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- PDB-6gka: 20 minute Fe2+ soak structure of SynFtn -

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Basic information

Entry
Database: PDB / ID: 6gka
Title20 minute Fe2+ soak 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 / Resolution: 1.76 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
DepositionMay 18, 2018Deposition 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 1.3May 15, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)20,0175
Polymers19,8141
Non-polymers2034
Water3,999222
1
A: Ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)480,405120
Polymers475,53324
Non-polymers4,87296
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
Buried area102600 Å2
ΔGint-1344 kcal/mol
Surface area132120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.260, 177.260, 177.260
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-203-

FE

21A-452-

HOH

31A-519-

HOH

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Components

#1: Protein Ferritin


Mass: 19813.893 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: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / 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.: 222 / 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: 2.93 Å3/Da / Density % sol: 57.99 %
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
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97953 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97953 Å / Relative weight: 1
ReflectionResolution: 1.76→53.45 Å / Num. obs: 23392 / % possible obs: 97.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 26.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.028 / Rrim(I) all: 0.059 / Net I/σ(I): 15.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.76-1.83.50.73112990.5850.4280.85495.5
8.98-53.453.30.0272090.9990.0150.03191.8

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
PHENIXphasing
RefinementResolution: 1.76→40.666 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.2
RfactorNum. reflection% reflection
Rfree0.1865 1156 4.94 %
Rwork0.1565 --
obs0.158 23389 96.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.02 Å2 / Biso mean: 28.6336 Å2 / Biso min: 16.91 Å2
Refinement stepCycle: final / Resolution: 1.76→40.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1393 0 4 222 1619
Biso mean--29.32 40.94 -
Num. residues----178
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7604-1.84050.31111380.27222701283996
1.8405-1.93760.25841370.20822730286797
1.9376-2.0590.22931430.18172675281895
2.059-2.21790.17861270.15712705283295
2.2179-2.44110.19921540.15382735288996
2.4411-2.79420.18591280.162833296198
2.7942-3.52010.18451490.14492894304399
3.5201-40.67710.16251800.1422960314096
Refinement TLS params.Method: refined / Origin x: 28.6083 Å / Origin y: -10.3594 Å / Origin z: -37.8779 Å
111213212223313233
T0.2145 Å20.0018 Å20.0456 Å2-0.2146 Å2-0.0189 Å2--0.1907 Å2
L1.0495 °2-0.5132 °20.7374 °2-0.6405 °2-0.5071 °2--0.7632 °2
S0.0295 Å °0.0857 Å °-0.0452 Å °-0.0932 Å °-0.0309 Å °-0.0424 Å °0.0776 Å °0.0938 Å °0.0024 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 5 through 182)

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