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- PDB-7xa0: Thermotoga maritima ferritin variant-Tm-E(S111F) -

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Basic information

Entry
Database: PDB / ID: 7xa0
TitleThermotoga maritima ferritin variant-Tm-E(S111F)
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / protein assembly
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 / 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 speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsYu, L. / Guanghua, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Thermotoga maritima ferritin variant-Tm-E(S111F)
Authors: Yu, L. / Guanghua, Z.
History
DepositionMar 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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


Theoretical massNumber of molelcules
Total (without water)17,4951
Polymers17,4951
Non-polymers00
Water1,35175
1
A: Ferritin

A: Ferritin


Theoretical massNumber of molelcules
Total (without water)34,9892
Polymers34,9892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554-x+y,y,-z-1/31
Buried area2350 Å2
ΔGint-11 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.337, 55.337, 128.818
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-251-

HOH

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Components

#1: Protein Ferritin /


Mass: 17494.680 Da / Num. of mol.: 1 / Mutation: S111F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1128 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0L2, bacterial non-heme ferritin
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.25 Å3/Da / Density % sol: 62.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100mM MES pH 6.0, 200mM Lithium sulfate, 35% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.03→42.94 Å / Num. obs: 15978 / % possible obs: 98.65 % / Redundancy: 1.1 % / CC1/2: 1 / Net I/σ(I): 21.51
Reflection shellResolution: 2.03→2.103 Å / Num. unique obs: 1498 / CC1/2: 1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vlg

1vlg


Resolution: 2.03→42.94 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 23.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2453 1489 10.12 %
Rwork0.2034 13227 -
obs0.2076 14716 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.28 Å2 / Biso mean: 34.5583 Å2 / Biso min: 16.54 Å2
Refinement stepCycle: final / Resolution: 2.03→42.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1200 0 0 75 1275
Biso mean---40.9 -
Num. residues----143
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.03-2.10.2871300.22521151128196
2.1-2.170.2641320.22421190132298
2.17-2.260.2571310.21071173130498
2.26-2.360.29171380.20541190132899
2.36-2.480.27541320.20861184131698
2.48-2.640.25381380.21791208134699
2.64-2.840.2551310.22371185131699
2.84-3.130.27021360.20991222135899
3.13-3.580.25261390.19491219135899
3.58-4.510.23021370.182112341371100
4.52-42.940.2081450.20291271141699

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