[English] 日本語
Yorodumi
- PDB-4e2h: Crystal structure of the periplasmic domain of Shigella flexneri WzzB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4e2h
TitleCrystal structure of the periplasmic domain of Shigella flexneri WzzB
ComponentsChain length determinant protein
KeywordsMEMBRANE PROTEIN / Wzz / LPS O-antigen chain length determination / inner membrane / periplasmic space
Function / homologyBacterial polysaccharide co-polymerase-like / FepE-like / Polysaccharide chain length determinant N-terminal domain / Chain length determinant protein / lipopolysaccharide biosynthetic process / 2-Layer Sandwich / plasma membrane / Alpha Beta / Chain length determinant protein
Function and homology information
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.36 Å
AuthorsKalynych, S. / Yao, D. / Magee, J.D. / Cygler, M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Characterization of Closely Related O-antigen Lipopolysaccharide (LPS) Chain Length Regulators.
Authors: Kalynych, S. / Yao, D. / Magee, J. / Cygler, M.
History
DepositionMar 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Jun 20, 2012Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chain length determinant protein
C: Chain length determinant protein
B: Chain length determinant protein


Theoretical massNumber of molelcules
Total (without water)82,5063
Polymers82,5063
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-36 kcal/mol
Surface area32580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.514, 62.619, 90.740
Angle α, β, γ (deg.)90.000, 94.670, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Chain length determinant protein / Polysaccharide antigen chain regulator


Mass: 27502.115 Da / Num. of mol.: 3 / Fragment: Periplasmic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: wzzB, cld, rol, SF2089, S2210 / Plasmid: pFO4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37792
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG4000, 0.1M Hepes, 0.1M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97912 Å
DetectorDate: Jul 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.36→49.7 Å / Num. all: 24179 / Num. obs: 22670 / % possible obs: 94 % / Observed criterion σ(I): 22.6

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.36→49.597 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.7178 / SU ML: 0.38 / σ(F): 2 / Phase error: 34.6 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.3025 1509 5.12 %Random
Rwork0.2454 ---
obs0.2483 22670 77.96 %-
all-24179 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.383 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso max: 157.84 Å2 / Biso mean: 52.9407 Å2 / Biso min: 16 Å2
Baniso -1Baniso -2Baniso -3
1-18.672 Å2-0 Å2-2.6039 Å2
2---3.098 Å20 Å2
3----15.5741 Å2
Refinement stepCycle: LAST / Resolution: 2.36→49.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4929 0 0 78 5007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015000
X-RAY DIFFRACTIONf_angle_d1.3946795
X-RAY DIFFRACTIONf_chiral_restr0.09809
X-RAY DIFFRACTIONf_plane_restr0.007896
X-RAY DIFFRACTIONf_dihedral_angle_d20.1941832
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.36-2.43690.3627690.3381273134239
2.4369-2.5240.3767770.33871665174251
2.524-2.6250.3721000.32441939203960
2.625-2.74450.38351320.29992225235769
2.7445-2.88910.34271400.2762464260477
2.8891-3.07010.31291410.26452677281882
3.0701-3.30710.32731580.27112923308190
3.3071-3.63990.32881490.24553097324694
3.6399-4.16630.27691710.21323171334297
4.1663-5.24820.25811820.20593211339398
5.2482-49.60770.2831900.23273318350899

+
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