[English] 日本語
Yorodumi
- PDB-3w5j: Crystal structure of GDP-bound NfeoB from Gallionella capsiferrif... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3w5j
TitleCrystal structure of GDP-bound NfeoB from Gallionella capsiferriformans
ComponentsFerrous iron transport protein B
KeywordsMETAL TRANSPORT / G PROTEIN / IRON TRANSPORT / GTPASE / TRANSMEMBRANE / GDP
Function / homology
Function and homology information


ferrous iron transmembrane transporter activity / GTP binding / metal ion binding / plasma membrane
Similarity search - Function
Ferrous iron transport protein B, C-terminal / Ferrous iron transport protein B C terminus / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain / : / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain profile. / Nucleoside transporter/FeoB GTPase, Gate domain / Nucleoside recognition / GTP binding domain ...Ferrous iron transport protein B, C-terminal / Ferrous iron transport protein B C terminus / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain / : / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain profile. / Nucleoside transporter/FeoB GTPase, Gate domain / Nucleoside recognition / GTP binding domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ferrous iron transport protein B
Similarity search - Component
Biological speciesGallionella capsiferriformans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.932 Å
AuthorsDeshpande, C.N. / McGrath, A.P. / Jormakka, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of an atypical FeoB G-domain reveals a putative domain-swapped dimer.
Authors: Deshpande, C.N. / McGrath, A.P. / Font, J. / Guilfoyle, A.P. / Maher, M.J. / Jormakka, M.
History
DepositionJan 30, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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
A: Ferrous iron transport protein B
B: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0965
Polymers45,4652
Non-polymers6313
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-46 kcal/mol
Surface area17740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.760, 84.040, 95.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ferrous iron transport protein B


Mass: 22732.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallionella capsiferriformans (bacteria)
Strain: ES-2 / Gene: Galf_2203 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D9SIP4
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.02 Å3/Da / Density % sol: 39.06 % / Mosaicity: 0.67 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M Ammonium sulphate, 0.1M Bis-Tris pH 5.5, 25 % (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.93→63.08 Å / Num. all: 28390 / Num. obs: 28390 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 18.2 Å2 / Rsym value: 0.151 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.93-2.046.90.860.7960.92834740840.3230.860.7962.6100
2.04-2.167.10.5920.5491.42738238410.2190.5920.5493.8100
2.16-2.317.10.4130.3841.92598936450.1530.4130.3845.2100
2.31-2.497.10.3050.2832.62409433900.1130.3050.2836.7100
2.49-2.737.10.2290.2123.42216631270.0850.2290.2128.4100
2.73-3.057.10.1560.14452045028680.0580.1560.14410.9100
3.05-3.537.20.120.1115.91816825370.0440.120.11114.9100
3.53-4.327.10.0950.08871534221560.0350.0950.08819.2100
4.32-6.1170.0730.0678.71193217160.0270.0730.06719.9100
6.11-47.7256.40.0670.0618.3656510260.0260.0670.06118.399.9

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
MOSFLMdata reduction
PHASERMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IBY

3iby


Resolution: 1.932→47.72 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2235 / WRfactor Rwork: 0.1858 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8692 / SU B: 3.711 / SU ML: 0.108 / SU R Cruickshank DPI: 0.1798 / SU Rfree: 0.1574 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 1429 5 %RANDOM
Rwork0.1914 ---
all0.1934 28332 --
obs0.1934 28332 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 53.06 Å2 / Biso mean: 23.4563 Å2 / Biso min: 7.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.932→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 39 229 3212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223023
X-RAY DIFFRACTIONr_bond_other_d0.0010.021969
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.9974106
X-RAY DIFFRACTIONr_angle_other_deg0.86734853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7295383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76525.082122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81715528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4991517
X-RAY DIFFRACTIONr_chiral_restr0.0730.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213299
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02540
X-RAY DIFFRACTIONr_mcbond_it0.6841.51921
X-RAY DIFFRACTIONr_mcbond_other0.1551.5782
X-RAY DIFFRACTIONr_mcangle_it1.27823086
X-RAY DIFFRACTIONr_scbond_it2.16531102
X-RAY DIFFRACTIONr_scangle_it3.5874.51020
LS refinement shellResolution: 1.932→1.982 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 101 -
Rwork0.261 1964 -
all-2065 -
obs-1964 100 %

+
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