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- PDB-6ls3: cubic-shaped crystal of TmFtn mutant-T4FY stimulated by Mg -

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Basic information

Entry
Database: PDB / ID: 6ls3
Titlecubic-shaped crystal of TmFtn mutant-T4FY stimulated by Mg
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Mg
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: 2.815 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: cubic-shaped crystal of TmFtn mutant-T4FY stimulated by Mg
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)156,19827
Polymers155,2638
Non-polymers93519
Water54030
1
B: Ferritin
E: Ferritin
A: Ferritin
C: Ferritin
D: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)468,59481
Polymers465,78924
Non-polymers2,80557
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area76930 Å2
ΔGint-939 kcal/mol
Surface area152630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.737, 171.737, 384.289
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein
Ferritin


Mass: 19407.887 Da / Num. of mol.: 8
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.: 15 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.51 Å3/Da / Density % sol: 64.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Potassium phosphate monobasic, Sodium phosphate dibasic pH 6.2, and 2500 mM Sodium chloride, 60 mM MgCl2

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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 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.815→138.703 Å / Num. obs: 50424 / % possible obs: 95 % / Redundancy: 5 % / Biso Wilson estimate: 76.05 Å2 / CC1/2: 0.999 / Net I/σ(I): 4.64
Reflection shellResolution: 2.815→2.961 Å / Num. unique obs: 5252 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VLG

1vlg


Resolution: 2.815→138.703 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.75
RfactorNum. reflection% reflection
Rfree0.2427 2427 4.82 %
Rwork0.1868 --
obs0.1895 50348 94.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.8 Å2 / Biso mean: 67.876 Å2 / Biso min: 35.82 Å2
Refinement stepCycle: final / Resolution: 2.815→138.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10928 0 19 30 10977
Biso mean--86.05 62.03 -
Num. residues----1310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911168
X-RAY DIFFRACTIONf_angle_d0.95215028
X-RAY DIFFRACTIONf_chiral_restr0.0521550
X-RAY DIFFRACTIONf_plane_restr0.0051942
X-RAY DIFFRACTIONf_dihedral_angle_d18.1816684
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8153-2.87280.29431320.26722943100
2.8728-2.93530.30441460.25662946100
2.9353-3.00360.30371460.2432951100
3.0036-3.07870.31971610.25142918100
3.0787-3.16190.32171370.24692970100
3.1619-3.2550.3171640.23352913100
3.255-3.36010.31351570.22882959100
3.3601-3.48020.2851940.2266176460
3.4802-3.61950.30171410.22782962100
3.6195-3.78420.26641130.2112229377
3.7842-3.98380.27221180.2029226477
3.9838-4.23340.22651550.16992968100
4.2334-4.56030.19981440.1592981100
4.5603-5.01920.19671560.15512990100
5.0192-5.74550.24121500.17713009100
5.7455-7.23870.25621570.18873009100
7.2387-138.70.18581560.146308198

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