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- PDB-6gkc: 2 minute Fe2+ soak structure of SynFtn -

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Basic information

Entry
Database: PDB / ID: 6gkc
Title2 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 / 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: 1.97 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 1.3Jan 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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)19,9263
Polymers19,8141
Non-polymers1122
Water2,432135
1
A: Ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)478,21472
Polymers475,53324
Non-polymers2,68148
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_657-x+1,y,-z+21
crystal symmetry operation4_577x,-y+2,-z+21
crystal symmetry operation17_557x,z,-y+21
crystal symmetry operation18_655-x+1,z,y1
crystal symmetry operation19_677-x+1,-z+2,-y+21
crystal symmetry operation20_575x,-z+2,y1
crystal symmetry operation57_455y-1/2,z,x+1/21
crystal symmetry operation58_656-y+3/2,z,-x+3/21
crystal symmetry operation59_476y-1/2,-z+2,-x+3/21
crystal symmetry operation60_675-y+3/2,-z+2,x+1/21
crystal symmetry operation69_456z-1/2,y,-x+3/21
crystal symmetry operation70_475z-1/2,-y+2,x+1/21
crystal symmetry operation71_655-z+3/2,y,x+1/21
crystal symmetry operation72_676-z+3/2,-y+2,-x+3/21
crystal symmetry operation77_455z-1/2,x+1/2,y1
crystal symmetry operation78_467z-1/2,-x+3/2,-y+21
crystal symmetry operation79_665-z+3/2,-x+3/2,y1
crystal symmetry operation80_657-z+3/2,x+1/2,-y+21
crystal symmetry operation85_457y-1/2,x+1/2,-z+21
crystal symmetry operation86_667-y+3/2,-x+3/2,-z+21
crystal symmetry operation87_465y-1/2,-x+3/2,z1
crystal symmetry operation88_655-y+3/2,x+1/2,z1
Buried area99520 Å2
ΔGint-1050 kcal/mol
Surface area130780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.157, 177.157, 177.157
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-392-

HOH

21A-433-

HOH

31A-435-

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 / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.92 Å3/Da / Density % sol: 57.92 %
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: I04 / Wavelength: 0.97949 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: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.97→53.41 Å / Num. obs: 16769 / % possible obs: 97.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 32.64 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.044 / Rrim(I) all: 0.084 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.97-2.023.21.07311610.5090.6851.28397.7
9.03-53.412.80.0231970.9990.0150.02890.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
xia2data scaling
PHENIX1.13_2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EUM

1eum


Resolution: 1.97→53.41 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.58
RfactorNum. reflection% reflection
Rfree0.2012 823 4.91 %
Rwork0.1775 --
obs0.1787 16762 96.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.88 Å2 / Biso mean: 33.6594 Å2 / Biso min: 17.05 Å2
Refinement stepCycle: final / Resolution: 1.97→53.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1393 0 2 135 1530
Biso mean--44.99 42.64 -
Num. residues----178
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9704-2.09380.31251210.25382625274697
2.0938-2.25550.21731340.21332603273797
2.2555-2.48250.24331540.19692589274396
2.4825-2.84170.23551400.18672649278997
2.8417-3.58010.18551280.16592706283497
3.5801-53.43450.17041460.15932767291393
Refinement TLS params.Method: refined / Origin x: 50.6822 Å / Origin y: 187.5581 Å / Origin z: 205.7519 Å
111213212223313233
T0.2815 Å20.0174 Å20.0569 Å2-0.3247 Å2-0.0014 Å2--0.3082 Å2
L0.3195 °20.1062 °20.1619 °2-0.2976 °20.1184 °2--0.402 °2
S-0.0029 Å °-0.0571 Å °0.0509 Å °0.0619 Å °0.006 Å °0.1134 Å °-0.0651 Å °-0.0763 Å °-0.0087 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 5 through 182)

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