[English] 日本語
Yorodumi
- PDB-5cq6: Crystal structure of the bromodomain of bromodomain adjacent to z... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cq6
TitleCrystal structure of the bromodomain of bromodomain adjacent to zinc finger domain protein 2B (BAZ2B) in complex with 2,6-Pyridinedicarboxylic acid (SGC - Diamond I04-1 fragment screening)
ComponentsBromodomain adjacent to zinc finger domain protein 2B
KeywordsTRANSCRIPTION / Structural Genomics / Structural Genomics Consortium / SGC
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
PYRIDINE-2,6-DICARBOXYLIC ACID / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 Å
AuthorsBradley, A. / Pearce, N. / Krojer, T. / Ng, J. / Talon, R. / Vollmar, M. / Jose, B. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. ...Bradley, A. / Pearce, N. / Krojer, T. / Ng, J. / Talon, R. / Vollmar, M. / Jose, B. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Crystal structure of the second bromodomain of bromodomain adjancent to zinc finger domain protein 2B (BAZ2B) in complex with 2,6-Pyridinedicarboxylic acid (SGC - Diamond I04-1 fragment screening)
Authors: Bradley, A. / Pearce, N. / Krojer, T. / Ng, J. / Talon, R. / Vollmar, M. / Jose, B. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionJul 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
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)14,5165
Polymers14,0571
Non-polymers4584
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint8 kcal/mol
Surface area7970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.845, 96.600, 58.339
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-2118-

HOH

-
Components

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


Mass: 14057.129 Da / Num. of mol.: 1 / Fragment: Bromodomain, UNP residues 1858-1972
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2B, KIAA1476 / Plasmid: pNIC28 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UIF8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PDC / PYRIDINE-2,6-DICARBOXYLIC ACID / DIPICOLINIC ACID


Mass: 167.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 4.05 Å3/Da / Density % sol: 69.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 30% PEG600 , 0.1M MES pH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.987 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.97→29.17 Å / Num. obs: 16453 / % possible obs: 99.3 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.036 / Net I/σ(I): 15.9 / Num. measured all: 106277 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.97-2.025.90.8092.1664111290.790.35493.6
8.8-29.176.10.02957.613332170.9990.01397.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→19.535 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 23.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2217 763 4.65 %
Rwork0.1898 --
obs0.1914 16420 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.48 Å2 / Biso mean: 31.7177 Å2 / Biso min: 18.55 Å2
Refinement stepCycle: final / Resolution: 1.97→19.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms930 0 32 131 1093
Biso mean--43.88 38.38 -
Num. residues----115

+
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