[English] 日本語
Yorodumi
- PDB-5dh1: Structure of the siderophore periplasmic binding protein from the... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dh1
TitleStructure of the siderophore periplasmic binding protein from the fuscachelin gene cluster of Thermobifida fusca in P21
Componentssiderophore periplasmic binding protein
KeywordsPROTEIN BINDING / Siderophore / Periplasmic Binding Protein / fuscachelin
Function / homology
Function and homology information


iron coordination entity transport / 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
Similar to iron(III) dicitrate transport permease RBL00804
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.842 Å
AuthorsLi, K. / Bruner, S.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1411991 United States
CitationJournal: Proteins / Year: 2016
Title: Structure and functional analysis of the siderophore periplasmic binding protein from the fuscachelin gene cluster of Thermobifida fusca.
Authors: Li, K. / Bruner, S.D.
History
DepositionAug 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: siderophore periplasmic binding protein
B: siderophore periplasmic binding protein
C: siderophore periplasmic binding protein
D: siderophore periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)134,9414
Polymers134,9414
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-10 kcal/mol
Surface area49120 Å2
Unit cell
Length a, b, c (Å)64.406, 135.559, 80.935
Angle α, β, γ (deg.)90.00, 91.98, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
siderophore periplasmic binding protein


Mass: 33735.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (strain YX) (bacteria)
Strain: YX / Gene: Tfu_1864 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q47NS2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.08 % / Description: rod-shaped
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.16 M ammonium acetate 30% w/v polyethylene glycol 4,000 0.1 M sodium acetate pH 5.6
PH range: 4.6-7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 14, 2014
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.84→47.93 Å / Num. obs: 32629 / % possible obs: 99.7 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 13.7
Reflection shellResolution: 2.84→3 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 2.5 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSOSX10.9.5_Darwin13.4.0data reduction
Aimless0.5.8data scaling
PHASER2.5.6phasing
ARP3.3.1model building
RefinementMethod to determine structure: SAD / Resolution: 2.842→46.531 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2471 1622 4.98 %RANDOM
Rwork0.1828 ---
obs0.186 32581 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.842→46.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8524 0 0 23 8547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128696
X-RAY DIFFRACTIONf_angle_d1.3911843
X-RAY DIFFRACTIONf_dihedral_angle_d17.1253111
X-RAY DIFFRACTIONf_chiral_restr0.0541333
X-RAY DIFFRACTIONf_plane_restr0.0061593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8421-2.92570.30431270.26222514X-RAY DIFFRACTION97
2.9257-3.02010.37781390.27352569X-RAY DIFFRACTION100
3.0201-3.12810.37261280.26412573X-RAY DIFFRACTION100
3.1281-3.25330.34331200.24742608X-RAY DIFFRACTION100
3.2533-3.40130.26731640.22062556X-RAY DIFFRACTION100
3.4013-3.58060.2671220.20242594X-RAY DIFFRACTION100
3.5806-3.80480.26111300.18132564X-RAY DIFFRACTION100
3.8048-4.09840.21161420.16932585X-RAY DIFFRACTION100
4.0984-4.51050.20891520.15362581X-RAY DIFFRACTION100
4.5105-5.16250.2021430.13972582X-RAY DIFFRACTION100
5.1625-6.50140.2171480.16242599X-RAY DIFFRACTION100
6.5014-46.53720.20031070.1382634X-RAY DIFFRACTION99

+
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