[English] 日本語
Yorodumi
- PDB-4cur: Crystal structure of human BAZ2B in complex with fragment-3 N09555 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cur
TitleCrystal structure of human BAZ2B in complex with fragment-3 N09555
ComponentsBROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN PROTEIN 2B
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


chromatin remodeling / regulation of transcription by RNA polymerase II / DNA binding / metal 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
2-(hydroxymethyl)-6-methylpyridin-3-ol / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.842 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-3 N09553
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

-
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)13,8203
Polymers13,6191
Non-polymers2012
Water2,144119
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)27,6406
Polymers27,2372
Non-polymers4024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area1640 Å2
ΔGint-4.7 kcal/mol
Surface area14910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.100, 96.600, 57.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-LA7 / 2-(hydroxymethyl)-6-methylpyridin-3-ol


Mass: 139.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 4.38 Å3/Da / Density % sol: 71.97 % / Description: NONE
Crystal growpH: 6.5 / Details: 31% PEG SMEAR LOW, 0.1M MES PH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: May 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.84→48.3 Å / Num. obs: 20037 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 34.41 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.1
Reflection shellResolution: 1.84→1.89 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 3.1 / % possible all: 99

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.842→40.55 Å / SU ML: 0.22 / σ(F): 1.91 / Phase error: 25.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2019 1016 5.1 %
Rwork0.1713 --
obs0.1727 20017 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.842→40.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms930 0 14 119 1063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006990
X-RAY DIFFRACTIONf_angle_d1.0031335
X-RAY DIFFRACTIONf_dihedral_angle_d13.498378
X-RAY DIFFRACTIONf_chiral_restr0.035143
X-RAY DIFFRACTIONf_plane_restr0.004171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8416-1.93860.39771500.31142669X-RAY DIFFRACTION99
1.9386-2.06010.2271450.22582649X-RAY DIFFRACTION100
2.0601-2.21910.24971390.1762684X-RAY DIFFRACTION99
2.2191-2.44240.19431540.16692701X-RAY DIFFRACTION100
2.4424-2.79580.19681400.16672697X-RAY DIFFRACTION100
2.7958-3.52210.20161620.18122723X-RAY DIFFRACTION100
3.5221-40.55980.17561260.15222878X-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)
14.51030.1254-5.17730.0004-0.12315.8792-0.422-1.2096-0.9124-0.0857-0.25670.2897-0.2730.67810.67030.45290.0295-0.00490.49570.1330.583342.318813.901819.1048
25.5534-1.5166-5.36374.41544.40627.3746-0.36050.1628-0.93760.24390.02440.3040.8367-0.05290.28590.38470.02910.00070.29890.00140.448420.10518.685326.8365
38.6498-4.32494.27072.93390.25279.4414-0.5858-0.63280.03381.07950.67260.5545-0.4023-1.0681-0.14450.41690.09430.06190.3760.03020.3412.664629.927934.0299
47.9863.4913-1.17378.40290.12245.30040.16640.17531.4814-1.0795-0.30840.7141-0.8134-0.41150.15280.53960.1399-0.0630.3881-0.00690.517311.869541.139923.1382
53.4292-1.4776-0.61976.31953.18162.60380.18570.31840.195-0.7614-0.005-0.2383-0.55350.1578-0.11260.41350.0201-0.00950.25920.01330.211120.040733.789920.8878
65.5071-3.3838-1.02157.11252.5174.98430.01210.0210.23070.11390.1115-0.3851-0.16120.423-0.18150.2999-0.0244-0.00480.27910.02080.258926.260330.225825.3738
77.1169-3.6219-1.01886.8831.1455.9924-0.6007-0.727-0.13691.12710.46960.07330.00790.28150.04890.43040.0544-0.02210.36010.03070.225122.124229.453236.8163
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1856 THROUGH 1868 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 1869 THROUGH 1882 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 1883 THROUGH 1889 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 1890 THROUGH 1900 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 1901 THROUGH 1920 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 1921 THROUGH 1943 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 1944 THROUGH 1970 )

+
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