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- PDB-7dy9: Thermotoga maritima ferritin mutant-FLAL -

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Basic information

Entry
Database: PDB / ID: 7dy9
TitleThermotoga maritima ferritin mutant-FLAL
ComponentsFerritin
KeywordsRECOMBINATION / Thermotoga maritima ferritin / mutant
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: 2.303 Å
AuthorsZhao, G. / Zhang, X.
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
B: Ferritin
A: Ferritin


Theoretical massNumber of molelcules
Total (without water)38,6902
Polymers38,6902
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-12 kcal/mol
Surface area15920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.305, 83.399, 103.802
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 30% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.987 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: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.303→45 Å / Num. obs: 14942 / % possible obs: 95.24 % / Redundancy: 7.6 % / CC1/2: 0.997 / Net I/σ(I): 6.5
Reflection shellResolution: 2.303→2.64 Å / Num. unique obs: 9361 / CC1/2: 0.935

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VLG

1vlg


Resolution: 2.303→44.065 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 46.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3858 728 4.87 %
Rwork0.2915 14214 -
obs0.2959 14942 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.56 Å2 / Biso mean: 52.5145 Å2 / Biso min: 31.01 Å2
Refinement stepCycle: final / Resolution: 2.303→44.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 0 20 2724
Biso mean---51.62 -
Num. residues----325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112764
X-RAY DIFFRACTIONf_angle_d1.2053724
X-RAY DIFFRACTIONf_chiral_restr0.057389
X-RAY DIFFRACTIONf_plane_restr0.006481
X-RAY DIFFRACTIONf_dihedral_angle_d19.4031646
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3033-2.48110.49291460.384261792
2.4811-2.73080.43311360.3507283098
2.7308-3.12580.4111450.3214283999
3.1258-3.93780.38821340.2899291299
3.9378-7.50.34731670.2541301699

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