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- PDB-7x9x: Thermotoga Maritima ferritin variant-Tm-E(G40E) with Zn -

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Basic information

Entry
Database: PDB / ID: 7x9x
TitleThermotoga Maritima ferritin variant-Tm-E(G40E) with Zn
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / protein assembly
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, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLiu, Y. / Zhao, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Nano / Year: 2022
Title: Directed Self-Assembly of Dimeric Building Blocks into Networklike Protein Origami to Construct Hydrogels.
Authors: Liu, Y. / Chen, X. / Yin, S. / Chang, X. / Lv, C. / Zang, J. / Leng, X. / Zhang, T. / Zhao, G.
History
DepositionMar 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 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)35,56411
Polymers35,0132
Non-polymers5509
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-254 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.500, 66.620, 92.340
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25mM HEPES pH 8.0, 35% MPD, 2mM Zinc chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 1.276911 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.276911 Å / Relative weight: 1
ReflectionResolution: 2.3→28.56 Å / Num. obs: 31502 / % possible obs: 99.69 % / Redundancy: 1.9 % / CC1/2: 0.997 / Net I/σ(I): 5.9
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 3042 / CC1/2: 0.699

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VLG

1vlg


Resolution: 2.3→28.56 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2511 2915 9.95 %
Rwork0.1896 26369 -
obs0.1957 29284 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.16 Å2 / Biso mean: 40.5182 Å2 / Biso min: 17.15 Å2
Refinement stepCycle: final / Resolution: 2.3→28.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2424 0 9 26 2459
Biso mean--39.18 33.3 -
Num. residues----289
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.340.34581350.291612231358100
2.34-2.380.30581410.290712591400100
2.38-2.420.31921420.270112601402100
2.42-2.470.31351400.253512491389100
2.47-2.520.28721390.232712771416100
2.52-2.570.3141340.227212461380100
2.57-2.630.25951430.223112681411100
2.63-2.70.31661370.216712631400100
2.7-2.770.25461420.202212561398100
2.77-2.850.26381330.20071226135999
2.85-2.940.23531390.191212811420100
2.94-3.050.25941450.192212361381100
3.05-3.170.29371390.191812891428100
3.17-3.320.23971430.185712421385100
3.32-3.490.24441370.175112711408100
3.49-3.710.27641440.17512641408100
3.71-3.990.22891380.164312421380100
3.99-4.390.18811380.13912561394100
4.4-5.030.17051320.134212581390100
5.03-6.320.24321420.199112651407100
6.32-28.560.26531320.18341238137098

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