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- PDB-7dlb: Crassostrea gigas ferritin mutant-D119K -

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Basic information

Entry
Database: PDB / ID: 7dlb
TitleCrassostrea gigas ferritin mutant-D119K
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Crassostrea gigas / Ferritin / Iron
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain ...Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesCrassostrea gigas (Pacific oyster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsLi, H. / Zang, J. / Wang, Z. / Du, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31730069 China
CitationJournal: To Be Published
Title: Crassostrea gigas ferritin mutant-D119K
Authors: Li, H. / Zang, J. / Wang, Z. / Du, M.
History
DepositionNov 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 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
A: Ferritin
B: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1344
Polymers40,0232
Non-polymers1122
Water2,180121
1
A: Ferritin
B: Ferritin
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)481,61148
Polymers480,27124
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
Buried area101660 Å2
ΔGint-434 kcal/mol
Surface area129340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.702, 150.702, 150.702
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

21A-305-

HOH

31B-302-

HOH

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Components

#1: Protein Ferritin


Mass: 20011.283 Da / Num. of mol.: 2 / Mutation: D119K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crassostrea gigas (Pacific oyster) / Gene: fer, CGI_10027591 / Production host: Escherichia coli (E. coli) / References: UniProt: Q70MM3, ferroxidase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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 K / Method: evaporation / Details: MPD, Tris base/ Hydrochloric acid, Sodium chloride

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9375 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9375 Å / Relative weight: 1
ReflectionResolution: 2.5→29.555 Å / Num. obs: 19777 / % possible obs: 100 % / Redundancy: 9.5 % / CC1/2: 1 / Net I/σ(I): 5.1
Reflection shellResolution: 2.5→2.592 Å / Num. unique obs: 1972 / CC1/2: 1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FHA

1fha


Resolution: 2.502→29.555 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2405 1010 5.11 %
Rwork0.195 --
obs0.1976 19749 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.2 Å2 / Biso mean: 41.4874 Å2 / Biso min: 27.84 Å2
Refinement stepCycle: final / Resolution: 2.502→29.555 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2776 0 2 121 2899
Biso mean--54.22 44.33 -
Num. residues----338

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