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- PDB-5n5f: Crystal structure of Haliangium ochraceum encapsulated ferritin -

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Basic information

Entry
Database: PDB / ID: 5n5f
TitleCrystal structure of Haliangium ochraceum encapsulated ferritin
Componentsencapsulated ferritin
KeywordsOXIDOREDUCTASE / ferritin / encapsulin / encapsulated ferritin
Function / homology
Function and homology information


encapsulin nanocompartment / ferroxidase / ferroxidase activity / iron ion transport / intracellular iron ion homeostasis / metal ion binding
Similarity search - Function
Helix Hairpins - #1960 / Ferritin-like protein / Helix Hairpins / Ferritin-like superfamily / Helix non-globular / Special
Similarity search - Domain/homology
Encapsulated ferritin-like protein
Similarity search - Component
Biological speciesHaliangium ochraceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.057 Å
AuthorsMarles-Wright, J. / He, D.
CitationJournal: Biochem.J. / Year: 2019
Title: Conservation of the structural and functional architecture of encapsulated ferritins in bacteria and archaea.
Authors: He, D. / Piergentili, C. / Ross, J. / Tarrant, E. / Tuck, L.R. / Mackay, C.L. / McIver, Z. / Waldron, K.J. / Clarke, D.J. / Marles-Wright, J.
History
DepositionFeb 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: encapsulated ferritin
B: encapsulated ferritin
C: encapsulated ferritin
D: encapsulated ferritin
E: encapsulated ferritin
F: encapsulated ferritin
G: encapsulated ferritin
H: encapsulated ferritin
I: encapsulated ferritin
J: encapsulated ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,89311
Polymers115,87010
Non-polymers231
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39430 Å2
ΔGint-228 kcal/mol
Surface area32960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.629, 92.652, 119.291
Angle α, β, γ (deg.)90.00, 106.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
encapsulated ferritin


Mass: 11587.021 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliangium ochraceum (bacteria) / Gene: Hoch_3836 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0LZ73
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M NaCl, 0.1 M Bis-Tris.HCl pH 5.5, 20 % (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.72 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 2, 2016
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.72 Å / Relative weight: 1
ReflectionResolution: 2.057→47.82 Å / Num. obs: 57293 / % possible obs: 96 % / Redundancy: 5.2 % / Biso Wilson estimate: 31.57 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.09437 / Rsym value: 0.1047 / Net I/σ(I): 10.16
Reflection shellResolution: 2.057→2.131 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.5965 / Mean I/σ(I) obs: 2.37 / Num. unique obs: 5570 / CC1/2: 0.909 / Rsym value: 0.6668 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5da5

5da5


Resolution: 2.057→47.82 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.8
RfactorNum. reflection% reflectionSelection details
Rfree0.2447 2765 4.84 %Random
Rwork0.1989 ---
obs0.2011 57083 96.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.057→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7644 0 1 168 7813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037821
X-RAY DIFFRACTIONf_angle_d0.45510603
X-RAY DIFFRACTIONf_dihedral_angle_d11.724783
X-RAY DIFFRACTIONf_chiral_restr0.0321167
X-RAY DIFFRACTIONf_plane_restr0.0031384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0573-2.09280.39211350.31322639X-RAY DIFFRACTION93
2.0928-2.13090.29591490.26052640X-RAY DIFFRACTION95
2.1309-2.17190.2971310.24982676X-RAY DIFFRACTION95
2.1719-2.21620.27881170.23052635X-RAY DIFFRACTION95
2.2162-2.26440.27811310.23492693X-RAY DIFFRACTION95
2.2644-2.3170.31681310.2282711X-RAY DIFFRACTION96
2.317-2.3750.31071460.22122666X-RAY DIFFRACTION96
2.375-2.43920.25891370.21032698X-RAY DIFFRACTION96
2.4392-2.5110.25861350.20772720X-RAY DIFFRACTION97
2.511-2.5920.27751630.20652698X-RAY DIFFRACTION97
2.592-2.68460.26621520.20162706X-RAY DIFFRACTION97
2.6846-2.79210.24651210.20622734X-RAY DIFFRACTION97
2.7921-2.91920.26491420.20422744X-RAY DIFFRACTION97
2.9192-3.07310.23961450.20832772X-RAY DIFFRACTION98
3.0731-3.26560.25971470.21332772X-RAY DIFFRACTION98
3.2656-3.51760.25891620.19892719X-RAY DIFFRACTION98
3.5176-3.87150.21111630.1822741X-RAY DIFFRACTION97
3.8715-4.43130.20421040.16752787X-RAY DIFFRACTION97
4.4313-5.58170.19031090.17632794X-RAY DIFFRACTION97
5.5817-47.83290.22441450.18172773X-RAY DIFFRACTION96

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