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- PDB-6son: 2 minute Fe2+ soak structure of SynFtn variant D137A -

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Basic information

Entry
Database: PDB / ID: 6son
Title2 minute Fe2+ soak structure of SynFtn variant D137A
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Ferritin / Iron Storage
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. CC9311 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHemmings, A.M. / Bradley, J.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/R003203/1 United Kingdom
CitationJournal: Dalton Trans / Year: 2020
Title: Routes of iron entry into, and exit from, the catalytic ferroxidase sites of the prokaryotic ferritin SynFtn.
Authors: Bradley, J.M. / Pullin, J. / Moore, G.R. / Svistunenko, D.A. / Hemmings, A.M. / Le Brun, N.E.
History
DepositionAug 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3354
Polymers20,1881
Non-polymers1473
Water3,801211
1
A: Ferritin
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A: Ferritin
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A: Ferritin
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A: Ferritin
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A: Ferritin
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A: Ferritin
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A: Ferritin
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A: Ferritin
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A: Ferritin
hetero molecules

A: Ferritin
hetero molecules

A: Ferritin
hetero molecules

A: Ferritin
hetero molecules

A: Ferritin
hetero molecules

A: Ferritin
hetero molecules

A: Ferritin
hetero molecules

A: Ferritin
hetero molecules

A: Ferritin
hetero molecules

A: Ferritin
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A: Ferritin
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A: Ferritin
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A: Ferritin
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A: Ferritin
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Theoretical massNumber of molelcules
Total (without water)488,05296
Polymers484,52024
Non-polymers3,53172
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Unit cell
Length a, b, c (Å)176.900, 176.900, 176.900
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-509-

HOH

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Components

#1: Protein Ferritin


Mass: 20188.346 Da / Num. of mol.: 1 / Mutation: D137A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. CC9311 (bacteria) / Gene: sync_1539 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0I9X8, bacterial non-heme ferritin
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.92 Å3/Da / Density % sol: 57.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M sodium acetate 2.0 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→62.54 Å / Num. obs: 31809 / % possible obs: 99.9 % / Redundancy: 19.2 % / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.012 / Rrim(I) all: 0.054 / Net I/σ(I): 26.1 / Num. measured all: 609755
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.6-1.6419.72.2214555123150.6330.5122.281.5100
7.16-62.5414.90.03671845110.0070.0372.799.4

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHENIX1.15_3459refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EUM

1eum


Resolution: 1.6→51.067 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.55
RfactorNum. reflection% reflection
Rfree0.1891 1539 4.84 %
Rwork0.1582 --
obs0.1597 31807 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.03 Å2 / Biso mean: 34.8093 Å2 / Biso min: 25.17 Å2
Refinement stepCycle: final / Resolution: 1.6→51.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1390 0 3 211 1604
Biso mean--45.2 46.58 -
Num. residues----178
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.6003-1.6520.27871410.23112699
1.652-1.7110.28471490.2022682
1.711-1.77950.22571370.17772680
1.7795-1.86050.22781250.15762711
1.8605-1.95860.20811320.15622723
1.9586-2.08140.2021540.14832710
2.0814-2.24210.17391160.13932736
2.2421-2.46770.1681420.14472742
2.4677-2.82470.17631460.15992768
2.8247-3.55870.16791400.16042819
3.5587-51.0670.19931570.15892998

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