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- PDB-7pfh: 2 minute Fe2+ soak structure of SynFtn E141D -

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Basic information

Entry
Database: PDB / ID: 7pfh
Title2 minute Fe2+ soak structure of SynFtn E141D
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / iron binding protein
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
ACETATE ION / : / Ferritin
Similarity search - Component
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
Model detailsstructure determined from crystals of SynFtn D65A that have not been soaked in Fe2+
AuthorsHemmings, A.M. / Bradley, J.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R002363/1 United Kingdom
CitationJournal: Microbiology (Reading, Engl.) / Year: 2021
Title: Key carboxylate residues for iron transit through the prokaryotic ferritin Syn Ftn.
Authors: Bradley, J.M. / Fair, J. / Hemmings, A.M. / Le Brun, N.E.
History
DepositionAug 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5518
Polymers20,2181
Non-polymers3337
Water3,657203
1
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
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
hetero molecules

A: Ferritin
hetero molecules

A: Ferritin
hetero molecules

A: Ferritin
hetero molecules

A: Ferritin
hetero molecules

A: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)493,230192
Polymers485,24024
Non-polymers7,991168
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)176.870, 176.870, 176.870
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-450-

HOH

31A-497-

HOH

41A-500-

HOH

51A-503-

HOH

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Components

#1: Protein Ferritin


Mass: 20218.330 Da / Num. of mol.: 1 / Fragment: ferritin / Mutation: E141D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (strain CC9311) (bacteria)
Strain: CC9311 / Gene: sync_1539 / Plasmid: pET21a / 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.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.85 Å3/Da / Density % sol: 56.85 % / Mosaicity: 0.051 °
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 2M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.41→53.3 Å / Num. obs: 45787 / % possible obs: 99.7 % / Redundancy: 15 % / Rpim(I) all: 0.011 / Rrim(I) all: 0.047 / Net I/σ(I): 23.3 / Num. measured all: 685729
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.41-1.444.10.2889221920.8711.80296.9
3.83-53.34171284368925630.0070.02999.7

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OUW

5ouw


Resolution: 1.5→44.218 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1711 1810 4.72 %
Rwork0.1527 36577 -
obs0.1536 38387 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.7 Å2 / Biso mean: 30.7856 Å2 / Biso min: 21.6 Å2
Refinement stepCycle: final / Resolution: 1.5→44.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1392 0 13 203 1608
Biso mean--54.21 42.44 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041450
X-RAY DIFFRACTIONf_angle_d0.6611977
X-RAY DIFFRACTIONf_chiral_restr0.041221
X-RAY DIFFRACTIONf_plane_restr0.004266
X-RAY DIFFRACTIONf_dihedral_angle_d12.412886
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5002-1.54080.24481320.21122758100
1.5408-1.58610.2241380.1692273099
1.5861-1.63730.19091410.14732752100
1.6373-1.69580.18321320.13532774100
1.6958-1.76370.171120.13632787100
1.7637-1.8440.18041460.13272770100
1.844-1.94120.15581560.1342755100
1.9412-2.06280.15861340.14562810100
2.0628-2.22210.16681480.13652801100
2.2221-2.44570.16031370.14922810100
2.4457-2.79950.17491330.15662864100
2.7995-3.52690.15531430.14932888100
3.5269-44.2180.18011580.16223078100

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