[English] 日本語
Yorodumi
- PDB-1k7s: FhuD complexed with albomycin-delta 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k7s
TitleFhuD complexed with albomycin-delta 2
ComponentsFerrichrome-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / two mixed domains connected by an alpha helix
Function / homology
Function and homology information


iron ion import across plasma membrane / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space
Similarity search - Function
ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DELTA-2-ALBOMYCIN A1 / Iron(3+)-hydroxamate-binding protein FhuD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsClarke, T.E. / Braun, V. / Winkelmann, G. / Tari, L.W. / Vogel, H.J.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: X-ray crystallographic structures of the Escherichia coli periplasmic protein FhuD bound to hydroxamate-type siderophores and the antibiotic albomycin.
Authors: Clarke, T.E. / Braun, V. / Winkelmann, G. / Tari, L.W. / Vogel, H.J.
#1: Journal: Nat.Struct.Biol. / Year: 2000
Title: The structure of the ferric siderophore binding protein FhuD complexed with gallichrome
Authors: Clarke, T.E. / Ku, S.-Y. / Dougan, D.R. / Vogel, H.J. / Tari, L.W.
History
DepositionOct 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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
N: Ferrichrome-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6552
Polymers29,6091
Non-polymers1,0461
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.57, 85.57, 91.60
Angle α, β, γ (deg.)90, 90, 120
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein Ferrichrome-binding periplasmic protein


Mass: 29609.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pMR21 / Production host: Escherichia coli (E. coli) / References: UniProt: P07822
#2: Chemical ChemComp-ALB / DELTA-2-ALBOMYCIN A1


Mass: 1045.828 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H57FeN12O18S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.27 Å3/Da / Density % sol: 62.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 16% PEG 4000, 0.1M Na acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18.3 mg/mlprotein1drop
28 %PEG40001drop
30.05 Msodium acetate1droppH5.2
416 %PEG40001reservoir
50.1 Msodium acetate1reservoirpH5.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 20, 2000 / Details: Osmic confocal multilayer optics
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 11873 / Num. obs: 10715 / % possible obs: 90.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 94.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 95.5 % / Rmerge(I) obs: 0.646 / % possible all: 90.2
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 94.8 % / Rmerge(I) obs: 0.0099
Reflection shell
*PLUS
% possible obs: 95.5 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 1.6

-
Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EFD

1efd


Resolution: 2.6→30 Å / σ(F): 1 / σ(I): 2 / Stereochemistry target values: mlf
RfactorNum. reflection% reflectionSelection details
Rfree0.243 484 -random
obs0.194 10715 90.2 %-
all-11873 --
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 41 38 2092
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007144
X-RAY DIFFRACTIONc_angle_d1.36891
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor obs: 0.194 / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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://pdbjlvh1.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