→17.866 Å / SU ML: 0.23 / σ(F): 1.89 / Phase error: 23.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2257 680 5 %
Rwork0.1671 --
obs0.1699 13558 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.11→17.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms926 0 13 127 1066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007965
X-RAY DIFFRACTIONf_angle_d0.9921301
X-RAY DIFFRACTIONf_dihedral_angle_d14.352367
X-RAY DIFFRACTIONf_chiral_restr0.035140
X-RAY DIFFRACTIONf_plane_restr0.004166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.27260.31151350.23582534X-RAY DIFFRACTION99
2.2726-2.50080.24721460.19372532X-RAY DIFFRACTION100
2.5008-2.86140.2181350.16822563X-RAY DIFFRACTION100
2.8614-3.60020.23871480.1762557X-RAY DIFFRACTION99
3.6002-17.86680.19361160.14492692X-RAY DIFFRACTION100
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)
16.7915-1.207-0.87386.1072-0.33870.9160.0675-0.5312-0.6199-0.72270.23640.15810.0407-0.47330.18750.2759-0.2244-0.17210.57340.17740.605851.50116.803715.9869
24.0919-3.2613-0.8093.46591.78841.6673-1.47070.1136-1.5329-0.0179-1.25130.39120.51180.7252-0.12780.56530.24360.00270.71320.15010.831637.107612.536421.5441
37.9337-2.0179-3.31493.10271.83372.9589-0.40690.1837-1.36470.4849-0.38960.99330.7573-0.25880.33250.44690.0108-0.02770.3394-0.07960.747425.646915.627122.744
43.95950.4607-4.53424.47582.81778.7121-0.4276-1.0219-2.11110.67950.01631.1621.39380.07330.23280.4051-0.01580.00090.32280.1510.631619.369718.748228.4654
58.5363-2.5799-0.33736.46941.24184.159-0.1344-0.7908-0.68451.17840.35710.53190.7476-0.91540.30320.42340.04480.04180.44750.10810.472814.135323.858132.5588
66.291-2.2645-0.91113.39290.42881.8552-0.2101-0.4488-0.3520.28770.33970.592-0.4802-0.42770.04120.39520.01810.03710.31260.04180.35612.684931.658129.6436
74.5795-4.1801-0.97464.3852-0.32092.87951.02540.18960.0085-0.3357-0.8550.8599-0.68120.0769-0.24390.4990.0773-0.08950.35460.020.533510.99142.876821.2076
88.3617-0.6857-2.11936.1425-0.38892.6610.41710.65430.5585-0.5601-0.30450.0035-0.4726-0.175-0.32590.5163-0.01280.06240.2980.00110.389216.938946.588923.6632
97.0758-2.4316-1.0972.1993.21626.64780.44450.18640.8714-0.38970.3719-1.61620.03220.4877-0.31270.421-0.03570.08650.3636-0.0330.519723.482942.250422.5782
105.9513-1.1038-2.18664.5854-1.75481.89490.12960.4157-0.2842-0.473-0.30550.2936-0.37360.10370.04680.35780.0309-0.02270.3399-0.05810.300317.958130.390922.624
115.9601-1.2138-0.99895.00231.0791.06270.42721.3206-0.7994-0.4156-0.51871.07140.349-0.57740.16360.37630.0431-0.10840.4398-0.13540.421119.873224.727318.3175
126.5575-1.8912-0.41914.22361.18783.88220.33490.2127-0.0926-0.7472-0.53640.23330.23820.62690.15680.48870.0412-0.07180.5051-0.10910.363125.111724.015414.9724
134.81750.11962.43240.16310.06371.23950.06080.5293-0.60780.9462-0.2756-0.37990.29050.90810.09050.4330.01470.00330.5066-0.03680.398330.74723.921922.419
144.2484-2.5892-0.70884.31410.04321.823-0.27820.10530.32540.02080.1605-0.2175-0.43990.11660.00410.3604-0.0104-0.02270.3366-0.02170.267426.503130.709226.4352
155.4769-2.8377-2.09876.41040.36750.8769-0.2577-0.70990.59770.54020.2915-0.45040.02180.2646-0.17310.3945-0.0477-0.03580.3888-0.03920.378223.275737.654431.6226
165.538-0.7944-1.85762.9981-0.58541.5195-0.3426-1.12840.40281.68751.2768-0.4078-0.6239-0.22-0.08730.65870.087-0.02050.4844-0.11230.333618.746543.178936.5096
172.0907-1.2108-2.15984.87311.93392.3634-0.1829-1.55780.36821.99520.13510.6598-0.8638-0.3648-0.04250.82940.2006-0.0160.5873-0.08350.377714.956738.014140.0767
184.083-3.9141-2.66844.81510.77824.5684-0.8313-0.662-0.30481.41670.65730.0684-0.8050.57840.01670.51240.0908-0.02690.50360.0010.320.92131.070536.8802
196.9474-2.0432-0.86534.4869-1.98393.1255-0.6866-1.6729-1.01970.87350.1296-0.11541.04381.06710.08060.49750.13790.01420.4810.11530.342924.831623.804535.9396
201.09712.37961.24095.62260.71462.0095-0.8141-0.7874-1.73681.68590.9206-0.73790.94012.55410.5020.58520.27610.07690.38070.18620.478529.390418.146832.35
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1856:1861)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 1862:1867)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 1868:1874)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 1875:1879)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 1880:1884)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 1885:1892)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 1893:1897)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 1898:1903)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 1904:1908)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 1909:1913)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 1914:1918)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 1919:1924)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 1925:1929)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 1930:1936)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 1937:1942)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 1943:1946)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 1947:1952)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 1953:1958)
19X-RAY DIFFRACTION19(CHAIN A AND RESID 1959:1963)
20X-RAY DIFFRACTION20(CHAIN A AND RESID 1964:1970)

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