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- PDB-6kh0: Design and crystal structure of protein MOFs with ferritin nanoca... -

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Basic information

Entry
Database: PDB / ID: 6kh0
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
Biological speciesPenaeus japonicus (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGu, C. / Zhang, T. / 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 ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,54412
Polymers117,2096
Non-polymers3356
Water31,9591774
1
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)470,17648
Polymers468,83624
Non-polymers1,34024
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area94490 Å2
ΔGint-642 kcal/mol
Surface area134350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.304, 125.304, 175.655
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11C-454-

HOH

21C-604-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 10 or resid 12...
21(chain B and (resid 2 through 10 or resid 12...
31(chain C and (resid 2 through 10 or resid 12...
41(chain D and (resid 2 through 10 or resid 12...
51(chain E and (resid 2 through 10 or resid 12...
61(chain F and (resid 2 through 10 or resid 12...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 10 or resid 12...A2 - 10
121(chain A and (resid 2 through 10 or resid 12...A12 - 15
131(chain A and (resid 2 through 10 or resid 12...A18 - 60
141(chain A and (resid 2 through 10 or resid 12...A62 - 98
151(chain A and (resid 2 through 10 or resid 12...A104 - 106
161(chain A and (resid 2 through 10 or resid 12...A118 - 11
171(chain A and (resid 2 through 10 or resid 12...A121 - 141
181(chain A and (resid 2 through 10 or resid 12...A143 - 172
211(chain B and (resid 2 through 10 or resid 12...B2 - 10
221(chain B and (resid 2 through 10 or resid 12...B12 - 15
231(chain B and (resid 2 through 10 or resid 12...B18 - 60
241(chain B and (resid 2 through 10 or resid 12...B62 - 98
251(chain B and (resid 2 through 10 or resid 12...B104 - 106
261(chain B and (resid 2 through 10 or resid 12...B118 - 11
271(chain B and (resid 2 through 10 or resid 12...B121 - 141
281(chain B and (resid 2 through 10 or resid 12...B143 - 172
311(chain C and (resid 2 through 10 or resid 12...C2 - 10
321(chain C and (resid 2 through 10 or resid 12...C12 - 15
331(chain C and (resid 2 through 10 or resid 12...C18 - 60
341(chain C and (resid 2 through 10 or resid 12...C62 - 98
351(chain C and (resid 2 through 10 or resid 12...C104 - 106
361(chain C and (resid 2 through 10 or resid 12...C118 - 11
371(chain C and (resid 2 through 10 or resid 12...C121 - 141
381(chain C and (resid 2 through 10 or resid 12...C143 - 172
411(chain D and (resid 2 through 10 or resid 12...D2 - 10
421(chain D and (resid 2 through 10 or resid 12...D12 - 15
431(chain D and (resid 2 through 10 or resid 12...D2 - 172
441(chain D and (resid 2 through 10 or resid 12...D0
451(chain D and (resid 2 through 10 or resid 12...D1 - 10106
461(chain D and (resid 2 through 10 or resid 12...D108 - 109
471(chain D and (resid 2 through 10 or resid 12...D8 - 109
481(chain D and (resid 2 through 10 or resid 12...D112 - 116
491(chain D and (resid 2 through 10 or resid 12...D118 - 119
4101(chain D and (resid 2 through 10 or resid 12...D121 - 141
4111(chain D and (resid 2 through 10 or resid 12...D143 - 172
511(chain E and (resid 2 through 10 or resid 12...E2 - 10
521(chain E and (resid 2 through 10 or resid 12...E12 - 15
531(chain E and (resid 2 through 10 or resid 12...E2 - 172
541(chain E and (resid 2 through 10 or resid 12...E0
551(chain E and (resid 2 through 10 or resid 12...E1 - 10106
561(chain E and (resid 2 through 10 or resid 12...E108 - 109
571(chain E and (resid 2 through 10 or resid 12...E8 - 109
581(chain E and (resid 2 through 10 or resid 12...E112 - 116
591(chain E and (resid 2 through 10 or resid 12...E118 - 119
5101(chain E and (resid 2 through 10 or resid 12...E121 - 141
5111(chain E and (resid 2 through 10 or resid 12...E143 - 172
611(chain F and (resid 2 through 10 or resid 12...F2 - 10
621(chain F and (resid 2 through 10 or resid 12...F12 - 15
631(chain F and (resid 2 through 10 or resid 12...F18 - 60
641(chain F and (resid 2 through 10 or resid 12...F62 - 98
651(chain F and (resid 2 through 10 or resid 12...F104 - 106
661(chain F and (resid 2 through 10 or resid 12...F118 - 11
671(chain F and (resid 2 through 10 or resid 12...F121 - 141
681(chain F and (resid 2 through 10 or resid 12...F143 - 172

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Components

#1: Protein
Ferritin


Mass: 19534.824 Da / Num. of mol.: 6 / 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.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1774 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.94 Å3/Da / Density % sol: 58.18 % / Description: octahedral
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 1 M NH4H2PO4, 100 mM Tris ( pH = 8.5 )

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
Reflection twinOperator: -h,k,-l / Fraction: 0.23
ReflectionResolution: 2→50 Å / Num. obs: 90921 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.04 / Rrim(I) all: 0.106 / Χ2: 0.978 / Net I/σ(I): 5.9 / Num. measured all: 620700
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2-2.076.80.33790720.9060.140.3650.654
2.07-2.156.90.26791120.9410.1090.2890.781
2.15-2.256.80.22590200.9530.0930.2440.858
2.25-2.376.50.19290780.9640.0820.2090.948
2.37-2.527.10.16790700.9720.0680.1810.993
2.52-2.716.90.13791040.9790.0560.1491.085
2.71-2.996.60.11390630.9850.0470.1221.134
2.99-3.4270.0990940.9910.0370.0971.215
3.42-4.316.80.06891360.9950.0280.0741.221
4.31-506.80.05591720.9970.0230.060.887

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A4U

6a4u


Resolution: 2→29.946 Å / Cross valid method: THROUGHOUT / σ(F): 307.24 / Phase error: 16.81 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1411 2009 2.21 %
Rwork0.101 88811 -
obs0.1069 90893 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.17 Å2 / Biso mean: 24.1938 Å2 / Biso min: 8.89 Å2
Refinement stepCycle: final / Resolution: 2→29.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8232 0 6 1774 10012
Biso mean--32.85 35.68 -
Num. residues----1020
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4574X-RAY DIFFRACTION7.736TORSIONAL
12B4574X-RAY DIFFRACTION7.736TORSIONAL
13C4574X-RAY DIFFRACTION7.736TORSIONAL
14D4574X-RAY DIFFRACTION7.736TORSIONAL
15E4574X-RAY DIFFRACTION7.736TORSIONAL
16F4574X-RAY DIFFRACTION7.736TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0013-2.05130.17341310.142763396470
2.0513-2.10670.161470.135363466493
2.1067-2.16870.17861490.124163036452
2.1687-2.23860.13611400.124263416481
2.2386-2.31850.15821430.115163346477
2.3185-2.41120.1591470.11363246471
2.4112-2.52080.16471410.116763076448
2.5208-2.65350.15491480.107463396487
2.6535-2.81940.1331440.102163146458
2.8194-3.03650.151460.096863616507
3.0365-3.34110.14071360.096363586494
3.3411-3.82230.14951480.091263416489
3.8223-4.80690.11831410.079563906531
4.8069-21.62470.1391480.122564146562

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