[English] 日本語
Yorodumi
- PDB-8vv5: The crystal structure of Brucella abortus FtrA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vv5
TitleThe crystal structure of Brucella abortus FtrA
ComponentsFtrA
KeywordsMETAL BINDING PROTEIN / Brucella abortus / iron transport / FtrABCD
Function / homologyPeriplasmic metal-binding protein Tp34-type / Periplasmic metal-binding protein Tp34-type superfamily / Fe2+ transport protein / COPPER (II) ION / UPF0423 protein BRA0381/BS1330_II0378
Function and homology information
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsRoy, S. / Garcia, B.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structures of FtrA and FtrB of the Brucella abortus ferrous iron transporter FtrABCD system
Authors: Roy, S. / Kerkan, A. / Martin, D.W. / Banerjee, S. / Garcia, B.L.
History
DepositionJan 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FtrA
B: FtrA
C: FtrA
D: FtrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0738
Polymers69,8194
Non-polymers2544
Water9,422523
1
A: FtrA
B: FtrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0374
Polymers34,9102
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-50 kcal/mol
Surface area13950 Å2
MethodPISA
2
C: FtrA
D: FtrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0374
Polymers34,9102
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-49 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.759, 58.161, 100.907
Angle α, β, γ (deg.)90.000, 130.060, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein
FtrA / UPF0423 protein BRA0381/BS1330_II0378


Mass: 17454.777 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Gene: BRA0381, BS1330_II0378 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8FWR4
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 6.5, 25% PEG3350

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→38.62 Å / Num. obs: 53016 / % possible obs: 97.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 27.08 Å2 / CC1/2: 0.992 / Rpim(I) all: 0.058 / Rrim(I) all: 0.113 / Net I/σ(I): 13
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-ID
3.99-38.6216.151210.9920.0320.0621
3.16-3.9920.752830.9890.0420.0821
2.76-3.1616.553820.9820.0590.1151
2.51-2.7611.452600.9750.0820.1551
2.51-2.76852720.9580.1130.2141
2.33-2.516.253180.9490.1350.2591
2.08-2.194.7253030.9090.1750.3421
1.99-2.083.4553860.9020.220.4341
1.92-1.992.553470.8520.2880.571
1.84-1.921.853440.7780.3690.7181

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5I0V

5i0v


Resolution: 1.84→38.62 Å / SU ML: 0.2176 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.5159
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2255 1992 3.8 %
Rwork0.1911 50479 -
obs0.1924 52471 95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.46 Å2
Refinement stepCycle: LAST / Resolution: 1.84→38.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4660 0 4 523 5187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00374851
X-RAY DIFFRACTIONf_angle_d0.65626593
X-RAY DIFFRACTIONf_chiral_restr0.0502669
X-RAY DIFFRACTIONf_plane_restr0.0062882
X-RAY DIFFRACTIONf_dihedral_angle_d13.83891793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.890.33331310.28432993X-RAY DIFFRACTION79.55
1.89-1.940.31450.24093631X-RAY DIFFRACTION96.33
1.94-1.990.23241300.22773618X-RAY DIFFRACTION96.52
1.99-2.060.27831530.22163668X-RAY DIFFRACTION97.23
2.06-2.130.25981460.21853675X-RAY DIFFRACTION96.96
2.13-2.220.26361610.20853647X-RAY DIFFRACTION97.27
2.22-2.320.23551290.20343687X-RAY DIFFRACTION97.25
2.32-2.440.24631370.20723685X-RAY DIFFRACTION97.01
2.44-2.590.2641410.21673549X-RAY DIFFRACTION93.56
2.59-2.790.29071410.20913700X-RAY DIFFRACTION97.71
2.79-3.070.24551550.20233762X-RAY DIFFRACTION98.74
3.07-3.520.1991480.17923723X-RAY DIFFRACTION98.07
3.52-4.430.17851380.16163517X-RAY DIFFRACTION91.93
4.43-38.620.18651370.16363624X-RAY DIFFRACTION92.11

+
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