[English] 日本語
Yorodumi
- PDB-6kh5: Design and crystal structure of protein MOFs with ferritin nanoca... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kh5
TitleDesign and crystal structure of protein MOFs with ferritin nanocages as linkers and nickel clusters as nodes
ComponentsFerritin
KeywordsOXIDOREDUCTASE / protein MOF / ferritin / nickel
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, 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
: / NICKEL (II) ION / Ferritin
Similarity search - Component
Biological speciesPenaeus japonicus (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.294 Å
AuthorsGu, C. / Chen, H. / Wang, Y. / Zhang, T. / Wang, H. / Zhao, G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31730069 China
National Natural Science Foundation of China (NSFC)31671805 China
CitationJournal: Chemistry / Year: 2020
Title: Structural Insight into Binary Protein Metal-Organic Frameworks with Ferritin Nanocages as Linkers and Nickel Clusters as Nodes.
Authors: Gu, C. / Chen, H. / Wang, Y. / Zhang, T. / Wang, H. / Zhao, G.
History
DepositionJul 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7675
Polymers19,5351
Non-polymers2324
Water97354
1
A: Ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)474,402120
Polymers468,83624
Non-polymers5,56696
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_654-x+1,y,-z-11
crystal symmetry operation4_564x,-y+1,-z-11
crystal symmetry operation5_654z+1,x,y-11
crystal symmetry operation6_665z+1,-x+1,-y1
crystal symmetry operation7_564-z,-x+1,y-11
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_564y,z+1,x-11
crystal symmetry operation10_665-y+1,z+1,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_654-y+1,-z,x-11
crystal symmetry operation13_554y,x,-z-11
crystal symmetry operation14_664-y+1,-x+1,-z-11
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
crystal symmetry operation17_565x,z+1,-y1
crystal symmetry operation18_664-x+1,z+1,y-11
crystal symmetry operation19_655-x+1,-z,-y1
crystal symmetry operation20_554x,-z,y-11
crystal symmetry operation21_655z+1,y,-x1
crystal symmetry operation22_664z+1,-y+1,x-11
crystal symmetry operation23_554-z,y,x-11
crystal symmetry operation24_565-z,-y+1,-x1
Buried area105490 Å2
ΔGint-1197 kcal/mol
Surface area130730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.533, 118.533, 118.533
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-347-

HOH

-
Components

#1: Protein Ferritin


Mass: 19534.824 Da / Num. of mol.: 1 / Mutation: T161H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penaeus japonicus (crustacean) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: T2B7E1, ferroxidase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.55 Å3/Da / Density % sol: 65.37 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 1 M NH4H2PO4, 100 mM Tris ( pH = 8.5 )

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.4938 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4938 Å / Relative weight: 1
ReflectionResolution: 2.294→50 Å / Num. obs: 24172 / % possible obs: 100 % / Redundancy: 22 % / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.041 / Rrim(I) all: 0.194 / Χ2: 0.892 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.38191.08312870.9680.2511.1120.65100
2.38-2.4821.60.99613080.9710.2171.020.673100
2.48-2.5921.80.76112880.9770.1660.780.722100
2.59-2.7323.60.54912990.9870.1150.5610.763100
2.73-2.922.80.39513280.9910.0840.4040.871100
2.9-3.1223.50.24513140.9940.0510.251.053100
3.12-3.4422.90.17613210.9950.0380.181.031100
3.44-3.93230.12713410.9950.0270.131.053100
3.93-4.9521.80.10813800.9970.0230.110.998100
4.95-5020.40.09214810.9980.0210.0941.02399.6

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A4U

6a4u


Resolution: 2.294→39.511 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2029 2425 10.03 %
Rwork0.1587 21747 -
obs0.1631 24172 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 192.36 Å2 / Biso mean: 31.7986 Å2 / Biso min: 14.65 Å2
Refinement stepCycle: final / Resolution: 2.294→39.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1372 0 4 54 1430
Biso mean--107.88 35.35 -
Num. residues----170
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.294-2.34080.26981410.21304
2.3408-2.39170.24371390.19141272
2.3917-2.44730.21731440.18061272
2.4473-2.50850.24561420.18421285
2.5085-2.57630.291430.17161290
2.5763-2.65210.2191400.17321263
2.6521-2.73770.22151420.16191281
2.7377-2.83550.19941470.17171259
2.8355-2.9490.23161390.16431288
2.949-3.08310.2341410.16881264
3.0831-3.24560.20711440.16961281
3.2456-3.44890.19211420.16591272
3.4489-3.7150.2231460.15331285
3.715-4.08850.1761430.13491292
4.0885-4.67930.14161440.12421266
4.6793-5.89220.20381410.15161283
5.8922-39.5110.17251470.16261290

+
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