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- PDB-7x9z: Thermotoga maritima ferritin variant-Tm-E(G40E) with Co -

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Basic information

Entry
Database: PDB / ID: 7x9z
TitleThermotoga maritima ferritin variant-Tm-E(G40E) with Co
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: 2.29 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(G40E) with Co
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
B: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,66213
Polymers35,0132
Non-polymers64811
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-137 kcal/mol
Surface area14890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.517, 65.809, 91.064
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ferritin /


Mass: 17506.645 Da / Num. of mol.: 2 / Mutation: G40E
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: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25mM HEPES, pH 8.0, 55% MPD, 5mM Cobalt chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 1.597735 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.597735 Å / Relative weight: 1
ReflectionResolution: 2.29→53.34 Å / Num. obs: 29843 / % possible obs: 98.61 % / Redundancy: 2 % / CC1/2: 0.991 / Net I/σ(I): 13.89
Reflection shellResolution: 2.29→2.372 Å / Num. unique obs: 2470 / CC1/2: 0.976

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Processing

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

1vlg


Resolution: 2.29→53.34 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 2781 10.03 %
Rwork0.1881 24948 -
obs0.1939 27729 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.5 Å2 / Biso mean: 23.5665 Å2 / Biso min: 8.04 Å2
Refinement stepCycle: final / Resolution: 2.29→53.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2424 0 11 38 2473
Biso mean--47.23 23.91 -
Num. residues----289
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.29-2.330.25571030.1663973107677
2.33-2.370.24081310.18411142127386
2.37-2.420.26851380.18941197133596
2.42-2.470.23721330.18491255138899
2.47-2.520.241430.18991284142798
2.52-2.580.26081440.193612861430100
2.58-2.640.32431380.213512711409100
2.64-2.720.29451440.22011269141398
2.72-2.80.29041430.19712651408100
2.8-2.890.26031440.190912711415100
2.89-2.990.2291400.204912671407100
2.99-3.110.26621430.191412901433100
3.11-3.250.24231440.202912691413100
3.25-3.420.21381440.191299144399
3.42-3.630.27711370.19471273141099
3.64-3.920.23921450.17631257140299
3.92-4.310.2241420.156412811423100
4.31-4.930.18071470.153412691416100
4.93-6.210.27171390.218312891428100
6.21-53.340.24141390.19051241138097

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