[English] 日本語
Yorodumi
- PDB-7eml: Structure of IrCp* immobilized apo-D38H-rHLFr -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7eml
TitleStructure of IrCp* immobilized apo-D38H-rHLFr
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / Iron storage protein / Ir binding
Function / homology
Function and homology information


intracellular ferritin complex / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / 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
: / : / Chem-RIR / Ferritin light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsTaher, M. / Maity, B. / Nakane, T. / Abe, S. / Ueno, T. / Mazumdar, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Controlled Uptake of an Iridium Complex inside Engineered apo-Ferritin Nanocages: Study of Structure and Catalysis.
Authors: Taher, M. / Maity, B. / Nakane, T. / Abe, S. / Ueno, T. / Mazumdar, S.
History
DepositionApr 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,90616
Polymers19,8951
Non-polymers2,01015
Water4,288238
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)525,734384
Polymers477,49224
Non-polymers48,242360
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 area100840 Å2
ΔGint-1111 kcal/mol
Surface area138150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.937, 181.937, 181.937
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
11A-206-

CD

21A-207-

CD

31A-208-

CD

41A-210-

CD

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Ferritin light chain / / Ferritin L subunit


Mass: 19895.486 Da / Num. of mol.: 1 / Mutation: D38H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: FTL / Production host: Escherichia coli (E. coli) / References: UniProt: P02791

-
Non-polymers , 7 types, 253 molecules

#2: Chemical ChemComp-RIR / [(1,2,3,4,5-Eta)-1,2,3,4,5-Pentamethylcyclopentadienyl]iridium(III)


Mass: 327.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15Ir / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CD / CADMIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-IR / IRIDIUM ION


Mass: 192.217 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ir / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Ammonium sulfate (0.5-1.0M), Cadmium sulfate(12-20mM)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.05 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.25→45.526 Å / Num. obs: 71305 / % possible obs: 100 % / Redundancy: 72.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.2 / Net I/σ(I): 23.1
Reflection shellResolution: 1.25→1.27 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 71305 / CC1/2: 0.82

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DAT

1dat


Resolution: 1.25→41.739 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.177 / WRfactor Rwork: 0.167 / SU B: 0.482 / SU ML: 0.021 / Average fsc free: 0.9589 / Average fsc work: 0.9613 / Cross valid method: FREE R-VALUE / ESU R: 0.037 / ESU R Free: 0.038
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1828 3571 5.008 %
Rwork0.1714 67732 -
all0.172 --
obs-71303 99.989 %
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: 14.399 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.25→41.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 39 238 1658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0131573
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171486
X-RAY DIFFRACTIONr_angle_refined_deg2.2011.6622162
X-RAY DIFFRACTIONr_angle_other_deg1.5811.593463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6545210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33922.26897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42715296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.421513
X-RAY DIFFRACTIONr_chiral_restr0.1240.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021775
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02340
X-RAY DIFFRACTIONr_nbd_refined0.2930.2403
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.21308
X-RAY DIFFRACTIONr_nbtor_refined0.1930.2727
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0970.2643
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2490.2144
X-RAY DIFFRACTIONr_metal_ion_refined0.3120.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.330.221
X-RAY DIFFRACTIONr_nbd_other0.2050.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.170.235
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.410.22
X-RAY DIFFRACTIONr_mcbond_it1.491.242731
X-RAY DIFFRACTIONr_mcbond_other1.4821.237730
X-RAY DIFFRACTIONr_mcangle_it2.2931.861921
X-RAY DIFFRACTIONr_mcangle_other2.2921.866922
X-RAY DIFFRACTIONr_scbond_it2.6951.557842
X-RAY DIFFRACTIONr_scbond_other2.6111.548835
X-RAY DIFFRACTIONr_scangle_it3.982.2311201
X-RAY DIFFRACTIONr_scangle_other3.9642.211190
X-RAY DIFFRACTIONr_lrange_it5.9817.0611926
X-RAY DIFFRACTIONr_lrange_other5.70416.1161859
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
1.25-1.2820.3762660.39348980.39251640.9190.9151000.363
1.282-1.3180.3542480.30547940.30850430.9260.9399.98020.275
1.318-1.3560.2522540.24546780.24549320.9460.9451000.217
1.356-1.3970.2142370.20845390.20847760.9480.9541000.178
1.397-1.4430.1982360.18544010.18646370.9540.9551000.159
1.443-1.4940.182330.15642740.15745070.9590.9671000.137
1.494-1.550.1672200.14641240.14743440.9670.9721000.131
1.55-1.6130.162250.14539450.14641700.9720.9731000.133
1.613-1.6850.1531840.13938470.1440310.9730.9761000.129
1.685-1.7670.1582030.14336520.14438550.970.9751000.135
1.767-1.8620.161730.14634990.14736720.9740.9761000.14
1.862-1.9750.1721790.15733050.15834840.9720.9741000.154
1.975-2.1110.1731530.16231550.16233080.9720.9761000.161
2.111-2.280.1461630.14629060.14630690.980.981000.148
2.28-2.4970.1611520.1426900.14128420.9750.9771000.147
2.497-2.790.1651210.14624820.14726030.9720.9741000.155
2.79-3.2190.1651160.15421990.15423150.970.9691000.168
3.219-3.9370.177960.15918860.1619820.9680.9711000.178
3.937-5.5430.191750.19515100.19515860.9720.97499.9370.219
5.543-41.7390.345370.3199480.329850.9280.9391000.347

+
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