[English] 日本語
Yorodumi
- PDB-2d28: Structure of the N-terminal domain of XpsE (crystal form P43212) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2d28
TitleStructure of the N-terminal domain of XpsE (crystal form P43212)
Componentstype II secretion ATPase XpsEType II secretion system
KeywordsPROTEIN TRANSPORT / alpha-beta sandwich
Function / homology
Function and homology information


protein-exporting ATPase activity / protein-secreting ATPase / protein secretion by the type II secretion system / type II protein secretion system complex / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Ribonucleotide Reductase Protein R1; domain 1 - #70 / Type II secretion system, protein E, N-terminal domain / Type II secretion system protein GspE / Type II secretion system protein GspE, N-terminal / MshEN domain / Type II secretion system protein GspE, N-terminal superfamily / Bacterial type II secretion system protein E signature. / Type II/IV secretion system protein / Type II/IV secretion system protein / Ribonucleotide Reductase Protein R1; domain 1 ...Ribonucleotide Reductase Protein R1; domain 1 - #70 / Type II secretion system, protein E, N-terminal domain / Type II secretion system protein GspE / Type II secretion system protein GspE, N-terminal / MshEN domain / Type II secretion system protein GspE, N-terminal superfamily / Bacterial type II secretion system protein E signature. / Type II/IV secretion system protein / Type II/IV secretion system protein / Ribonucleotide Reductase Protein R1; domain 1 / GMP Synthetase; Chain A, domain 3 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / Type II secretion system protein E
Similarity search - Component
Biological speciesXanthomonas campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsChen, Y. / Shiue, S.-J. / Huang, C.-W. / Chang, J.-L. / Chien, Y.-L. / Hu, N.-T. / Chan, N.-L.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structure and Function of the XpsE N-Terminal Domain, an Essential Component of the Xanthomonas campestris Type II Secretion System
Authors: Chen, Y. / Shiue, S.-J. / Huang, C.-W. / Chang, J.-L. / Chien, Y.-L. / Hu, N.-T. / Chan, N.-L.
History
DepositionSep 3, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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
C: type II secretion ATPase XpsE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0812
Polymers16,9441
Non-polymers1371
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.914, 55.914, 104.813
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein type II secretion ATPase XpsE / Type II secretion system / XpsE


Mass: 16943.967 Da / Num. of mol.: 1 / Fragment: N-terminal domain / Mutation: L26V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris (bacteria) / Gene: xpsE / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P31742
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.56 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: magnesium acetate, sodium cacodylate pH 6.5, PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.9537, 0.97990, 0.97980
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 11, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97991
30.97981
ReflectionResolution: 2→28 Å / Num. obs: 12460 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.045
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.09 / Num. unique all: 1161 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→28 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.28 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 570 4.8 %RANDOM
Rwork0.189 ---
all0.192 12460 --
obs0.192 11783 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.385 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 2→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1136 0 5 152 1293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211155
X-RAY DIFFRACTIONr_bond_other_d0.0030.021122
X-RAY DIFFRACTIONr_angle_refined_deg2.17521560
X-RAY DIFFRACTIONr_angle_other_deg1.03532577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.2735141
X-RAY DIFFRACTIONr_chiral_restr0.1120.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021269
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02237
X-RAY DIFFRACTIONr_nbd_refined0.2660.2282
X-RAY DIFFRACTIONr_nbd_other0.2640.21308
X-RAY DIFFRACTIONr_nbtor_other0.0910.2730
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.298
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3790.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3420.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.228
X-RAY DIFFRACTIONr_mcbond_it1.4281.5711
X-RAY DIFFRACTIONr_mcangle_it2.50721131
X-RAY DIFFRACTIONr_scbond_it3.6573444
X-RAY DIFFRACTIONr_scangle_it5.554.5429
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.289 49
Rwork0.15 807
all-856

+
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