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- PDB-5n5e: Crystal structure of encapsulated ferritin domain from Pyrococcus... -

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Basic information

Entry
Database: PDB / ID: 5n5e
TitleCrystal structure of encapsulated ferritin domain from Pyrococcus furiosus PFC_05175
ComponentsPFC_05175
KeywordsOXIDOREDUCTASE / ferritin / encapsulin / encapsulated ferritin
Function / homology
Function and homology information


peptidase activity / oxidoreductase activity / defense response to bacterium / metal ion binding
Similarity search - Function
Rubrerythrin, diiron-binding domain / Rubrerythrin / Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / Rubrerythrin domain-containing protein
Similarity search - Component
Biological speciesPyrococcus furiosus COM1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.026 Å
AuthorsMarles-Wright, J. / He, D.
Funding support United Kingdom, China, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/N005570/1 United Kingdom
China Scholarships Council China
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.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.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.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_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
e: PFC_05175
A: PFC_05175
B: PFC_05175
C: PFC_05175
D: PFC_05175
E: PFC_05175
F: PFC_05175
G: PFC_05175
H: PFC_05175
I: PFC_05175
J: PFC_05175
K: PFC_05175
L: PFC_05175
M: PFC_05175
N: PFC_05175
O: PFC_05175
P: PFC_05175
Q: PFC_05175
R: PFC_05175
T: PFC_05175
U: PFC_05175
V: PFC_05175
W: PFC_05175
X: PFC_05175
Y: PFC_05175
Z: PFC_05175
a: PFC_05175
b: PFC_05175
c: PFC_05175
d: PFC_05175
hetero molecules


Theoretical massNumber of molelcules
Total (without water)341,15560
Polymers339,47930
Non-polymers1,67530
Water36,2822014
1
e: PFC_05175
C: PFC_05175
D: PFC_05175
H: PFC_05175
J: PFC_05175
K: PFC_05175
P: PFC_05175
Q: PFC_05175
R: PFC_05175
d: PFC_05175
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,71820
Polymers113,16010
Non-polymers55810
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48820 Å2
ΔGint-413 kcal/mol
Surface area33310 Å2
MethodPISA
2
A: PFC_05175
E: PFC_05175
F: PFC_05175
M: PFC_05175
N: PFC_05175
O: PFC_05175
W: PFC_05175
Z: PFC_05175
a: PFC_05175
c: PFC_05175
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,71820
Polymers113,16010
Non-polymers55810
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49140 Å2
ΔGint-406 kcal/mol
Surface area33320 Å2
MethodPISA
3
B: PFC_05175
G: PFC_05175
I: PFC_05175
L: PFC_05175
T: PFC_05175
U: PFC_05175
V: PFC_05175
X: PFC_05175
Y: PFC_05175
b: PFC_05175
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,71820
Polymers113,16010
Non-polymers55810
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48660 Å2
ΔGint-410 kcal/mol
Surface area33470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.853, 110.057, 136.271
Angle α, β, γ (deg.)90.00, 91.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ...
PFC_05175


Mass: 11315.974 Da / Num. of mol.: 30
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_05175 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I6U7J4
#2: Chemical...
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2014 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M lithium chloride 20 % (w/v) PEG3350 Drops:100 nl protein, 100 nl reservoir solution. Reservoir: 70 ul.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.74 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2015
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74 Å / Relative weight: 1
ReflectionResolution: 2.026→47.19 Å / Num. obs: 374905 / % possible obs: 99.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 22.88 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.07968 / Rsym value: 0.0953 / Net I/σ(I): 10.48
Reflection shellResolution: 2.026→2.099 Å / Redundancy: 3 % / Rmerge(I) obs: 0.3627 / Mean I/σ(I) obs: 4.02 / Num. unique obs: 36076 / CC1/2: 0.902 / Rsym value: 0.4412 / % possible all: 99

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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: 2.026→47.19 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.26
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 17934 4.91 %Random Selection
Rwork0.1741 ---
obs0.1652 365595 96.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.026→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23400 0 30 2014 25444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223978
X-RAY DIFFRACTIONf_angle_d0.43532365
X-RAY DIFFRACTIONf_dihedral_angle_d17.02615171
X-RAY DIFFRACTIONf_chiral_restr0.0363779
X-RAY DIFFRACTIONf_plane_restr0.0024231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0262-2.04920.24615840.223610852X-RAY DIFFRACTION91
2.0492-2.07330.22315740.201811808X-RAY DIFFRACTION98
2.0733-2.09860.22775390.201711679X-RAY DIFFRACTION97
2.0986-2.12510.24995450.198711698X-RAY DIFFRACTION97
2.1251-2.15310.24286540.195211193X-RAY DIFFRACTION95
2.1531-2.18260.21296140.175811624X-RAY DIFFRACTION98
2.1826-2.21380.21315670.174311653X-RAY DIFFRACTION97
2.2138-2.24680.21785400.178211405X-RAY DIFFRACTION95
2.2468-2.28190.21046090.172211860X-RAY DIFFRACTION99
2.2819-2.31930.21265760.16711776X-RAY DIFFRACTION99
2.3193-2.35930.21745890.164811764X-RAY DIFFRACTION98
2.3593-2.40220.2246240.172611641X-RAY DIFFRACTION98
2.4022-2.44840.21085810.169411368X-RAY DIFFRACTION95
2.4484-2.49840.20496590.165711686X-RAY DIFFRACTION98
2.4984-2.55270.20316190.161311673X-RAY DIFFRACTION98
2.5527-2.61210.20675790.161811378X-RAY DIFFRACTION95
2.6121-2.67740.19816450.164811728X-RAY DIFFRACTION99
2.6774-2.74980.20766390.16711900X-RAY DIFFRACTION99
2.7498-2.83070.20656340.1611793X-RAY DIFFRACTION99
2.8307-2.92210.1825510.172111564X-RAY DIFFRACTION97
2.9221-3.02650.21896340.173611752X-RAY DIFFRACTION98
3.0265-3.14770.19696260.171811664X-RAY DIFFRACTION98
3.1477-3.29090.20275190.168811501X-RAY DIFFRACTION96
3.2909-3.46440.18516170.177411677X-RAY DIFFRACTION98
3.4644-3.68140.19526330.160411688X-RAY DIFFRACTION98
3.6814-3.96550.18236920.144911383X-RAY DIFFRACTION96
3.9655-4.36430.15184970.128511689X-RAY DIFFRACTION97
4.3643-4.99540.14286070.124911477X-RAY DIFFRACTION96
4.9954-6.29160.22885790.172311593X-RAY DIFFRACTION97
6.2916-47.190.15636080.159611190X-RAY DIFFRACTION94

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