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- PDB-7v4v: polylysine induce assembly of Thermotoga maritima ferritin -

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Basic information

Entry
Database: PDB / ID: 7v4v
Titlepolylysine induce assembly of Thermotoga maritima ferritin
ComponentsFerritin
KeywordsPEPTIDE BINDING PROTEIN / polylysine / Thermotoga maritima ferritin / 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 MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhang, X. / Zhao, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31972018 China
CitationJournal: To Be Published
Title: polylysine induce assembly of Thermotoga maritima ferritin
Authors: Zhang, X. / Zhao, G.
History
DepositionAug 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2022Provider: 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

Downloads & links

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Assembly

Deposited unit
H: Ferritin
A: Ferritin
B: Ferritin
C: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,05412
Polymers77,6074
Non-polymers4478
Water2,180121
1
C: Ferritin
hetero molecules

H: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0276
Polymers38,8042
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area3000 Å2
ΔGint-66 kcal/mol
Surface area15580 Å2
MethodPISA
2
A: Ferritin
B: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0276
Polymers38,8042
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-66 kcal/mol
Surface area15510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.808, 94.495, 108.121
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: 19401.840 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / Gene: TM_1128 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0L2, bacterial non-heme ferritin
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.97919 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.3→38.78 Å / Num. obs: 38772 / % possible obs: 98.69 % / Redundancy: 10 % / CC1/2: 0.996 / Net I/σ(I): 8.5
Reflection shellResolution: 2.3→2.382 Å / CC1/2: 0.996

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VLG

1vlg


Resolution: 2.3→38.687 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 1998 5.15 %
Rwork0.2013 36761 -
obs0.2042 38759 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.89 Å2 / Biso mean: 57.1346 Å2 / Biso min: 27.21 Å2
Refinement stepCycle: final / Resolution: 2.3→38.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5428 0 8 121 5557
Biso mean--61.26 50.44 -
Num. residues----651
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3001-2.35760.37291250.2823230888
2.3576-2.42140.32341360.2627248595
2.4214-2.49260.31051420.24472622100
2.4926-2.5730.30051420.232609100
2.573-2.6650.29681410.2282613100
2.665-2.77170.29011440.21962639100
2.7717-2.89780.26581410.2212617100
2.8978-3.05050.28551460.21812674100
3.0505-3.24150.32061430.22522639100
3.2415-3.49170.29991450.22652662100
3.4917-3.84270.2821460.19622668100
3.8427-4.39810.2191450.17772685100
4.3981-5.53860.2011480.1682720100
5.5386-80.21691540.1804282099

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