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- PDB-8hct: Crystal structure of Cu2+ binding to Dendrorhynchus zhejiangensis... -

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Basic information

Entry
Database: PDB / ID: 8hct
TitleCrystal structure of Cu2+ binding to Dendrorhynchus zhejiangensis ferritin
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Cu2+-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
COPPER (II) ION / : / Ferritin
Similarity search - Component
Biological speciesDendrorhynchus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 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
DepositionNov 3, 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)20,0449
Polymers19,5221
Non-polymers5228
Water2,792155
1
A: Ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)481,044216
Polymers468,52824
Non-polymers12,516192
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 area122320 Å2
ΔGint-2236 kcal/mol
Surface area128980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.011, 151.011, 151.011
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-204-

CU

21A-205-

CU

31A-206-

CU

41A-207-

CU

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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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 3.68 Å3/Da / Density % sol: 66.62 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium citrate tribasic dihydrate, 0.1 M Tris hydrochloride pH 8.5, 30% v/v polyethyene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.38→106.9 Å / Num. obs: 13361 / % possible obs: 80.66 % / Redundancy: 7.6 % / Biso Wilson estimate: 36.35 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.022 / Rrim(I) all: 0.069 / Net I/σ(I): 5.3
Reflection shellResolution: 1.38→2.97 Å / Num. unique obs: 68702 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
REFMACccp4-7.0.024refinement
HKL-3000data reduction
HKL-3000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→106.78 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.938 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22639 667 4.8 %RANDOM
Rwork0.16406 ---
obs0.16689 13361 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.186 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.26→106.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 13 155 1534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191398
X-RAY DIFFRACTIONr_bond_other_d0.0030.021248
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.9451876
X-RAY DIFFRACTIONr_angle_other_deg1.02432907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8025168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45724.80577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00115254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.763158
X-RAY DIFFRACTIONr_chiral_restr0.1090.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021569
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02287
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_it2.812.867675
X-RAY DIFFRACTIONr_mcbond_other2.7922.857674
X-RAY DIFFRACTIONr_mcangle_it4.0274.276842
X-RAY DIFFRACTIONr_mcangle_other4.034.288843
X-RAY DIFFRACTIONr_scbond_it4.3383.352722
X-RAY DIFFRACTIONr_scbond_other4.3213.353722
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5384.8221034
X-RAY DIFFRACTIONr_long_range_B_refined7.88235.1691687
X-RAY DIFFRACTIONr_long_range_B_other7.83734.7041651
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.263→2.322 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 46 -
Rwork0.242 975 -
obs--100 %

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