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- PDB-6lk9: Coho salmon ferritin -

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Basic information

Entry
Database: PDB / ID: 6lk9
TitleCoho salmon ferritin
ComponentsCoho salmon ferritin
KeywordsMETAL BINDING PROTEIN / coho salmon / ferritin
Function / homologyFerritin, core subunit, four-helix bundle / Ferritin / Up-down Bundle / Mainly Alpha / :
Function and homology information
Biological speciesOncorhynchus kisutch (coho salmon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å
AuthorsWang, Z. / Zang, J. / Li, H. / Tan, X. / Du, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31730069 China
CitationJournal: To Be Published
Title: Coho salmon ferritin
Authors: Wang, Z. / Zang, J. / Li, H. / Tan, X. / Du, M.
History
DepositionDec 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
A: Coho salmon ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1302
Polymers20,0741
Non-polymers561
Water1,36976
1
A: Coho salmon ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)483,12748
Polymers481,78724
Non-polymers1,34024
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area97670 Å2
ΔGint-669 kcal/mol
Surface area130850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.092, 182.092, 182.092
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

21A-320-

HOH

31A-343-

HOH

41A-346-

HOH

51A-372-

HOH

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Components

#1: Protein Coho salmon ferritin


Mass: 20074.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oncorhynchus kisutch (coho salmon) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
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: 3.13 Å3/Da / Density % sol: 60.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG 2000 MME,Tris base

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.099→41.775 Å / Num. obs: 15705 / % possible obs: 100 % / Redundancy: 1 % / CC1/2: 1 / Net I/σ(I): 1.35
Reflection shellResolution: 2.099→2.174 Å / Num. unique obs: 1535 / CC1/2: 1

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Processing

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

1fha


Resolution: 2.099→41.775 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.18
RfactorNum. reflection% reflection
Rfree0.2328 772 4.92 %
Rwork0.1959 --
obs0.1978 15705 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.75 Å2 / Biso mean: 23.6158 Å2 / Biso min: 13.24 Å2
Refinement stepCycle: final / Resolution: 2.099→41.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1411 0 1 76 1488
Biso mean--41.37 26.73 -
Num. residues----171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061443
X-RAY DIFFRACTIONf_angle_d0.7811942
X-RAY DIFFRACTIONf_chiral_restr0.046200
X-RAY DIFFRACTIONf_plane_restr0.004257
X-RAY DIFFRACTIONf_dihedral_angle_d16.473873
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.099-2.23020.22551390.18862414
2.2302-2.40240.2469980.19962450
2.4024-2.64410.24661030.20792460
2.6441-3.02660.24321230.21432465
3.0266-3.81280.24611500.20132482
3.8128-41.7750.21651590.18222662

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