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- PDB-8x3h: Crystal structure of iron-bound recombinant ovotransferrin N-lobe... -

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Basic information

Entry
Database: PDB / ID: 8x3h
TitleCrystal structure of iron-bound recombinant ovotransferrin N-lobe at 0.93 angstrom resolution
ComponentsOvotransferrin
KeywordsMETAL TRANSPORT / transferrin / atomic resolution
Function / homology
Function and homology information


iron ion transport / recycling endosome / antibacterial humoral response / early endosome / extracellular space / metal ion binding / plasma membrane
Similarity search - Function
Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin / Transferrin-like domain / Transferrin / Transferrin-like domain profile. / Transferrin
Similarity search - Domain/homology
CARBONATE ION / : / Ovotransferrin
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.93 Å
AuthorsToyoda, M. / Mikami, B. / Mizutani, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of iron-bound ovotransferrin N-lobe at atomic resolution
Authors: Toyoda, M. / Tanabe, A. / Mikami, B. / Hirose, M. / Mizutani, K.
History
DepositionNov 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ovotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7364
Polymers36,5281
Non-polymers2083
Water9,728540
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-13 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.346, 75.518, 84.647
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ovotransferrin


Mass: 36528.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TFEW / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71 / References: UniProt: Q4ADJ7
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3 / 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: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 100mM HEPES-Na buffer, 21% PEG 3350, 200mM Sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.7 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 0.93→50 Å / Num. obs: 190261 / % possible obs: 95.4 % / Redundancy: 7.8 % / CC1/2: 0.997 / Rpim(I) all: 0.015 / Rrim(I) all: 0.045 / Net I/σ(I): 62.5
Reflection shellResolution: 0.93→0.95 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 5.2 / Num. unique obs: 7502 / CC1/2: 0.865 / Rpim(I) all: 0.188 / Rrim(I) all: 0.491 / % possible all: 76.1

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Processing

Software
NameClassification
SHELXLrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.93→10 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1237 --
Rwork0.1029 --
obs-180290 90.58 %
Refinement stepCycle: LAST / Resolution: 0.93→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2563 0 11 540 3114

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