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- PDB-7dy8: Thermotoga maritima ferritin mutant-FLAL -

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Basic information

Entry
Database: PDB / ID: 7dy8
TitleThermotoga maritima ferritin mutant-FLAL
ComponentsFerritin
KeywordsRECOMBINATION / Thermotoga maritima ferritin
Function / homology
Function and homology information


bacterial non-heme ferritin / ferroxidase activity / ferric iron binding / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / identical protein binding / cytoplasm / cytosol
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: 2.103 Å
AuthorsZhang, X. / Zhao, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31730069 China
CitationJournal: Nat Commun / Year: 2021
Title: Protein interface redesign facilitates the transformation of nanocage building blocks to 1D and 2D nanomaterials.
Authors: Zhang, X. / Liu, Y. / Zheng, B. / Zang, J. / Lv, C. / Zhang, T. / Wang, H. / Zhao, G.
History
DepositionJan 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: 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
H: Ferritin
A: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,11411
Polymers38,6902
Non-polymers4249
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-113 kcal/mol
Surface area15750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.418, 85.981, 107.090
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: 19344.898 Da / Num. of mol.: 2 / Mutation: E112L, E113A, K114L, N147F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1128 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0L2, bacterial non-heme ferritin
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.1M Ca(Ac)2, 20% PEG 1000, and 100 mM Imidazole/HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.103→29.1 Å / Num. obs: 21568 / % possible obs: 98.44 % / Redundancy: 7.3 % / CC1/2: 0.982 / Net I/σ(I): 22.845
Reflection shellResolution: 2.103→2.179 Å / Num. unique obs: 2073 / CC1/2: 0.969

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VLG

1vlg


Resolution: 2.103→29.054 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2646 1997 9.27 %
Rwork0.2118 19542 -
obs0.2167 21539 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.08 Å2 / Biso mean: 40.083 Å2 / Biso min: 23.09 Å2
Refinement stepCycle: final / Resolution: 2.103→29.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 9 26 2739
Biso mean--50.67 37.51 -
Num. residues----325
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1035-2.15610.31891360.235132695
2.1561-2.21440.32651400.23971368100
2.2144-2.27950.37451330.2572131794
2.2795-2.3530.29481410.2253138499
2.353-2.43710.29391430.22421397100
2.4371-2.53460.25691430.21431387100
2.5346-2.64990.29221440.22911416100
2.6499-2.78950.30511430.2295140099
2.7895-2.96410.27741420.23421386100
2.9641-3.19270.29141440.2351140799
3.1927-3.51350.25731430.2232140198
3.5135-4.02080.25551430.2045140298
4.0208-5.06140.2021460.1783142097
5.0614-6.50.24871560.19121531100

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