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- PDB-6gkb: Iron soak structure of Y40F SynFtn -

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Basic information

Entry
Database: PDB / ID: 6gkb
TitleIron soak structure of Y40F SynFtn
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Ferritin
Function / homology
Function and homology information


bacterial non-heme ferritin / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytosol
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: 1.9 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 / 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)19,9103
Polymers19,7981
Non-polymers1122
Water2,756153
1
A: Ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)477,83072
Polymers475,14924
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 area95820 Å2
ΔGint-713 kcal/mol
Surface area133180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.679, 176.679, 176.679
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-202-

FE

21A-411-

HOH

31A-440-

HOH

41A-448-

HOH

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Components

#1: Protein Ferritin


Mass: 19797.893 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.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.9 Å3/Da / Density % sol: 57.61 %
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: 1.9→62.47 Å / Num. obs: 18124 / % possible obs: 95.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.036 / Rrim(I) all: 0.059 / Net I/σ(I): 14.4
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4 % / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1149 / Rpim(I) all: 0.648 / Rrim(I) all: 1.078 / % possible all: 98.1

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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: 1.9→62.465 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.27
RfactorNum. reflection% reflection
Rfree0.2099 906 5 %
Rwork0.167 --
obs0.169 18123 94.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.05 Å2 / Biso mean: 39.4616 Å2 / Biso min: 24.81 Å2
Refinement stepCycle: final / Resolution: 1.9→62.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1392 0 2 153 1547
Biso mean--46.4 48.77 -
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 (%)
1.9003-2.01940.29441570.24452829298696
2.0194-2.17530.23131640.18312834299897
2.1753-2.39420.19761330.16322866299995
2.3942-2.74070.2191690.16882832300195
2.7407-3.4530.21151300.16872894302494
3.453-62.49920.19661530.15672962311591
Refinement TLS params.Method: refined / Origin x: 50.6379 Å / Origin y: 187.0773 Å / Origin z: 205.1403 Å
111213212223313233
T0.2552 Å20.0275 Å20.0995 Å2-0.3324 Å2-0.012 Å2--0.2965 Å2
L0.6245 °20.1988 °20.3158 °2-0.5713 °20.245 °2--0.8174 °2
S0.0097 Å °-0.1471 Å °0.0964 Å °0.1525 Å °-0.0216 Å °0.1877 Å °-0.0415 Å °-0.1678 Å °0.0045 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 182
2X-RAY DIFFRACTION1allB1 - 3
3X-RAY DIFFRACTION1allS1 - 153

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