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- PDB-6txn: Crystal structure of thermotoga maritima Ferritin in apo form -

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Basic information

Entry
Database: PDB / ID: 6txn
TitleCrystal structure of thermotoga maritima Ferritin in apo form
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Metal binding / engineered protein
Function / homology
Function and homology information


bacterial non-heme ferritin / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / intracellular iron ion homeostasis / 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsWilk, P. / Grudnik, P. / Kumar, M. / Heddle, J. / Chakraborti, S.
Funding support Poland, 1items
OrganizationGrant numberCountry
Foundation for Polish ScienceHoming/2017-3/22 Poland
CitationJournal: Nanoscale / Year: 2021
Title: A single residue can modulate nanocage assembly in salt dependent ferritin.
Authors: Kumar, M. / Markiewicz-Mizera, J. / Janna Olmos, J.D. / Wilk, P. / Grudnik, P. / Biela, A.P. / Jemiola-Rzeminska, M. / Gorecki, A. / Chakraborti, S. / Heddle, J.G.
History
DepositionJan 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,61342
Polymers155,2158
Non-polymers3,39834
Water11,584643
1
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)475,839126
Polymers465,64424
Non-polymers10,195102
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area96420 Å2
ΔGint-1017 kcal/mol
Surface area147920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.020, 176.020, 356.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Ferritin


Mass: 19401.840 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Gene: TM_1128 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0L2, bacterial non-heme ferritin

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Non-polymers , 5 types, 677 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H42 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 643 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.42 Å3/Da / Density % sol: 64.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2 M MgCl2, 2.4 M (NH4)2 SO4, 0.1M MES. pH 6.0. 1ul of 10mg/mL protein was mixed with same amount of well solution, crystals normally appears in 2 days

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.978631 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 30, 2018
RadiationMonochromator: 0.978631 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978631 Å / Relative weight: 1
ReflectionResolution: 2.01→49.22 Å / Num. obs: 140330 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.084 / Net I/σ(I): 11
Reflection shellResolution: 2.01→7.78 Å / Rmerge(I) obs: 1.526 / Num. unique obs: 13704 / CC1/2: 0.395 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vlg

1vlg


Resolution: 2.01→48.276 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.83
RfactorNum. reflection% reflection
Rfree0.2214 1999 1.42 %
Rwork0.1931 --
obs0.1935 140306 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 343.19 Å2 / Biso mean: 57.4759 Å2 / Biso min: 27.95 Å2
Refinement stepCycle: final / Resolution: 2.01→48.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10916 0 406 643 11965
Biso mean--76.93 53.1 -
Num. residues----1312
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.01-2.06030.29841410.3219833100
2.0603-2.1160.30351420.28919811100
2.116-2.17830.28081420.26869785100
2.1783-2.24860.28211420.24989816100
2.2486-2.32890.28671420.24199839100
2.3289-2.42220.26711420.22519842100
2.4222-2.53240.25781420.21999840100
2.5324-2.66590.27351430.22169857100
2.6659-2.83290.27871430.21919877100
2.8329-3.05160.28141420.20689865100
3.0516-3.35870.22281430.1979870100
3.3587-3.84450.1871440.17599936100
3.8445-4.84290.16161430.15079967100
4.8429-48.2760.20231480.17361016999

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