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- PDB-7pfj: 20 minute Fe2+ soaked structure of SynFtn Variant E141A -

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Basic information

Entry
Database: PDB / ID: 7pfj
Title20 minute Fe2+ soaked structure of SynFtn Variant E141A
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: 1.65 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)20,5189
Polymers20,1741
Non-polymers3438
Water4,017223
1
A: Ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)492,427216
Polymers484,18424
Non-polymers8,243192
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_545z,-y-1,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_545-z,-y-1,-x1
crystal symmetry operation29_545z,x-1/2,y+1/21
crystal symmetry operation30_544z,-x-1/2,-y-1/21
crystal symmetry operation31_545-z,-x-1/2,y+1/21
crystal symmetry operation32_544-z,x-1/2,-y-1/21
crystal symmetry operation41_544x,z-1/2,-y-1/21
crystal symmetry operation42_545-x,z-1/2,y+1/21
crystal symmetry operation43_544-x,-z-1/2,-y-1/21
crystal symmetry operation44_545x,-z-1/2,y+1/21
crystal symmetry operation81_545y+1/2,z-1/2,x1
crystal symmetry operation82_445-y-1/2,z-1/2,-x1
crystal symmetry operation83_545y+1/2,-z-1/2,-x1
crystal symmetry operation84_445-y-1/2,-z-1/2,x1
crystal symmetry operation85_545y+1/2,x-1/2,-z1
crystal symmetry operation86_445-y-1/2,-x-1/2,-z1
crystal symmetry operation87_545y+1/2,-x-1/2,z1
crystal symmetry operation88_445-y-1/2,x-1/2,z1
Buried area103160 Å2
ΔGint-916 kcal/mol
Surface area129280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.670, 176.670, 176.670
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-207-

NA

31A-454-

HOH

41A-519-

HOH

51A-521-

HOH

61A-523-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ferritin


Mass: 20174.320 Da / Num. of mol.: 1 / Fragment: ferritin / Mutation: E141A
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

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Non-polymers , 5 types, 231 molecules

#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.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 56.8 % / 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: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.59→62.46 Å / Num. obs: 32306 / % possible obs: 100 % / Redundancy: 78.5 % / Biso Wilson estimate: 29.92 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.008 / Rrim(I) all: 0.071 / Net I/σ(I): 41.8 / Num. measured all: 2536613 / Scaling rejects: 4
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
1.59-1.6380.63.25118919823460.8270.3633.2712.1100
7.11-62.4663.50.0292932546210.0040.03154.799.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OUW

5ouw


Resolution: 1.65→40.531 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1743 1412 4.87 %
Rwork0.1502 27570 -
obs0.1513 28982 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.13 Å2 / Biso mean: 31.1358 Å2 / Biso min: 20.98 Å2
Refinement stepCycle: final / Resolution: 1.65→40.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 13 223 1625
Biso mean--55.86 43.14 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051442
X-RAY DIFFRACTIONf_angle_d0.6921964
X-RAY DIFFRACTIONf_chiral_restr0.041220
X-RAY DIFFRACTIONf_plane_restr0.004263
X-RAY DIFFRACTIONf_dihedral_angle_d13.341879
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.65-1.7090.22911330.15622699
1.709-1.77740.22121410.15082686
1.7774-1.85830.19861410.14692692
1.8583-1.95630.16681430.13612708
1.9563-2.07890.20631420.14012724
2.0789-2.23940.16481440.13212713
2.2394-2.46470.17141410.14222758
2.4647-2.82130.18081500.15332752
2.8213-3.55420.14191330.14492826
3.5542-40.5310.18541440.16053012

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