[English] 日本語
Yorodumi
- PDB-7usn: Crystal structure of ferritin 1 from Caenorhabditis elegans, FTN-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7usn
TitleCrystal structure of ferritin 1 from Caenorhabditis elegans, FTN-1
ComponentsFerritin
KeywordsOXIDOREDUCTASE / Ferroxidase
Function / homology
Function and homology information


Iron uptake and transport / Neutrophil degranulation / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / intracellular iron ion homeostasis / identical protein binding / cytoplasm
Similarity search - Function
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 speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.789 Å
AuthorsMalcolm, T.R. / Maher, M.J. / Mubarak, S.S.M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Biochemistry / Year: 2023
Title: Biochemical Characterization of Caenorhabditis elegans Ferritins.
Authors: Mubarak, S.S.M. / Malcolm, T.R. / Brown, H.G. / Hanssen, E. / Maher, M.J. / McColl, G. / Jameson, G.N.L.
History
DepositionApr 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
O: Ferritin
H: Ferritin
I: Ferritin
J: Ferritin
K: Ferritin
L: Ferritin
M: Ferritin
N: Ferritin
P: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,83371
Polymers309,28816
Non-polymers4,54555
Water43,2902403
1
A: Ferritin
C: Ferritin
D: Ferritin
F: Ferritin
O: Ferritin
H: Ferritin
I: Ferritin
J: Ferritin
hetero molecules

A: Ferritin
C: Ferritin
D: Ferritin
F: Ferritin
O: Ferritin
H: Ferritin
I: Ferritin
J: Ferritin
hetero molecules

A: Ferritin
C: Ferritin
D: Ferritin
F: Ferritin
O: Ferritin
H: Ferritin
I: Ferritin
J: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)471,182111
Polymers463,93324
Non-polymers7,24987
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area112190 Å2
ΔGint-827 kcal/mol
Surface area131550 Å2
MethodPISA
2
B: Ferritin
E: Ferritin
G: Ferritin
K: Ferritin
L: Ferritin
M: Ferritin
N: Ferritin
P: Ferritin
hetero molecules

B: Ferritin
E: Ferritin
G: Ferritin
K: Ferritin
L: Ferritin
M: Ferritin
N: Ferritin
P: Ferritin
hetero molecules

B: Ferritin
E: Ferritin
G: Ferritin
K: Ferritin
L: Ferritin
M: Ferritin
N: Ferritin
P: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)470,317102
Polymers463,93324
Non-polymers6,38578
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation12_665-y+1,-z+1,x1
Buried area112070 Å2
ΔGint-755 kcal/mol
Surface area130560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)227.763, 227.763, 227.763
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23
Components on special symmetry positions
IDModelComponents
11A-382-

HOH

21A-422-

HOH

31B-362-

HOH

41B-408-

HOH

51I-2059-

HOH

61I-2073-

HOH

71L-387-

HOH

81L-422-

HOH

-
Components

#1: Protein
Ferritin


Mass: 19330.527 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ftn-1, C54F6.14, CELE_C54F6.14 / Production host: Escherichia coli (E. coli) / References: UniProt: O16453, ferroxidase
#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2403 / 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: 3.18 Å3/Da / Density % sol: 61.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: Ammonium sulfate, Bis-Tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 1.789→50 Å / Num. obs: 365928 / % possible obs: 99.9 % / Redundancy: 21.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.036 / Net I/σ(I): 12.2
Reflection shellResolution: 1.79→1.82 Å / Rmerge(I) obs: 1.567 / Num. unique obs: 17721 / CC1/2: 0.806 / Rpim(I) all: 0.347

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.789→48.559 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.176 / WRfactor Rwork: 0.158 / SU B: 1.21 / SU ML: 0.041 / Average fsc free: 0.9847 / Average fsc work: 0.9889 / Cross valid method: FREE R-VALUE / ESU R: 0.02 / ESU R Free: 0.019
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1885 17988 4.916 %
Rwork0.1657 347910 -
all0.167 --
obs-365898 99.892 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.536 Å2
Baniso -1Baniso -2Baniso -3
1--14.794 Å26.306 Å2-19.507 Å2
2---14.976 Å2-19.43 Å2
3---29.77 Å2
Refinement stepCycle: LAST / Resolution: 1.789→48.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21792 0 235 2403 24430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01322551
X-RAY DIFFRACTIONr_bond_other_d0.0010.01621002
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.63730347
X-RAY DIFFRACTIONr_angle_other_deg1.3861.58448104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.59252706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55222.6271500
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.889153979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.40215188
X-RAY DIFFRACTIONr_chiral_restr0.0740.22785
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0226192
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025620
X-RAY DIFFRACTIONr_nbd_refined0.2060.24897
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1630.218656
X-RAY DIFFRACTIONr_nbtor_refined0.1640.211119
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.29971
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.22038
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1060.23
X-RAY DIFFRACTIONr_metal_ion_refined0.0530.223
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1880.2111
X-RAY DIFFRACTIONr_nbd_other0.1850.2604
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.2196
X-RAY DIFFRACTIONr_mcbond_it1.3162.44310821
X-RAY DIFFRACTIONr_mcbond_other1.3162.44310820
X-RAY DIFFRACTIONr_mcangle_it1.8183.65813528
X-RAY DIFFRACTIONr_mcangle_other1.8183.65813529
X-RAY DIFFRACTIONr_scbond_it2.4532.82411730
X-RAY DIFFRACTIONr_scbond_other2.4472.80611671
X-RAY DIFFRACTIONr_scangle_it3.7834.11316817
X-RAY DIFFRACTIONr_scangle_other3.7854.08316728
X-RAY DIFFRACTIONr_lrange_it4.98430.25926991
X-RAY DIFFRACTIONr_lrange_other4.79329.70626392
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.789-1.8360.27413480.228251590.23268890.9880.99298.57930.223
1.836-1.8860.23713310.192249360.195262670.9880.9921000.186
1.886-1.9410.23212170.182242800.185254970.9860.9921000.172
1.941-20.20712740.17235970.171248720.9870.99199.9960.157
2-2.0660.19111600.161228640.163240240.9870.9911000.147
2.066-2.1380.19111320.158221350.159232670.9850.991000.143
2.138-2.2190.18811330.155213350.156224680.9840.991000.139
2.219-2.3090.1810800.153205620.155216420.9840.9891000.138
2.309-2.4110.16710020.145197760.146207780.9860.991000.129
2.411-2.5290.1749670.148189130.149198800.9840.9891000.132
2.529-2.6650.1799490.154179360.155188850.9820.9871000.138
2.665-2.8260.1778630.154170790.155179420.9830.9871000.138
2.826-3.0210.1787920.16160070.161167990.9820.9861000.147
3.021-3.2620.1877320.171150110.172157430.980.9841000.16
3.262-3.5710.1787300.168137190.169144490.9840.9851000.161
3.571-3.990.1716400.156124850.157131260.9850.98799.99240.151
3.99-4.6020.1585740.143110790.144116530.9860.9891000.141
4.602-5.6240.2074890.19193840.19298730.9830.9861000.186
5.624-7.8990.2453700.2373650.2377450.9730.97699.87090.219
7.899-48.0090.2152050.20242880.20244950.9840.98299.95550.224

+
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://pdbjlvh1.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