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- PDB-5ouz: Metal free structure of Y40F SynFtn -

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Basic information

Entry
Database: PDB / ID: 5ouz
TitleMetal free structure of Y40F SynFtn
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Ferritin
Function / homology
Function and homology information


bacterial non-heme ferritin / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Ferritin, prokaryotic-type / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Biological speciesSynechococcus sp. CC9311 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.081 Å
AuthorsHemmings, A.M. / Bradley, J.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/IO21884/1 United Kingdom
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Reaction of O2with a diiron protein generates a mixed-valent Fe2+/Fe3+center and peroxide.
Authors: Bradley, J.M. / Svistunenko, D.A. / Pullin, J. / Hill, N. / Stuart, R.K. / Palenik, B. / Wilson, M.T. / Hemmings, A.M. / Moore, G.R. / Le Brun, N.E.
History
DepositionAug 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 30, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 2024Group: 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

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Assembly

Deposited unit
A: Ferritin


Theoretical massNumber of molelcules
Total (without water)20,2161
Polymers20,2161
Non-polymers00
Water2,504139
1
A: Ferritin
x 24


Theoretical massNumber of molelcules
Total (without water)485,19324
Polymers485,19324
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_655-x+1,z,y1
crystal symmetry operation19_655-x+1,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation57_554y+1/2,z,x-1/21
crystal symmetry operation58_555-y+1/2,z,-x+1/21
crystal symmetry operation59_555y+1/2,-z,-x+1/21
crystal symmetry operation60_554-y+1/2,-z,x-1/21
crystal symmetry operation69_555z+1/2,y,-x+1/21
crystal symmetry operation70_554z+1/2,-y,x-1/21
crystal symmetry operation71_554-z+1/2,y,x-1/21
crystal symmetry operation72_555-z+1/2,-y,-x+1/21
crystal symmetry operation77_545z+1/2,x-1/2,y1
crystal symmetry operation78_555z+1/2,-x+1/2,-y1
crystal symmetry operation79_555-z+1/2,-x+1/2,y1
crystal symmetry operation80_545-z+1/2,x-1/2,-y1
crystal symmetry operation85_545y+1/2,x-1/2,-z1
crystal symmetry operation86_555-y+1/2,-x+1/2,-z1
crystal symmetry operation87_555y+1/2,-x+1/2,z1
crystal symmetry operation88_545-y+1/2,x-1/2,z1
Buried area90640 Å2
ΔGint-348 kcal/mol
Surface area134120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.920, 176.920, 176.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-298-

HOH

21A-336-

HOH

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Components

#1: Protein Ferritin /


Mass: 20216.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. CC9311 (bacteria) / Strain: CC9311 / Gene: sync_1539 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0I9X8, bacterial non-heme ferritin
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium acetate 2.0 M sodium chloride pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.08→53.34 Å / Num. obs: 14805 / % possible obs: 100 % / Redundancy: 56.6 % / CC1/2: 1 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.01 / Rrim(I) all: 0.077 / Net I/σ(I): 46.9
Reflection shellRmerge(I) obs: 0.658 / CC1/2: 0.985 / Rpim(I) all: 0.088 / Rrim(I) all: 0.664

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EUM

1eum


Resolution: 2.081→53.34 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20
RfactorNum. reflection% reflection
Rfree0.2045 752 5.08 %
Rwork0.1538 --
obs0.1563 14801 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.081→53.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1392 0 0 139 1531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051417
X-RAY DIFFRACTIONf_angle_d0.6611923
X-RAY DIFFRACTIONf_dihedral_angle_d13.75852
X-RAY DIFFRACTIONf_chiral_restr0.041215
X-RAY DIFFRACTIONf_plane_restr0.004257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0811-2.24180.24191340.13342731X-RAY DIFFRACTION100
2.2418-2.46740.19151470.13072754X-RAY DIFFRACTION100
2.4674-2.82440.21631480.14672760X-RAY DIFFRACTION100
2.8244-3.55840.21161560.15752815X-RAY DIFFRACTION100
3.5584-53.36090.19481670.16192989X-RAY DIFFRACTION100

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