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- PDB-6ljg: Crassostrea gigas ferritin mutant-D119G -

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Basic information

Entry
Database: PDB / ID: 6ljg
TitleCrassostrea gigas ferritin mutant-D119G
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Crassostrea gigas / ferritin / mutant / iron
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / 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, core subunit, four-helix bundle / Ferritin / 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: 1.799 Å
AuthorsLi, H. / Zang, J. / Tan, X. / 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-D119G
Authors: Li, H. / Zang, J. / Tan, X. / Wang, Z. / Du, M.
History
DepositionDec 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 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: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9242
Polymers19,8681
Non-polymers561
Water3,801211
1
A: Ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)478,17448
Polymers476,83424
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 area100260 Å2
ΔGint-457 kcal/mol
Surface area133250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.134, 151.134, 151.134
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-450-

HOH

21A-459-

HOH

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Components

#1: Protein Ferritin


Mass: 19868.078 Da / Num. of mol.: 1 / Mutation: D119G
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.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 3.62 Å3/Da / Density % sol: 66.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG 8000, CAPS/Sodium hydroxide, Sodium chloride

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.799→26.72 Å / Num. obs: 27659 / % possible obs: 99.93 % / Redundancy: 38.8 % / CC1/2: 1 / Net I/σ(I): 311
Reflection shellResolution: 1.799→1.864 Å / Num. unique obs: 2700 / CC1/2: 1

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Processing

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

1fha


Resolution: 1.799→26.717 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.21
RfactorNum. reflection% reflection
Rfree0.2147 2000 7.25 %
Rwork0.192 --
obs0.1936 27569 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 60.74 Å2 / Biso mean: 29.2704 Å2 / Biso min: 16.44 Å2
Refinement stepCycle: final / Resolution: 1.799→26.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1391 0 1 211 1603
Biso mean--28.87 38.55 -
Num. residues----170
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.799-1.84390.30481410.2931813
1.8439-1.89380.31181400.29851772
1.8938-1.94950.31981390.27621787
1.9495-2.01240.29921410.26961805
2.0124-2.08430.26361410.25221794
2.0843-2.16770.27811410.23451801
2.1677-2.26630.2371410.2121804
2.2663-2.38570.25391410.2141822
2.3857-2.53510.20921420.20921802
2.5351-2.73070.24971430.19491828
2.7307-3.00510.24311430.18491833
3.0051-3.43920.18331450.17111855
3.4392-4.330.15611470.1461867
4.33-26.7170.18341550.1711986

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