[English] 日本語
Yorodumi
- PDB-3e13: Iron reconstituted ferric binding protein from Campylobacter jejuni -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 30000000000000
TitleIron reconstituted ferric binding protein from Campylobacter jejuni
ComponentsPutative iron-uptake ABC transport system,periplasmic iron-binding protein
KeywordsMETAL BINDING PROTEIN / Beta sheet surrounded by alpha helices / anti-parallel beta sheet containing hinge region
Function / homology
Function and homology information


outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Ferric binding protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Iron-uptake ABC transport system,periplasmic iron-binding protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMurphy, M.E.P. / Tom-Yew, S.A.L. / Bekker, E.G.
CitationJournal: To be Published
Title: Small hinge motion by the anion-independent ferric binding protein from Campylobacter jejuni
Authors: Tom-Yew, S.A.L. / Shilton, B.H. / Bekker, E.G. / Gaynor, E.C. / Murphy, M.E.P.
History
DepositionAug 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: 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 / database_2 / pdbx_initial_refinement_model / 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_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
X: Putative iron-uptake ABC transport system,periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1762
Polymers36,1201
Non-polymers561
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.113, 54.740, 92.237
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Putative iron-uptake ABC transport system,periplasmic iron-binding protein


Mass: 36119.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: NCTC 11168 / Gene: cfbpA, Cj0175c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Hms174(de3) / References: UniProt: Q0PBW4
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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 Å3/Da / Density % sol: 38.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 24% PEG 4000, 0.1M Tris-HCl, 60 mM sodium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-3 / Wavelength: 0.974609 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2004
Details: Flat mirror (vertical focusing) ; single crystal (311) bent monochromator (horizontal focusing)
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974609 Å / Relative weight: 1
ReflectionResolution: 1.6→48.8 Å / Num. obs: 38962 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 8.6
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 3 / % possible all: 73.9

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Y4T

1y4t


Resolution: 1.6→48.8 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.552 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18595 1771 5 %RANDOM
Rwork0.14468 ---
all0.14677 38897 --
obs0.14677 33603 90.94 %-
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: 11.729 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2---0.18 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.6→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2505 0 1 480 2986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222547
X-RAY DIFFRACTIONr_bond_other_d0.0020.022303
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.9553427
X-RAY DIFFRACTIONr_angle_other_deg0.87635409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4375316
X-RAY DIFFRACTIONr_chiral_restr0.110.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022814
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02483
X-RAY DIFFRACTIONr_nbd_refined0.2160.2502
X-RAY DIFFRACTIONr_nbd_other0.2460.22670
X-RAY DIFFRACTIONr_nbtor_other0.0860.21370
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2307
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.231
X-RAY DIFFRACTIONr_mcbond_it0.8991.51579
X-RAY DIFFRACTIONr_mcangle_it1.58222544
X-RAY DIFFRACTIONr_scbond_it2.8123968
X-RAY DIFFRACTIONr_scangle_it4.6484.5883
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.23 105
Rwork0.171 1995

+
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