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- PDB-8w94: Azumapecten Farreri homopolymeric ferritin (ApF) mutant-H2KE expo... -

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Basic information

Entry
Database: PDB / ID: 8w94
TitleAzumapecten Farreri homopolymeric ferritin (ApF) mutant-H2KE exposed to H2O2 for 2 s
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
: / HYDROGEN PEROXIDE / Ferritin
Similarity search - Component
Biological speciesAzumapecten farreri (Farrer's scallop)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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)20,1625
Polymers19,9601
Non-polymers2024
Water2,180121
1
b: Ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)483,885120
Polymers479,04824
Non-polymers4,83796
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 area94040 Å2
ΔGint-167 kcal/mol
Surface area130940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.652, 152.652, 152.652
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-201-

FE

21b-383-

HOH

31b-394-

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: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 3.71 Å3/Da / Density % sol: 66.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM MOPS, pH7, 500 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→29.94 Å / Num. obs: 13688 / % possible obs: 99 % / Redundancy: 36.6 % / CC1/2: 0.987 / Net I/σ(I): 18.12
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 1313 / CC1/2: 0.76

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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: 2.3→29.94 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1998 1374 10.01 %
Rwork0.1604 --
obs0.1643 13688 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1386 0 5 121 1512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.796
X-RAY DIFFRACTIONf_dihedral_angle_d4.921184
X-RAY DIFFRACTIONf_chiral_restr0.042192
X-RAY DIFFRACTIONf_plane_restr0.006251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.25041330.19211201X-RAY DIFFRACTION98
2.38-2.480.21431330.17831190X-RAY DIFFRACTION98
2.48-2.590.23891340.17431208X-RAY DIFFRACTION99
2.59-2.730.19341350.16481214X-RAY DIFFRACTION99
2.73-2.890.21361340.16781208X-RAY DIFFRACTION99
2.9-3.120.2011370.16721228X-RAY DIFFRACTION100
3.12-3.430.19361360.16141233X-RAY DIFFRACTION99
3.43-3.930.19091390.15021253X-RAY DIFFRACTION100
3.93-4.940.16921420.14051272X-RAY DIFFRACTION100
4.95-100.21151510.16611351X-RAY DIFFRACTION99

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