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- PDB-7dl5: Crystal structure of Thermotoga Maritima ferritin mutant at 2.3 A... -

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Basic information

Entry
Database: PDB / ID: 7dl5
TitleCrystal structure of Thermotoga Maritima ferritin mutant at 2.3 Angstrom resolution
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


bacterial non-heme ferritin / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / 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: 2.3 Å
AuthorsLiu, Y. / Leng, X. / Zang, J. / Zhao, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)No. 31671805 and 31730069 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: A short helix regulates conversion of dimeric and 24-meric ferritin architectures.
Authors: Liu, Y. / Zang, J. / Leng, X. / Zhao, G.
History
DepositionNov 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 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)34,86410
Polymers34,6072
Non-polymers2588
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-63 kcal/mol
Surface area13800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.093, 107.093, 110.589
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11H-202-

MG

21A-203-

MG

31H-345-

HOH

41H-375-

HOH

51A-350-

HOH

61A-369-

HOH

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Components

#1: Protein Ferritin /


Mass: 17303.385 Da / Num. of mol.: 2
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: Tmari_1134 / Production host: Escherichia coli (E. coli) / References: UniProt: G4FEM0, bacterial non-heme ferritin
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 3.56 Å3/Da / Density % sol: 65.48 %
Crystal growTemperature: 293.2 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.5 1.6M Magnesium Sulfate Hexahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9787 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.3→29.61 Å / Num. obs: 20913 / % possible obs: 99.68 % / Redundancy: 2.5 % / Biso Wilson estimate: 38.22 Å2 / CC1/2: 0.99 / Net I/σ(I): 5.5
Reflection shellResolution: 2.3→2.384 Å / Num. unique obs: 2059 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VLG

1vlg


Resolution: 2.3→29.61 Å / SU ML: 0.2783 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 23.5291
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2274 2013 9.63 %
Rwork0.1777 18891 -
obs0.1824 20904 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.82 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 8 151 2570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742486
X-RAY DIFFRACTIONf_angle_d0.76823349
X-RAY DIFFRACTIONf_chiral_restr0.0423347
X-RAY DIFFRACTIONf_plane_restr0.0043432
X-RAY DIFFRACTIONf_dihedral_angle_d4.5301319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.28831390.21171313X-RAY DIFFRACTION98.04
2.36-2.420.25631420.19181362X-RAY DIFFRACTION100
2.42-2.490.23211490.19551368X-RAY DIFFRACTION100
2.49-2.570.23631420.18431359X-RAY DIFFRACTION100
2.57-2.670.22781450.18521356X-RAY DIFFRACTION100
2.67-2.770.28891410.18571330X-RAY DIFFRACTION100
2.77-2.90.27271440.18231365X-RAY DIFFRACTION99.8
2.9-3.050.20921440.17571343X-RAY DIFFRACTION99.93
3.05-3.240.26381430.17971355X-RAY DIFFRACTION100
3.24-3.490.20651440.18061347X-RAY DIFFRACTION99.93
3.49-3.840.23081450.17141360X-RAY DIFFRACTION99.87
3.84-4.40.21391440.1711343X-RAY DIFFRACTION99.8
4.4-5.530.18481440.17061353X-RAY DIFFRACTION99.67
5.54-29.610.23251470.17331337X-RAY DIFFRACTION99.13
Refinement TLS params.Method: refined / Origin x: -27.4052487341 Å / Origin y: -14.7261557493 Å / Origin z: 36.4947159836 Å
111213212223313233
T0.31912204809 Å20.0317497008637 Å2-0.0131425006114 Å2-0.284196623101 Å2-0.0120915310943 Å2--0.340355325181 Å2
L1.13025150986 °20.439135454683 °20.246182337634 °2-0.624328660192 °20.128978608324 °2--0.40211929884 °2
S0.024030226488 Å °0.034385381744 Å °-0.0496193982163 Å °0.0365474649942 Å °-0.0213206150059 Å °-0.0342570106873 Å °0.0285022404241 Å °0.0417013673157 Å °-0.00284403775843 Å °
Refinement TLS groupSelection details: all

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