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- PDB-6ls0: rod-shaped crystal of TmFtn mutant-T4FY stimulited by PLL15 -

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Basic information

Entry
Database: PDB / ID: 6ls0
Titlerod-shaped crystal of TmFtn mutant-T4FY stimulited by PLL15
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Iron
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 / 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: 1.87 Å
AuthorsZhao, G. / Zhang, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31730069 China
CitationJournal: To Be Published
Title: rod-shaped crystal of TmFtn mutant-T4FY stimulited by PLL15
Authors: Zhao, G. / Zhang, X.
History
DepositionJan 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,02211
Polymers77,6324
Non-polymers3917
Water6,431357
1
H: Ferritin
B: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0396
Polymers38,8162
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-66 kcal/mol
Surface area15830 Å2
MethodPISA
2
A: Ferritin
hetero molecules

C: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9835
Polymers38,8162
Non-polymers1683
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_454x-1/2,-y+1/2,-z-11
Buried area2890 Å2
ΔGint-51 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.480, 94.120, 109.160
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: 19407.887 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (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


Mass: 55.845 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris base/Hydrochloric acid pH 8.5,

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.87→47.215 Å / Num. obs: 72846 / % possible obs: 99 % / Redundancy: 1 % / CC1/2: 0.996 / Net I/σ(I): 8.5
Reflection shellResolution: 1.87→1.937 Å / Num. unique obs: 7030 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VLG

1vlg


Resolution: 1.87→47.215 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.96
RfactorNum. reflection% reflection
Rfree0.2524 1997 2.75 %
Rwork0.2252 --
obs0.226 72707 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.76 Å2 / Biso mean: 43.5361 Å2 / Biso min: 22.68 Å2
Refinement stepCycle: final / Resolution: 1.87→47.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5432 0 7 357 5796
Biso mean--48.44 46.45 -
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 (%)
1.87-1.91680.52331350.4743480396
1.9168-1.96860.5081410.4077494998
1.9686-2.02650.38641410.30655013100
2.0265-2.09190.36371420.28595049100
2.0919-2.16670.31721420.27454988100
2.1667-2.25350.38521400.3144495498
2.2535-2.3560.31731420.27895062100
2.356-2.48020.3121430.25415060100
2.4802-2.63560.25121430.2475056100
2.6356-2.83910.2391440.2395097100
2.8391-3.12470.25771440.23185093100
3.1247-3.57670.23481430.21585119100
3.5767-4.50580.21071470.18155174100
4.5058-33.650.19011500.1755529398

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