[English] 日本語
Yorodumi
- PDB-4e2c: Crystal Structure of the periplasmic domain of the chimeric LPS O... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4e2c
TitleCrystal Structure of the periplasmic domain of the chimeric LPS O-antigen chain length regulator protein
Componentschimeric WzzB Chain length determinant protein
KeywordsMEMBRANE PROTEIN / Chimeric polysaccharide co-polymerase / Bacterial inner membrane
Function / homology
Function and homology information


lipopolysaccharide biosynthetic process / protein tyrosine kinase activity / identical protein binding / plasma membrane
Similarity search - Function
Bacterial polysaccharide co-polymerase-like / FepE-like / Polysaccharide chain length determinant N-terminal domain / Chain length determinant protein / : / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chain length determinant protein / Chain length determinant protein
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
Salmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
Revision 1.3Jul 5, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: chimeric WzzB Chain length determinant protein
B: chimeric WzzB Chain length determinant protein


Theoretical massNumber of molelcules
Total (without water)55,4762
Polymers55,4762
Non-polymers00
Water1,49583
1
A: chimeric WzzB Chain length determinant protein
B: chimeric WzzB Chain length determinant protein

A: chimeric WzzB Chain length determinant protein
B: chimeric WzzB Chain length determinant protein

A: chimeric WzzB Chain length determinant protein
B: chimeric WzzB Chain length determinant protein

A: chimeric WzzB Chain length determinant protein
B: chimeric WzzB Chain length determinant protein


Theoretical massNumber of molelcules
Total (without water)221,9058
Polymers221,9058
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area30600 Å2
ΔGint-145 kcal/mol
Surface area81230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.946, 116.946, 219.126
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

-
Components

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


Mass: 27738.133 Da / Num. of mol.: 2 / Fragment: Periplasmic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria), (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Gene: cld, rol, S2210, SF2089, wzzB, STM2079 / Plasmid: pF04 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37792, UniProt: Q04866
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 3.38 Å3/Da / Density % sol: 63.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 2.0M Sodium Citrate, 5% w/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorDetector: CCD / Date: May 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionRedundancy: 7.9 % / Av σ(I) over netI: 43.99 / Number: 151373 / Rmerge(I) obs: 0.064 / Χ2: 1.93 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 19253 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.595097.910.0332.5047.1
6.037.5910010.0412.3467.8
5.276.0399.910.0462.0758
4.795.2799.810.0442.1998
4.444.7999.710.0452.3918
4.184.4499.610.0542.6338
3.974.1899.810.0632.7498
3.83.9799.910.0662.268
3.653.899.810.0812.9967.2
3.533.659910.0842.0716.9
3.423.5310010.0811.628.1
3.323.4210010.0911.5488.2
3.233.3210010.1131.5678.2
3.153.2399.910.1351.4528.2
3.083.1599.910.151.4528.2
3.023.0810010.1731.4348.2
2.963.0299.910.1871.4138.2
2.92.9610010.2191.3418.3
2.852.910010.2291.2988.2
2.82.8599.610.2431.2366.4
ReflectionResolution: 2.8→50 Å / Num. obs: 23646 / % possible obs: 99.7 % / Observed criterion σ(I): 12.2 / Redundancy: 7.9 % / Rmerge(I) obs: 0.064 / Χ2: 1.926 / Net I/σ(I): 19.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.856.40.2439221.236199.6
2.85-2.98.20.2299521.2981100
2.9-2.968.30.2199431.3411100
2.96-3.028.20.1879501.413199.9
3.02-3.088.20.1739581.4341100
3.08-3.158.20.159411.452199.9
3.15-3.238.20.1359431.452199.9
3.23-3.328.20.1139651.5671100
3.32-3.428.20.0919441.5481100
3.42-3.538.10.0819721.621100
3.53-3.656.90.0849362.071199
3.65-3.87.20.0819562.996199.8
3.8-3.9780.0669512.26199.9
3.97-4.1880.0639712.749199.8
4.18-4.4480.0549592.633199.6
4.44-4.7980.0459712.391199.7
4.79-5.2780.0449722.199199.8
5.27-6.0380.0469902.075199.9
6.03-7.597.80.04110032.3461100
7.59-507.10.03310542.504197.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→42.5 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.296 1182 RANDOM
Rwork0.235 --
obs-19253 -
Displacement parametersBiso max: 156.14 Å2 / Biso mean: 30.7549 Å2 / Biso min: 3.73 Å2
Refinement stepCycle: LAST / Resolution: 2.8→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3502 0 0 83 3585
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_deg1.14

+
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