[English] 日本語
Yorodumi
- PDB-5mbt: CeuE (H227L, Y288F variant) a periplasmic protein from Campylobac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mbt
TitleCeuE (H227L, Y288F variant) a periplasmic protein from Campylobacter jejuni
ComponentsEnterochelin uptake periplasmic binding protein
KeywordsMETAL TRANSPORT / Periplasmic / Iron-Uptake / Tetradentate / Siderophore / mutation
Function / homology
Function and homology information


iron ion transport / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
FatB domain / : / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Enterochelin uptake periplasmic binding protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWilde, E.J. / Blagova, E.V. / Hughes, A. / Raines, D.J. / Moroz, O.V. / Turkenburg, J.P. / Duhme-Klair, A.-K. / Wilson, K.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/L024829/1 United Kingdom
CitationJournal: Sci Rep / Year: 2017
Title: Interactions of the periplasmic binding protein CeuE with Fe(III) n-LICAM(4-) siderophore analogues of varied linker length.
Authors: Wilde, E.J. / Hughes, A. / Blagova, E.V. / Moroz, O.V. / Thomas, R.P. / Turkenburg, J.P. / Raines, D.J. / Duhme-Klair, A.K. / Wilson, K.S.
History
DepositionNov 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enterochelin uptake periplasmic binding protein
B: Enterochelin uptake periplasmic binding protein
C: Enterochelin uptake periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)96,1233
Polymers96,1233
Non-polymers00
Water2,180121
1
A: Enterochelin uptake periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)32,0411
Polymers32,0411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Enterochelin uptake periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)32,0411
Polymers32,0411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Enterochelin uptake periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)32,0411
Polymers32,0411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.163, 62.684, 67.092
Angle α, β, γ (deg.)82.73, 77.33, 76.54
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Enterochelin uptake periplasmic binding protein


Mass: 32040.998 Da / Num. of mol.: 3 / Mutation: H227L Y288F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: ceuE, Cj1355 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0P8Q4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1M MIB, pH 9.0; 25% Peg 1500.

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→60.77 Å / Num. obs: 78620 / % possible obs: 96.2 % / Redundancy: 3.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.085 / Net I/σ(I): 7.4
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.983 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.459 / % possible all: 96.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZKW

3zkw


Resolution: 1.8→60.77 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.129 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.131 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23981 3985 5.1 %RANDOM
Rwork0.19473 ---
obs0.19708 74635 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.981 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-2.13 Å20.6 Å2
2--0.6 Å21.09 Å2
3----0.88 Å2
Refinement stepCycle: 1 / Resolution: 1.8→60.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6342 0 0 121 6463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0196467
X-RAY DIFFRACTIONr_bond_other_d0.0020.026380
X-RAY DIFFRACTIONr_angle_refined_deg1.8641.9838757
X-RAY DIFFRACTIONr_angle_other_deg1.083314665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.525849
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.10926.653242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.695151145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8831510
X-RAY DIFFRACTIONr_chiral_restr0.1170.21052
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217300
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021311
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1823.4013393
X-RAY DIFFRACTIONr_mcbond_other3.183.4013392
X-RAY DIFFRACTIONr_mcangle_it4.2645.0754225
X-RAY DIFFRACTIONr_mcangle_other4.2645.0764226
X-RAY DIFFRACTIONr_scbond_it3.8743.7023074
X-RAY DIFFRACTIONr_scbond_other3.8743.7033075
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6715.3874527
X-RAY DIFFRACTIONr_long_range_B_refined6.87140.6116972
X-RAY DIFFRACTIONr_long_range_B_other6.87440.6016962
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 284 -
Rwork0.332 5594 -
obs--96.38 %

+
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