[English] 日本語
Yorodumi
- PDB-8t7m: Iron and Copper bound HftA from Treponema denticola -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8t7m
TitleIron and Copper bound HftA from Treponema denticola
ComponentsPathogen-specific surface antigen, putative
KeywordsMETAL BINDING PROTEIN / Lipoprotein / Iron transport / Periplasmic
Function / homologyPeriplasmic metal-binding protein Tp34-type / Periplasmic metal-binding protein Tp34-type superfamily / Fe2+ transport protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / COPPER (II) ION / : / Pathogen-specific surface antigen, putative
Function and homology information
Biological speciesTreponema denticola ATCC 35405 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsCorbett, B.W. / Suits, M.D.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2022-05457 Canada
CitationJournal: To Be Published
Title: Structural and functional characterization of the high-affinity ferrous iron transport protein HftA from Treponema denticola
Authors: Corbett, B.W. / Suits, M.D.
History
DepositionJun 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pathogen-specific surface antigen, putative
B: Pathogen-specific surface antigen, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3907
Polymers35,0552
Non-polymers3355
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-87 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.250, 105.250, 79.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein Pathogen-specific surface antigen, putative


Mass: 17527.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola ATCC 35405 (bacteria)
Gene: TDE_1511 / Production host: Escherichia coli (E. coli) / References: UniProt: Q73MJ7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 66.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Sodium citrate, Ammonium sulphate, glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.82→45.57 Å / Num. obs: 44957 / % possible obs: 99.9 % / Redundancy: 19.3 % / Biso Wilson estimate: 37.13 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Net I/σ(I): 18.1
Reflection shellResolution: 1.82→1.92 Å / Rmerge(I) obs: 0.3945 / Num. unique obs: 4462 / CC1/2: 0.848 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata processing
SCALAdata scaling
PHASERphasing
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PJL

3pjl


Resolution: 1.82→39.79 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2331 2288 5.1 %RANDOM
Rwork0.2037 ---
obs0.205 44879 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→39.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2456 0 9 117 2582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.943
X-RAY DIFFRACTIONf_dihedral_angle_d7.106353
X-RAY DIFFRACTIONf_chiral_restr0.065369
X-RAY DIFFRACTIONf_plane_restr0.007490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.860.36631380.34182656X-RAY DIFFRACTION100
1.86-1.90.32741450.30592627X-RAY DIFFRACTION100
1.9-1.950.27841690.27572639X-RAY DIFFRACTION100
1.95-20.22821110.24422659X-RAY DIFFRACTION100
2-2.060.26391580.24652647X-RAY DIFFRACTION100
2.06-2.130.29831290.24382637X-RAY DIFFRACTION99
2.13-2.20.28481530.23932646X-RAY DIFFRACTION100
2.2-2.290.27531490.24252647X-RAY DIFFRACTION99
2.29-2.40.2561390.22862677X-RAY DIFFRACTION100
2.4-2.520.27481300.23742641X-RAY DIFFRACTION100
2.52-2.680.26511700.23172649X-RAY DIFFRACTION100
2.68-2.890.26061540.2392654X-RAY DIFFRACTION100
2.89-3.180.25911410.22892684X-RAY DIFFRACTION100
3.18-3.640.24221450.20262668X-RAY DIFFRACTION100
3.64-4.580.15481110.16352728X-RAY DIFFRACTION100
4.58-39.790.21441460.17082732X-RAY DIFFRACTION100

+
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