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- PDB-7pf9: SynFtn Variant E141D -

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Basic information

Entry
Database: PDB / ID: 7pf9
TitleSynFtn Variant 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
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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

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Assembly

Deposited unit
A: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3485
Polymers20,2181
Non-polymers1294
Water3,423190
1
A: Ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)488,344120
Polymers485,24024
Non-polymers3,10496
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 area102350 Å2
ΔGint-1105 kcal/mol
Surface area131710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.607, 176.607, 176.607
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Space group name HallF423
Components on special symmetry positions
IDModelComponents
11A-201-

NA

21A-424-

HOH

31A-485-

HOH

41A-490-

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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.84 Å3/Da / Density % sol: 56.66 % / Mosaicity: 0 °
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: 1.52→53.19 Å / Num. obs: 36931 / % possible obs: 100 % / Redundancy: 78.5 % / Biso Wilson estimate: 26.38 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.008 / Rrim(I) all: 0.067 / Net I/σ(I): 46.5
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
1.64-1.6879.13.3816725721140.8130.3813.4022100
7.33-53.1962.50.0272579441310.0030.027181.899.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OUW

5ouw


Resolution: 1.55→40.52 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.1144
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1805 1758 5.08 %
Rwork0.1595 32869 -
obs0.1606 34627 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.86 Å2
Refinement stepCycle: LAST / Resolution: 1.55→40.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1392 0 4 190 1586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511443
X-RAY DIFFRACTIONf_angle_d0.64541967
X-RAY DIFFRACTIONf_chiral_restr0.0391220
X-RAY DIFFRACTIONf_plane_restr0.0043264
X-RAY DIFFRACTIONf_dihedral_angle_d3.9744203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.31071260.26572375X-RAY DIFFRACTION95.42
1.59-1.640.27211190.22862482X-RAY DIFFRACTION99.43
1.64-1.690.24441070.20912525X-RAY DIFFRACTION100
1.69-1.750.22521210.18912479X-RAY DIFFRACTION100
1.75-1.820.20131570.17342473X-RAY DIFFRACTION100
1.82-1.910.21661640.15812465X-RAY DIFFRACTION100
1.91-2.010.18521430.15052501X-RAY DIFFRACTION100
2.01-2.130.18561300.14122527X-RAY DIFFRACTION100
2.13-2.30.16911310.13322527X-RAY DIFFRACTION100
2.3-2.530.18721440.15132530X-RAY DIFFRACTION100
2.53-2.890.16961250.15482591X-RAY DIFFRACTION100
2.89-3.640.17321540.14692583X-RAY DIFFRACTION100
3.64-40.520.16741370.16662811X-RAY DIFFRACTION100

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