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- PDB-6kh4: Design and crystal structure of protein MOFs with ferritin nanoca... -

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Basic information

Entry
Database: PDB / ID: 6kh4
TitleDesign and crystal structure of protein MOFs with ferritin nanocages as linkers and nickel clusters as nodes
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN
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: 2.302 Å
AuthorsGu, C. / Chen, H. / Wang, Y. / Zhang, T. / Wang, H. / Zhao, G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31730069 China
National Natural Science Foundation of China31671805 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7675
Polymers19,5351
Non-polymers2324
Water1,20767
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 area106160 Å2
ΔGint-1205 kcal/mol
Surface area129330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.579, 118.579, 118.579
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-353-

HOH

21A-364-

HOH

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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.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.56 Å3/Da / Density % sol: 65.41 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 1M NH4H2PO4, 100mM Tris ( pH = 8.5 )

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.4813 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: 1.4813 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 23946 / % possible obs: 99.9 % / Redundancy: 24.5 % / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.021 / Rrim(I) all: 0.103 / Χ2: 0.962 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.3825.70.37212750.9910.0750.380.705100
2.38-2.4825.30.29512970.9930.060.3020.806100
2.48-2.5924.60.22912770.9950.0470.2340.863100
2.59-2.7325.60.17912840.9950.0360.1830.991100
2.73-2.924.30.14313140.9970.030.1461.007100
2.9-3.1225.50.1113140.9970.0220.1131.087100
3.12-3.4424.30.09412970.9980.0190.0961.054100
3.44-3.9324.80.08313400.9990.0170.0850.981100
3.93-4.9523.70.07413590.9980.0150.0761.066100
4.95-5021.60.06614680.9990.0150.0681.06599.4

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Processing

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

6a4u


Resolution: 2.302→35.753 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 18.68
RfactorNum. reflection% reflection
Rfree0.1986 2390 9.98 %
Rwork0.16 --
obs0.1639 23946 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 199.63 Å2 / Biso mean: 35.3827 Å2 / Biso min: 16.45 Å2
Refinement stepCycle: final / Resolution: 2.302→35.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1372 0 4 67 1443
Biso mean--86.95 35.4 -
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
2.302-2.34870.27691410.18211289
2.3487-2.39980.2251410.17051254
2.3998-2.45560.24271370.17361266
2.4556-2.5170.25891430.17671258
2.517-2.5850.2171400.16971289
2.585-2.66110.25351470.16131261
2.6611-2.74690.17571320.15841260
2.7469-2.84510.21831400.16831268
2.8451-2.95890.20611370.16831255
2.9589-3.09350.21811400.17811265
3.0935-3.25650.2451370.16991278
3.2565-3.46040.19371430.17781250
3.4604-3.72730.20921470.15911282
3.7273-4.10190.1961350.13871272
4.1019-4.69430.13911440.12421252
4.6943-5.910.171430.14341275
5.91-35.7530.16661430.17811282

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