[English] 日本語
Yorodumi
- PDB-1h96: recombinant mouse L-chain ferritin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h96
Titlerecombinant mouse L-chain ferritin
ComponentsFERRITIN LIGHT CHAIN 1
KeywordsIRON STORAGE
Function / homology
Function and homology information


ferritin complex / autolysosome / endocytic vesicle lumen / ferric iron binding / autophagosome / iron ion transport / intracellular iron ion homeostasis / iron ion binding / extracellular region
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / 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 iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / 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
: / Ferritin light chain 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGranier, T. / Gallois, B. / D'Estaintot, B.L. / Dautant, A. / Chevalier, J.M. / Mellado, J.M. / Beaumont, C. / Santambrogio, P. / Arosio, P. / Precigoux, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of Mouse L-Chain Ferritin at 1.6 A Resolution
Authors: Granier, T. / Gallois, B. / D'Estaintot, B.L. / Dautant, A. / Chevalier, J.M. / Mellado, J.M. / Beaumont, C. / Santambrogio, P. / Arosio, P. / Precigoux, G.
History
DepositionFeb 28, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / diffrn_source / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _diffrn_source.pdbx_synchrotron_y_n / _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FERRITIN LIGHT CHAIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,77811
Polymers20,6701
Non-polymers1,10810
Water5,278293
1
A: FERRITIN LIGHT CHAIN 1
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)522,670264
Polymers496,08424
Non-polymers26,586240
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation24_555-z,-y,-x1
crystal symmetry operation14_555-y,-x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)180.820, 180.820, 180.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-489-

CD

21A-2162-

HOH

31A-2241-

HOH

-
Components

#1: Protein FERRITIN LIGHT CHAIN 1


Mass: 20670.164 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse)
Description: FOR DETAILS SEE BEAUMONT, C., DUGAST, I., RENAUDIE, F., SOUROUJON, M., GRANDCHAMP, B. J. BIOL. CHEM., 1989, VOL. 264, 13, PP 7498-7504
Organ: LIVER / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B / References: UniProt: P29391
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION THR121ALA (PCR ERROR)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.3 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.4
Details: HANGING DROP VAPOR DIFFUSION: DROPS MADE UP OF 3MICROL OF PROTEIN (3.5 MG/ML) IN 20 MM TRIS PH 7.4 AND 3 MICROL OF PRECIPITANT SOLUTION COMPOSED OF 0.92 M AMMONIUM SULFATE, 0.4% CDSO4 AND 3 MM NAN3
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
13.5 mg/mlprotein1drop
220 mMTris1droppH7.4
30.92 Mammonium sulfate1reservoir
40.4 %1reservoirCdSO4
53 mM1reservoirNaN3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: NONIUS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1999 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 32400 / % possible obs: 95.7 % / Redundancy: 4.9 % / Biso Wilson estimate: 11.83 Å2 / Rsym value: 0.071 / Net I/σ(I): 9.3
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.38 / % possible all: 83.8
Reflection
*PLUS
Num. obs: 32292 / Num. measured all: 158991 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 83.8 % / Num. unique obs: 2042 / Num. measured obs: 8894 / Rmerge(I) obs: 0.38

-
Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DAT

1dat


Resolution: 1.6→14 Å / SU B: 1.2 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.075
Details: THE C-TERMINAL RESIDUE WAS NOT SEEN IN THE DENSITY MAP
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1637 5 %RANDOM
Rwork0.16 ---
obs-32339 95.7 %-
Displacement parametersBiso mean: 13 Å2
Refinement stepCycle: LAST / Resolution: 1.6→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1340 0 14 293 1647
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0220.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0270.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.853
X-RAY DIFFRACTIONp_mcangle_it2.255.5
X-RAY DIFFRACTIONp_scbond_it3.54
X-RAY DIFFRACTIONp_scangle_it4.76.5
X-RAY DIFFRACTIONp_plane_restr0.0190.03
X-RAY DIFFRACTIONp_chiral_restr0.0960.15
X-RAY DIFFRACTIONp_singtor_nbd0.1690.5
X-RAY DIFFRACTIONp_multtor_nbd0.2850.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.5
X-RAY DIFFRACTIONp_xyhbond_nbd0.110.5
X-RAY DIFFRACTIONp_planar_tor3.37
X-RAY DIFFRACTIONp_staggered_tor13.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor20
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 19 Å / Rfactor obs: 0.16 / Rfactor Rfree: 0.19 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.64 Å / Rfactor Rfree: 0.27 / Rfactor obs: 0.22

+
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