[English] 日本語
Yorodumi
- PDB-5mij: X-ray structure of carboplatin-encapsulated horse spleen apoferritin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mij
TitleX-ray structure of carboplatin-encapsulated horse spleen apoferritin
ComponentsFerritin light chain
KeywordsMETAL TRANSPORT
Function / homology
Function and homology information


ferritin complex / autolysosome / ferric iron binding / autophagosome / iron ion transport / ferrous iron binding / 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, 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
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.49 Å
AuthorsPontillo, N. / Ferraro, G. / Helliwell, J.R. / Merlino, A.
CitationJournal: ACS Med Chem Lett / Year: 2017
Title: X-ray Structure of the Carboplatin-Loaded Apo-Ferritin Nanocage.
Authors: Pontillo, N. / Ferraro, G. / Helliwell, J.R. / Amoresano, A. / Merlino, A.
History
DepositionNov 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,73719
Polymers19,8721
Non-polymers1,86518
Water5,188288
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)521,688456
Polymers476,93824
Non-polymers44,749432
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_995-x+4,-y+4,z1
crystal symmetry operation3_955-x+4,y,-z1
crystal symmetry operation4_595x,-y+4,-z1
crystal symmetry operation5_753z+2,x,y-21
crystal symmetry operation6_797z+2,-x+4,-y+21
crystal symmetry operation7_793-z+2,-x+4,y-21
crystal symmetry operation8_757-z+2,x,-y+21
crystal symmetry operation9_573y,z+2,x-21
crystal symmetry operation10_977-y+4,z+2,-x+21
crystal symmetry operation11_577y,-z+2,-x+21
crystal symmetry operation12_973-y+4,-z+2,x-21
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_995-y+4,-x+4,-z1
crystal symmetry operation15_595y,-x+4,z1
crystal symmetry operation16_955-y+4,x,z1
crystal symmetry operation17_577x,z+2,-y+21
crystal symmetry operation18_973-x+4,z+2,y-21
crystal symmetry operation19_977-x+4,-z+2,-y+21
crystal symmetry operation20_573x,-z+2,y-21
crystal symmetry operation21_757z+2,y,-x+21
crystal symmetry operation22_793z+2,-y+4,x-21
crystal symmetry operation23_753-z+2,y,x-21
crystal symmetry operation24_797-z+2,-y+4,-x+21
Unit cell
Length a, b, c (Å)181.670, 181.670, 181.670
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-204-

CD

21A-206-

CD

31A-214-

CD

41A-494-

HOH

51A-559-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Ferritin light chain / Ferritin L subunit


Mass: 19872.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P02791

-
Non-polymers , 5 types, 306 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.7 / Details: 0.8 M (NH4)2SO4, 0.1 M Tris pH 7.7, 60 mM CdSO4.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.49→104.9 Å / Num. obs: 42236 / % possible obs: 99.7 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.8
Reflection shellResolution: 1.49→1.52 Å / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 4.2 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.49→104.89 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.058 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18101 2123 5.1 %RANDOM
Rwork0.15767 ---
obs0.15886 39899 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.699 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.49→104.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1371 0 22 288 1681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0191516
X-RAY DIFFRACTIONr_bond_other_d0.0020.021432
X-RAY DIFFRACTIONr_angle_refined_deg2.181.9652035
X-RAY DIFFRACTIONr_angle_other_deg1.1093.0013290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6245190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26224.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12615275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1841512
X-RAY DIFFRACTIONr_chiral_restr0.1240.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021765
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02369
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7481.21731
X-RAY DIFFRACTIONr_mcbond_other1.7471.212732
X-RAY DIFFRACTIONr_mcangle_it2.5831.806929
X-RAY DIFFRACTIONr_mcangle_other2.5821.805929
X-RAY DIFFRACTIONr_scbond_it3.6891.554782
X-RAY DIFFRACTIONr_scbond_other3.5181.528774
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5092.1471100
X-RAY DIFFRACTIONr_long_range_B_refined7.57312.4312076
X-RAY DIFFRACTIONr_long_range_B_other6.68210.7621878
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.492→1.531 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 153 -
Rwork0.242 2893 -
obs--98.86 %

+
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