[English] 日本語
Yorodumi
- PDB-7v4v: polylysine induce assembly of Thermotoga maritima ferritin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7v4v
Titlepolylysine induce assembly of Thermotoga maritima ferritin
ComponentsFerritin
KeywordsPEPTIDE BINDING PROTEIN / polylysine / Thermotoga maritima ferritin / assembly
Function / homology
Function and homology information


bacterial non-heme ferritin / ferroxidase activity / ferric iron binding / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhang, X. / Zhao, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31972018 China
CitationJournal: To Be Published
Title: polylysine induce assembly of Thermotoga maritima ferritin
Authors: Zhang, X. / Zhao, G.
History
DepositionAug 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Ferritin
A: Ferritin
B: Ferritin
C: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,05412
Polymers77,6074
Non-polymers4478
Water2,180121
1
C: Ferritin
hetero molecules

H: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0276
Polymers38,8042
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area3000 Å2
ΔGint-66 kcal/mol
Surface area15580 Å2
MethodPISA
2
A: Ferritin
B: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0276
Polymers38,8042
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-66 kcal/mol
Surface area15510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.808, 94.495, 108.121
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Ferritin


Mass: 19401.840 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / Gene: TM_1128 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0L2, bacterial non-heme ferritin
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: Tris-HCl pH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.97919 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.3→38.78 Å / Num. obs: 38772 / % possible obs: 98.69 % / Redundancy: 10 % / CC1/2: 0.996 / Net I/σ(I): 8.5
Reflection shellResolution: 2.3→2.382 Å / CC1/2: 0.996

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VLG

1vlg


Resolution: 2.3→38.687 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 1998 5.15 %
Rwork0.2013 36761 -
obs0.2042 38759 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.89 Å2 / Biso mean: 57.1346 Å2 / Biso min: 27.21 Å2
Refinement stepCycle: final / Resolution: 2.3→38.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5428 0 8 121 5557
Biso mean--61.26 50.44 -
Num. residues----651
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3001-2.35760.37291250.2823230888
2.3576-2.42140.32341360.2627248595
2.4214-2.49260.31051420.24472622100
2.4926-2.5730.30051420.232609100
2.573-2.6650.29681410.2282613100
2.665-2.77170.29011440.21962639100
2.7717-2.89780.26581410.2212617100
2.8978-3.05050.28551460.21812674100
3.0505-3.24150.32061430.22522639100
3.2415-3.49170.29991450.22652662100
3.4917-3.84270.2821460.19622668100
3.8427-4.39810.2191450.17772685100
4.3981-5.53860.2011480.1682720100
5.5386-80.21691540.1804282099

+
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