[English] 日本語
Yorodumi
- PDB-6l56: Fe(II) loaded Tegillarca granosa ferritin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6l56
TitleFe(II) loaded Tegillarca granosa ferritin
ComponentsFerritin
KeywordsOXIDOREDUCTASE / ferritin / copper / tegillarca granosa / Structural Genomics / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin, conserved site / 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 iron-binding regions signature 1. / Ferritin, conserved site / 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 speciesTegillarca granosa (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85300580472 Å
AuthorsJiang, Q.Q. / Su, X.R. / Ming, T.H. / Huan, H.S.
CitationJournal: Front Mol Biosci / Year: 2022
Title: Structural Insights Into the Effects of Interactions With Iron and Copper Ions on Ferritin From the Blood Clam Tegillarca granosa.
Authors: Ming, T.H. / Jiang, Q.Q. / Huo, C. / Huan, H.S. / Wu, Y. / Su, C. / Qiu, X. / Lu, C. / Zhou, J. / Li, Y. / Han, J. / Zhang, Z. / Su, X.R.
History
DepositionOct 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Nov 22, 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
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
I: Ferritin
J: Ferritin
K: Ferritin
L: Ferritin
M: Ferritin
N: Ferritin
O: Ferritin
P: Ferritin
Q: Ferritin
R: Ferritin
S: Ferritin
T: Ferritin
U: Ferritin
V: Ferritin
W: Ferritin
X: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)485,339132
Polymers480,49124
Non-polymers4,848108
Water48,9832719
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100690 Å2
ΔGint-1187 kcal/mol
Surface area132830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.900, 182.000, 182.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number16
Space group name H-MP222
Space group name HallP22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-205-

NA

21D-203-

NA

31F-203-

NA

41G-202-

NA

51J-203-

NA

61L-203-

NA

71M-203-

NA

81O-203-

NA

91R-203-

NA

101S-203-

NA

111V-203-

NA

121X-203-

NA

-
Components

#1: Protein ...
Ferritin


Mass: 20020.438 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tegillarca granosa (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D3JCC5, ferroxidase
#2: Chemical...
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2719 / 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: 3.18 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M sodium cacodylate trihydrate pH 6.5, 30% v/v (+/-)-2-Methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97892 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 505323 / % possible obs: 99.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 12.36317743 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.062 / Rrim(I) all: 0.158 / Rsym value: 0.145 / Χ2: 0.785 / Net I/av σ(I): 11.429 / Net I/σ(I): 11.429
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 1.833 / Num. unique obs: 24901 / CC1/2: 0.798 / Rpim(I) all: 0.34 / Rrim(I) all: 0.798 / Rsym value: 0.718 / Χ2: 0.446 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
xia2data reduction
HKL-3000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RCD

1rcd


Resolution: 1.85300580472→44.1186557677 Å / SU ML: 0.168946357154 / Cross valid method: FREE R-VALUE / σ(F): 1.96425499726 / Phase error: 17.9486605964
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.195768369097 25630 5.07822406797 %
Rwork0.16521311816 479074 -
obs0.166751590386 504704 99.4898401709 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.2235201556 Å2
Refinement stepCycle: LAST / Resolution: 1.85300580472→44.1186557677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32827 0 108 2719 35654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059762674374833451
X-RAY DIFFRACTIONf_angle_d0.731809417644987
X-RAY DIFFRACTIONf_chiral_restr0.04750760126414700
X-RAY DIFFRACTIONf_plane_restr0.004229442530345924
X-RAY DIFFRACTIONf_dihedral_angle_d14.0450898420400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8534-1.87410.2618135016087820.21629792730515420X-RAY DIFFRACTION96.3601760438
1.8741-1.89610.2308150011518290.20251556627515712X-RAY DIFFRACTION98.646230916
1.8961-1.91920.2395813671098920.1940363758315781X-RAY DIFFRACTION99.2381405869
1.9192-1.94350.2414235467668960.18930739552515734X-RAY DIFFRACTION99.2480305562
1.9435-1.96910.2325242906518890.1795291805715822X-RAY DIFFRACTION99.4288094246
1.9691-1.99610.2301407157218470.17127405701915840X-RAY DIFFRACTION99.015012164
1.9961-2.02460.2005283969617940.16841780503315870X-RAY DIFFRACTION99.1609639988
2.0246-2.05480.2001514939599390.17083833315515773X-RAY DIFFRACTION99.6185026228
2.0548-2.08690.2056994708367760.1617821388915936X-RAY DIFFRACTION99.6482022539
2.0869-2.12110.2073209208658410.15939937034915920X-RAY DIFFRACTION99.5308788599
2.1211-2.15770.1963538961697540.15649882312216005X-RAY DIFFRACTION99.809421714
2.1577-2.19690.1894561981768440.1585340762315997X-RAY DIFFRACTION99.692180193
2.1969-2.23920.1986298065127930.16177172330116018X-RAY DIFFRACTION99.8693043427
2.2392-2.28490.1854896439688030.15280935153216030X-RAY DIFFRACTION99.7806757558
2.2849-2.33460.1966059354378450.1675806493915893X-RAY DIFFRACTION99.7913313063
2.3346-2.38890.2183578512537590.15752527535516080X-RAY DIFFRACTION99.928787609
2.3889-2.44860.1860078117159200.17044354605815985X-RAY DIFFRACTION99.8405386251
2.4486-2.51480.2049409268349210.17115581003815862X-RAY DIFFRACTION99.9226006192
2.5148-2.58880.2063848255919050.16656657778115944X-RAY DIFFRACTION99.928829844
2.5888-2.67240.1956545625799660.16676480923615947X-RAY DIFFRACTION99.9645369112
2.6724-2.76790.2048959633438480.1752178835816172X-RAY DIFFRACTION99.9530185577
2.7679-2.87870.1982485878048130.16766034792615915X-RAY DIFFRACTION99.9820692128
2.8787-3.00960.1991393791018340.16976895115116087X-RAY DIFFRACTION99.9468399291
3.0096-3.16830.2000138622167660.16928448054116220X-RAY DIFFRACTION99.9705726561
3.1683-3.36670.2052388318539250.16907417837516080X-RAY DIFFRACTION99.9588525747
3.3667-3.62660.1888250775318360.16069283039416160X-RAY DIFFRACTION99.9470743899
3.6266-3.99130.18791266428430.15348801387716191X-RAY DIFFRACTION99.9589225984
3.9913-4.56830.1435491394259420.13384551545316164X-RAY DIFFRACTION99.9415751344
4.5683-5.75360.1706656672298860.15857665060616325X-RAY DIFFRACTION99.8839301259
5.7536-44.110.1770661400839420.17021646237416191X-RAY DIFFRACTION96.8349064602

+
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