[English] 日本語
Yorodumi
- PDB-6lij: Crassostrea gigas ferritin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lij
TitleCrassostrea gigas ferritin
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Crassostrea gigas / Ferritin / Iron
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Biological speciesCrassostrea gigas (Pacific oyster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLi, H. / Zang, J. / Tan, X. / Wang, Z. / Du, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31730069 China
CitationJournal: To Be Published
Title: Crassostrea gigas ferritin
Authors: Li, H. / Zang, J. / Tan, X. / Wang, Z. / Du, M.
History
DepositionDec 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8192
Polymers19,7951
Non-polymers241
Water1,20767
1
A: Ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)475,66148
Polymers475,07824
Non-polymers58324
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
crystal symmetry operation13_554y,x,-z-11
crystal symmetry operation14_554-y,-x,-z-11
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation33_554y,z+1/2,x-1/21
crystal symmetry operation34_554-y,z+1/2,-x-1/21
crystal symmetry operation35_544y,-z-1/2,-x-1/21
crystal symmetry operation36_544-y,-z-1/2,x-1/21
crystal symmetry operation41_554x,z+1/2,-y-1/21
crystal symmetry operation42_554-x,z+1/2,y-1/21
crystal symmetry operation43_544-x,-z-1/2,-y-1/21
crystal symmetry operation44_544x,-z-1/2,y-1/21
crystal symmetry operation53_554z+1/2,x,y-1/21
crystal symmetry operation54_554z+1/2,-x,-y-1/21
crystal symmetry operation55_454-z-1/2,-x,y-1/21
crystal symmetry operation56_454-z-1/2,x,-y-1/21
crystal symmetry operation69_554z+1/2,y,-x-1/21
crystal symmetry operation70_554z+1/2,-y,x-1/21
crystal symmetry operation71_454-z-1/2,y,x-1/21
crystal symmetry operation72_454-z-1/2,-y,-x-1/21
Buried area98460 Å2
ΔGint-344 kcal/mol
Surface area131740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.007, 183.007, 183.007
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-350-

HOH

-
Components

#1: Protein Ferritin /


Mass: 19794.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crassostrea gigas (Pacific oyster) / Gene: fer, CGI_10027591 / Production host: Escherichia coli (E. coli) / References: UniProt: Q70MM3, ferroxidase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.23 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: Magnesium chloride hexahydrate, Tris(hydroxymethyl)aminomethane, 1,6-Hexanediol

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.1→35.22 Å / Num. obs: 15887 / % possible obs: 100 % / Redundancy: 3 % / CC1/2: 0.75 / Net I/σ(I): 1.36
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 1533 / CC1/2: 0.75

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FHA

1fha


Resolution: 2.1→35.22 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.4
RfactorNum. reflection% reflection
Rfree0.2304 789 4.97 %
Rwork0.1928 --
obs0.1946 15882 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 57.51 Å2 / Biso mean: 22.9449 Å2 / Biso min: 15.43 Å2
Refinement stepCycle: final / Resolution: 2.1→35.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1387 0 1 67 1455
Biso mean--17.53 24.14 -
Num. residues----169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071411
X-RAY DIFFRACTIONf_angle_d0.7241895
X-RAY DIFFRACTIONf_chiral_restr0.045194
X-RAY DIFFRACTIONf_plane_restr0.004254
X-RAY DIFFRACTIONf_dihedral_angle_d16.791860
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1003-2.23190.2611280.18592449
2.2319-2.40420.20921400.19692444
2.4042-2.64610.23731340.19382451
2.6461-3.02880.22621300.20792507
3.0288-3.81520.26661210.2072531
3.8152-35.220.20661360.17562711

+
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