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- PDB-8w91: Azumapecten Farreri homopolymeric ferritin mutant - H2KE exposed ... -

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Basic information

Entry
Database: PDB / ID: 8w91
TitleAzumapecten Farreri homopolymeric ferritin mutant - H2KE exposed to H2O2 for 3 min
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / enzyme
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, conserved site / 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 speciesAzumapecten farreri (Farrer's scallop)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsZhang, T. / Jiao, R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Inorg.Chem. / Year: 2024
Title: Structural Insights into the Reaction between Hydrogen Peroxide and Di-iron Complexes at the Ferroxidase Center of Ferritin.
Authors: Jiao, R. / Zhao, G. / Zhang, T.
History
DepositionSep 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
b: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1284
Polymers19,9601
Non-polymers1683
Water3,351186
1
b: Ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)483,06996
Polymers479,04824
Non-polymers4,02172
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 area93350 Å2
ΔGint-217 kcal/mol
Surface area131500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.716, 153.716, 153.716
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11b-203-

FE

21b-417-

HOH

31b-446-

HOH

41b-478-

HOH

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Components

#1: Protein Ferritin


Mass: 19960.330 Da / Num. of mol.: 1 / Mutation: H10K,H121E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azumapecten farreri (Farrer's scallop) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A173CSP7
#2: Chemical ChemComp-FE / FE (III) ION


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


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.79 Å3/Da / Density % sol: 67.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM MOPS, pH 7, 500 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 1.6314 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6314 Å / Relative weight: 1
ReflectionResolution: 2.12→48.61 Å / Num. obs: 16848 / % possible obs: 94.28 % / Redundancy: 23.8 % / CC1/2: 0.999 / Net I/σ(I): 21.4
Reflection shellResolution: 2.122→2.198 Å / Num. unique obs: 1176 / CC1/2: 0.669

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→48.61 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1835 1480 4.76 %
Rwork0.1575 --
obs0.1587 16848 93.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.12→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1386 0 3 186 1575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.786
X-RAY DIFFRACTIONf_dihedral_angle_d4.671184
X-RAY DIFFRACTIONf_chiral_restr0.049192
X-RAY DIFFRACTIONf_plane_restr0.007251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.190.3039990.26131803X-RAY DIFFRACTION63
2.19-2.270.24681080.23082191X-RAY DIFFRACTION76
2.27-2.360.2651190.20032620X-RAY DIFFRACTION91
2.36-2.470.20081790.17542831X-RAY DIFFRACTION100
2.47-2.60.20021250.17012895X-RAY DIFFRACTION100
2.6-2.760.21821320.16042878X-RAY DIFFRACTION100
2.76-2.970.17241290.1582888X-RAY DIFFRACTION100
2.97-3.270.1721660.14432859X-RAY DIFFRACTION100
3.27-3.740.17851470.14272869X-RAY DIFFRACTION100
3.75-4.720.13481390.1282890X-RAY DIFFRACTION100
4.72-100.17021370.15032897X-RAY DIFFRACTION100

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