[English] 日本語
Yorodumi
- PDB-6trz: Crystal structure of horse L ferritin (HoLf) Fe(III)-loaded for 1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6trz
TitleCrystal structure of horse L ferritin (HoLf) Fe(III)-loaded for 15 minutes
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / horse L ferritin / HoLf / Fe(III) / trinuclear Fe(III) cluster
Function / homology
Function and homology information


ferritin complex / autolysosome / ferric iron binding / autophagosome / ferrous iron binding / iron ion transport / cytoplasmic vesicle / intracellular iron ion homeostasis / iron ion binding / cytoplasm
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
: / : / OXYGEN ATOM / Ferritin light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsPozzi, C. / Ciambellotti, S. / Turano, P. / Mangani, S.
CitationJournal: Chemistry / Year: 2020
Title: Iron Biomineral Growth from the Initial Nucleation Seed in L-Ferritin.
Authors: Ciambellotti, S. / Pozzi, C. / Mangani, S. / Turano, P.
History
DepositionDec 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _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.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_symmetry
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,57910
Polymers20,0801
Non-polymers4999
Water2,828157
1
AAA: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)493,888240
Polymers481,91424
Non-polymers11,974216
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area95050 Å2
ΔGint-470 kcal/mol
Surface area134120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.471, 180.471, 180.471
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
11AAA-206-

FE

21AAA-208-

CD

31AAA-452-

HOH

-
Components

-
Protein , 1 types, 1 molecules AAA

#1: Protein Ferritin light chain / Ferritin L subunit


Mass: 20079.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P02791

-
Non-polymers , 5 types, 166 molecules

#2: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 30 mM cadmium nitrate, 1 M ammonium sulfate, and 200 mM sodium acetate, pH 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 13, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.02→90.23 Å / Num. obs: 17109 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 21.6 % / Biso Wilson estimate: 33.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.02 / Rrim(I) all: 0.094 / Net I/σ(I): 19.8
Reflection shellResolution: 2.02→2.13 Å / Redundancy: 22 % / Rmerge(I) obs: 0.877 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2448 / CC1/2: 0.908 / Rpim(I) all: 0.194 / Rrim(I) all: 0.914 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LG2

5lg2


Resolution: 2.02→63.888 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.96 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.119
RfactorNum. reflection% reflection
Rfree0.1878 891 5.208 %
Rwork0.1648 --
all0.166 --
obs-17108 99.982 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.92 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 2.02→63.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1355 0 9 157 1521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131404
X-RAY DIFFRACTIONr_bond_other_d0.0350.0171301
X-RAY DIFFRACTIONr_angle_refined_deg1.991.6361895
X-RAY DIFFRACTIONr_angle_other_deg2.4311.5773001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4885175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46821.70588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61715249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.051513
X-RAY DIFFRACTIONr_chiral_restr0.1310.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021598
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02317
X-RAY DIFFRACTIONr_nbd_refined0.2470.2330
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.21091
X-RAY DIFFRACTIONr_nbtor_refined0.1920.2685
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.2604
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.286
X-RAY DIFFRACTIONr_metal_ion_refined0.0840.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2390.214
X-RAY DIFFRACTIONr_nbd_other0.2090.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1960.222
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0190.21
X-RAY DIFFRACTIONr_mcbond_it3.2593.707685
X-RAY DIFFRACTIONr_mcbond_other3.263.706684
X-RAY DIFFRACTIONr_mcangle_it4.1735.525856
X-RAY DIFFRACTIONr_mcangle_other4.1715.526857
X-RAY DIFFRACTIONr_scbond_it5.5344.166717
X-RAY DIFFRACTIONr_scbond_other5.534.165718
X-RAY DIFFRACTIONr_scangle_it7.7386.0231036
X-RAY DIFFRACTIONr_scangle_other7.7346.0221037
X-RAY DIFFRACTIONr_lrange_it8.84844.91664
X-RAY DIFFRACTIONr_lrange_other8.77544.5021641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.0730.21710.2081173X-RAY DIFFRACTION100
2.073-2.1290.207660.1971138X-RAY DIFFRACTION100
2.129-2.1910.232660.191095X-RAY DIFFRACTION99.9139
2.191-2.2590.169520.1741080X-RAY DIFFRACTION100
2.259-2.3330.176500.1541051X-RAY DIFFRACTION100
2.333-2.4140.16520.1551020X-RAY DIFFRACTION100
2.414-2.5060.233470.16993X-RAY DIFFRACTION100
2.506-2.6080.229420.17942X-RAY DIFFRACTION100
2.608-2.7240.193640.16910X-RAY DIFFRACTION100
2.724-2.8570.192470.147874X-RAY DIFFRACTION100
2.857-3.0110.212510.143826X-RAY DIFFRACTION100
3.011-3.1930.17490.144792X-RAY DIFFRACTION100
3.193-3.4140.165380.146750X-RAY DIFFRACTION100
3.414-3.6870.171410.14699X-RAY DIFFRACTION100
3.687-4.0380.174450.132640X-RAY DIFFRACTION100
4.038-4.5140.209320.133602X-RAY DIFFRACTION100
4.514-5.2110.16240.134538X-RAY DIFFRACTION100
5.211-6.3780.198210.213474X-RAY DIFFRACTION100
6.378-9.0030.158220.207373X-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