[English] 日本語
Yorodumi
- PDB-5e9k: Crystal Structure of BAZ2B bromodomain in complex with fragment F275 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5e9k
TitleCrystal Structure of BAZ2B bromodomain in complex with fragment F275
ComponentsBromodomain adjacent to zinc finger domain protein 2B
KeywordsTRANSCRIPTION / four helical bundle
Function / homology
Function and homology information


chromatin remodeling / chromatin / regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding
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
2-chloro-1H-imidazole / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.067 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 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,6342
Polymers13,5321
Non-polymers1031
Water1,17165
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.331, 96.181, 57.794
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
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-5KX / 2-chloro-1H-imidazole


Mass: 102.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H3ClN2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
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%)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.067→48.09 Å / Num. all: 14219 / Num. obs: 14219 / % possible obs: 99.6 % / Redundancy: 8.6 % / Biso Wilson estimate: 31.71 Å2 / Rpim(I) all: 0.019 / Rrim(I) all: 0.054 / Rsym value: 0.048 / Net I/av σ(I): 12.407 / Net I/σ(I): 26.3 / Num. measured all: 121784
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
2.067-2.188.50.3961.91715020120.1510.3966.197.8
2.18-2.318.30.2692.81630319550.1050.2698.699.9
2.31-2.478.20.1933.91473318030.0750.19310.5100
2.47-2.678.80.1315.81507517160.0490.13114.9100
2.67-2.929.20.089.41444715680.0290.0823.1100
2.92-3.279.10.05413.41295714290.020.05432100
3.27-3.778.60.035181100912730.0140.03547.699.9
3.77-4.627.60.02623.4830010860.0110.02658.6100
4.62-6.538.70.0242675278690.0090.02463.8100
6.53-48.098.40.0212842835080.0080.02176.299.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

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

4ir5


Resolution: 2.067→48.09 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 29.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2194 1342 5.04 %
Rwork0.1942 25280 -
obs0.1955 14219 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.09 Å2 / Biso mean: 49.5496 Å2 / Biso min: 30.52 Å2
Refinement stepCycle: final / Resolution: 2.067→48.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 6 65 1018
Biso mean--45.63 50.2 -
Num. residues----116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007981
X-RAY DIFFRACTIONf_angle_d1.0771320
X-RAY DIFFRACTIONf_chiral_restr0.038142
X-RAY DIFFRACTIONf_plane_restr0.004168
X-RAY DIFFRACTIONf_dihedral_angle_d13.49378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0665-2.14040.32721280.28872441X-RAY DIFFRACTION94
2.1404-2.22610.2761310.2632514X-RAY DIFFRACTION99
2.2261-2.32740.26721310.25062522X-RAY DIFFRACTION99
2.3274-2.45010.26031330.2282517X-RAY DIFFRACTION100
2.4501-2.60360.2731390.22522556X-RAY DIFFRACTION100
2.6036-2.80460.19321360.20822534X-RAY DIFFRACTION100
2.8046-3.08680.26161320.21012552X-RAY DIFFRACTION100
3.0868-3.53340.25121390.21582548X-RAY DIFFRACTION100
3.5334-4.45120.18871370.16462543X-RAY DIFFRACTION100
4.4512-48.090.16091360.14772553X-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)
12.8384-0.1690.216-0.0054-0.1102-0.0253-0.5178-0.69750.53280.05050.0002-0.03930.3203-0.19560.51890.3926-0.0297-0.00350.6332-0.04950.5843-1.352734.3013-9.6453
26.531-3.23353.92533.1929-2.2874.6301-0.12850.12670.25970.2836-0.0018-0.2237-0.28880.23550.10310.298-0.00570.04980.3179-0.00440.386420.48229.4867-2.2624
32.5508-0.07710.17592.46920.2632.86690.08610.1072-0.1072-0.0583-0.059-0.12720.4897-0.0362-0.05720.35750.02320.0180.321-0.00440.329220.630314.9628-4.3879
42.8462-0.56490.13544.297-0.12472.7307-0.3736-0.5530.09920.97150.26480.16320.0756-0.30580.02670.42590.07740.04770.4366-0.02690.316217.738119.66437.3286
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 1882 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1883 through 1943 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1944 through 1971 )A0

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more