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- PDB-5ouw: Metal free structure of SynFtn -

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Basic information

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


bacterial non-heme ferritin / ferric iron binding / iron ion transport / ferrous iron binding / 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. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsHemmings, A.M. / Bradley, J.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/I021884/1 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)19,7571
Polymers19,7571
Non-polymers00
Water2,666148
1
A: Ferritin
x 24


Theoretical massNumber of molelcules
Total (without water)474,16424
Polymers474,16424
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_545z,-y-1,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_545-z,-y-1,-x1
crystal symmetry operation29_545z,x-1/2,y+1/21
crystal symmetry operation30_544z,-x-1/2,-y-1/21
crystal symmetry operation31_545-z,-x-1/2,y+1/21
crystal symmetry operation32_544-z,x-1/2,-y-1/21
crystal symmetry operation41_544x,z-1/2,-y-1/21
crystal symmetry operation42_545-x,z-1/2,y+1/21
crystal symmetry operation43_544-x,-z-1/2,-y-1/21
crystal symmetry operation44_545x,-z-1/2,y+1/21
crystal symmetry operation81_545y+1/2,z-1/2,x1
crystal symmetry operation82_445-y-1/2,z-1/2,-x1
crystal symmetry operation83_545y+1/2,-z-1/2,-x1
crystal symmetry operation84_445-y-1/2,-z-1/2,x1
crystal symmetry operation85_545y+1/2,x-1/2,-z1
crystal symmetry operation86_445-y-1/2,-x-1/2,-z1
crystal symmetry operation87_545y+1/2,-x-1/2,z1
crystal symmetry operation88_445-y-1/2,x-1/2,z1
Buried area91210 Å2
ΔGint-404 kcal/mol
Surface area131610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.740, 177.740, 177.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-346-

HOH

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Components

#1: Protein Ferritin


Mass: 19756.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (strain 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


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.89 Å3/Da / Density % sol: 57.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: ammonium acetate, sodium chloride

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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: 2.05→53.59 Å / Num. obs: 15595 / % possible obs: 99.7 % / Redundancy: 54.9 % / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.01 / Rrim(I) all: 0.075 / Net I/σ(I): 53.2
Reflection shellResolution: 2.05→2.1 Å / Rmerge(I) obs: 0.644 / CC1/2: 0.986 / Rpim(I) all: 0.085 / Rrim(I) all: 0.649

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EUM

1eum


Resolution: 2.05→53.591 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1971 706 4.53 %
Rwork0.1539 14869 -
obs0.156 15575 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.23 Å2 / Biso mean: 31.8214 Å2 / Biso min: 16.49 Å2
Refinement stepCycle: final / Resolution: 2.05→53.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 0 148 1537
Biso mean---42.09 -
Num. residues----177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061437
X-RAY DIFFRACTIONf_angle_d0.6851957
X-RAY DIFFRACTIONf_chiral_restr0.041219
X-RAY DIFFRACTIONf_plane_restr0.004262
X-RAY DIFFRACTIONf_dihedral_angle_d15.271877
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0503-2.20860.25031460.1428753021100
2.2086-2.43090.20911260.152909303599
2.4309-2.78260.24891320.15852934306699
2.7826-3.50570.20631500.15382969311999
3.5057-53.60890.16531520.155731823334100

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