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- PDB-8gy1: Crystal structure of Ag+ binding to Dendrorhynchus zhejiangensis ... -

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Basic information

Entry
Database: PDB / ID: 8gy1
TitleCrystal structure of Ag+ binding to Dendrorhynchus zhejiangensis ferritin
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Ag+-bound DzFer
Function / homology
Function and homology information


ferroxidase / ferric iron binding / ferrous iron binding / iron ion transport / intracellular iron ion homeostasis / oxidoreductase activity / cytoplasm
Similarity search - Function
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 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
SILVER ION / Ferritin
Similarity search - Component
Biological speciesDendrorhynchus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMing, T.H. / Su, X.R. / Huo, C.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)41676159 China
CitationJournal: Polymers (Basel) / Year: 2023
Title: Structural and Biochemical Characterization of Silver/Copper Binding by Dendrorhynchus zhejiangensis Ferritin.
Authors: Huo, C. / Ming, T. / Wu, Y. / Huan, H. / Qiu, X. / Lu, C. / Li, Y. / Zhang, Z. / Han, J. / Su, X.
History
DepositionSep 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)20,2468
Polymers19,5221
Non-polymers7247
Water3,477193
1
A: Ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)485,892192
Polymers468,52824
Non-polymers17,365168
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
crystal symmetry operation5_564z,x+1,y-11
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_564-z,-x+1,y-11
crystal symmetry operation8_566-z,x+1,-y+11
crystal symmetry operation9_465y-1,z+1,x1
crystal symmetry operation10_665-y+1,z+1,-x1
crystal symmetry operation11_465y-1,-z+1,-x1
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation13_465y-1,x+1,-z1
crystal symmetry operation14_665-y+1,-x+1,-z1
crystal symmetry operation15_465y-1,-x+1,z1
crystal symmetry operation16_665-y+1,x+1,z1
crystal symmetry operation17_566x,z+1,-y+11
crystal symmetry operation18_564-x,z+1,y-11
crystal symmetry operation19_566-x,-z+1,-y+11
crystal symmetry operation20_564x,-z+1,y-11
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_575z,-y+2,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_575-z,-y+2,-x1
Buried area104940 Å2
ΔGint-688 kcal/mol
Surface area132550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.212, 148.212, 148.212
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
11A-206-

AG

21A-207-

AG

31A-470-

HOH

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Components

#1: Protein Ferritin


Mass: 19521.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dendrorhynchus (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8F4Y4C2, ferroxidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ag
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 3.65 Å3/Da / Density % sol: 66.33 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: DzFer crystals were grown in 0.2 M ammonium sulfate, 0.1 M sodium acetate trihydrate pH 4.6, 30% w/v PEG monomethyl ether 2000, followed by soaking for 10 min with 20% glycerol and 100 mM AgNO3.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL17B / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jan 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→106.78 Å / Num. obs: 21003 / % possible obs: 99.7 % / Redundancy: 11.3 % / CC1/2: 0.99 / Net I/σ(I): 7.2
Reflection shellResolution: 1.9→2 Å / Num. unique obs: 3175 / CC1/2: 0.92

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Processing

Software
NameVersionClassification
REFMACccp4-7.0.024refinement
PHENIX1.14-3260refinement
XDSdata reduction
autoPROCdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→104.8 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.349 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18965 1107 5 %RANDOM
Rwork0.1508 ---
obs0.15273 21003 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.17 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.9→104.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 17 193 1576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191413
X-RAY DIFFRACTIONr_bond_other_d0.0030.021260
X-RAY DIFFRACTIONr_angle_refined_deg1.8751.9461896
X-RAY DIFFRACTIONr_angle_other_deg1.09832937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3025170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.61324.87278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02315256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.748158
X-RAY DIFFRACTIONr_chiral_restr0.1350.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021587
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02289
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9043.096680
X-RAY DIFFRACTIONr_mcbond_other2.8223.087679
X-RAY DIFFRACTIONr_mcangle_it3.9134.616850
X-RAY DIFFRACTIONr_mcangle_other3.9254.629851
X-RAY DIFFRACTIONr_scbond_it5.2093.69732
X-RAY DIFFRACTIONr_scbond_other5.1693.691732
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5395.2851046
X-RAY DIFFRACTIONr_long_range_B_refined8.42640.1121919
X-RAY DIFFRACTIONr_long_range_B_other8.34839.1681857
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 73 -
Rwork0.219 1537 -
obs--100 %

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