[English] 日本語
Yorodumi
- PDB-5oah: THE PERIPLASMIC BINDING PROTEIN CEUE OF CAMPYLOBACTER JEJUNI BIND... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5oah
TitleTHE PERIPLASMIC BINDING PROTEIN CEUE OF CAMPYLOBACTER JEJUNI BINDS THE IRON(III) COMPLEX OF Azotochelin
ComponentsEnterochelin ABC transporter substrate-binding protein
KeywordsMETAL BINDING PROTEIN / IRON UPTAKE / TETRADENTATE SIDEROPHORE BINDING PROTEIN / AZOTOCHELIN
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
Azotochelin / : / Enterochelin ABC transporter substrate-binding protein / Enterochelin uptake periplasmic binding protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRaines, A.D.J. / Blagova, E. / Dodson, E.J. / Wilson, K.S. / Duhme-Klair, A.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
CitationJournal: Nat Catal / Year: 2018
Title: Redox-switchable siderophore anchor enables reversible artificial metalloenzyme assembly
Authors: Raines, A.D.J. / Clarke, J.E. / Blagova, E. / Dodson, E.J. / Wilson, K.S. / Duhme-Klair, A.K.
History
DepositionJun 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enterochelin ABC transporter substrate-binding protein
B: Enterochelin ABC transporter substrate-binding protein
C: Enterochelin ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5197
Polymers95,5703
Non-polymers9484
Water2,702150
1
A: Enterochelin ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3313
Polymers31,8571
Non-polymers4742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Enterochelin ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3313
Polymers31,8571
Non-polymers4742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Enterochelin ABC transporter substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)31,8571
Polymers31,8571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.139, 63.410, 67.674
Angle α, β, γ (deg.)82.710, 76.360, 79.030
Int Tables number1
Space group name H-MP1
Detailsbiological unit is the same as asym.

-
Components

#1: Protein Enterochelin ABC transporter substrate-binding protein


Mass: 31856.744 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: AD53_07815, BKM79_06765 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E7P069, UniProt: Q0P8Q4*PLUS
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-95B / Azotochelin


Mass: 418.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22N2O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.5 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 7.5 / Details: 0.2M NaF 20% PEG3350 Fe-Azotochelin stock solution

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→65.52 Å / Num. obs: 84430 / % possible obs: 99.1 % / Redundancy: 1.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1 / CC1/2: 0.589 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3zkw

3zkw


Resolution: 1.8→65.52 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.251 4314 5.1 %RANDOM
Rwork0.2047 80097 --
obs0.207 84411 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.96 Å2 / Biso mean: 39.161 Å2 / Biso min: 19.16 Å2
Baniso -1Baniso -2Baniso -3
1--2.05 Å2-1.05 Å20.91 Å2
2---0.29 Å22.39 Å2
3---2.29 Å2
Refinement stepCycle: LAST / Resolution: 1.8→65.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6729 0 62 150 6941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196902
X-RAY DIFFRACTIONr_bond_other_d00.026760
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.9879291
X-RAY DIFFRACTIONr_angle_other_deg3.7692.99315782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6135861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.79226.609289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.339151329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3471512
X-RAY DIFFRACTIONr_chiral_restr0.1220.21076
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217506
X-RAY DIFFRACTIONr_gen_planes_other0.0240.021188
X-RAY DIFFRACTIONr_mcbond_it3.4933.6223453
X-RAY DIFFRACTIONr_mcbond_other3.4933.6213452
X-RAY DIFFRACTIONr_mcangle_it4.625.424311
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 312 -
Rwork0.318 5872 -
all-6184 -
obs--98.03 %

+
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