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- PDB-6lij: Crassostrea gigas ferritin -

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Basic information

Entry
Database: PDB / ID: 6lij
TitleCrassostrea gigas ferritin
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Crassostrea gigas / Ferritin / 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: 2.1 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
Authors: Li, H. / Zang, J. / Tan, X. / Wang, Z. / Du, M.
History
DepositionDec 11, 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)19,8192
Polymers19,7951
Non-polymers241
Water1,20767
1
A: Ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)475,66148
Polymers475,07824
Non-polymers58324
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
crystal symmetry operation13_554y,x,-z-11
crystal symmetry operation14_554-y,-x,-z-11
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation33_554y,z+1/2,x-1/21
crystal symmetry operation34_554-y,z+1/2,-x-1/21
crystal symmetry operation35_544y,-z-1/2,-x-1/21
crystal symmetry operation36_544-y,-z-1/2,x-1/21
crystal symmetry operation41_554x,z+1/2,-y-1/21
crystal symmetry operation42_554-x,z+1/2,y-1/21
crystal symmetry operation43_544-x,-z-1/2,-y-1/21
crystal symmetry operation44_544x,-z-1/2,y-1/21
crystal symmetry operation53_554z+1/2,x,y-1/21
crystal symmetry operation54_554z+1/2,-x,-y-1/21
crystal symmetry operation55_454-z-1/2,-x,y-1/21
crystal symmetry operation56_454-z-1/2,x,-y-1/21
crystal symmetry operation69_554z+1/2,y,-x-1/21
crystal symmetry operation70_554z+1/2,-y,x-1/21
crystal symmetry operation71_454-z-1/2,y,x-1/21
crystal symmetry operation72_454-z-1/2,-y,-x-1/21
Buried area98460 Å2
ΔGint-344 kcal/mol
Surface area131740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.007, 183.007, 183.007
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-350-

HOH

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Components

#1: Protein Ferritin


Mass: 19794.918 Da / Num. of mol.: 1
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.23 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: Magnesium chloride hexahydrate, Tris(hydroxymethyl)aminomethane, 1,6-Hexanediol

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.1→35.22 Å / Num. obs: 15887 / % possible obs: 100 % / Redundancy: 3 % / CC1/2: 0.75 / Net I/σ(I): 1.36
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 1533 / CC1/2: 0.75

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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: 2.1→35.22 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.4
RfactorNum. reflection% reflection
Rfree0.2304 789 4.97 %
Rwork0.1928 --
obs0.1946 15882 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 57.51 Å2 / Biso mean: 22.9449 Å2 / Biso min: 15.43 Å2
Refinement stepCycle: final / Resolution: 2.1→35.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1387 0 1 67 1455
Biso mean--17.53 24.14 -
Num. residues----169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071411
X-RAY DIFFRACTIONf_angle_d0.7241895
X-RAY DIFFRACTIONf_chiral_restr0.045194
X-RAY DIFFRACTIONf_plane_restr0.004254
X-RAY DIFFRACTIONf_dihedral_angle_d16.791860
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1003-2.23190.2611280.18592449
2.2319-2.40420.20921400.19692444
2.4042-2.64610.23731340.19382451
2.6461-3.02880.22621300.20792507
3.0288-3.81520.26661210.2072531
3.8152-35.220.20661360.17562711

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