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- PDB-1ryx: Crystal structure of hen serum transferrin in apo- form -

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Basic information

Entry
Database: PDB / ID: 1ryx
TitleCrystal structure of hen serum transferrin in apo- form
ComponentsOvotransferrin
KeywordsMETAL TRANSPORT / Hen serum transferrin / Apo- form / Domain Orientation
Function / homology
Function and homology information


extracellular sequestering of iron ion / organomineral extracellular matrix / antimicrobial humoral response / intracellular sequestering of iron ion / ferric iron binding / acute-phase response / recycling endosome / iron ion transport / antibacterial humoral response / response to lipopolysaccharide ...extracellular sequestering of iron ion / organomineral extracellular matrix / antimicrobial humoral response / intracellular sequestering of iron ion / ferric iron binding / acute-phase response / recycling endosome / iron ion transport / antibacterial humoral response / response to lipopolysaccharide / early endosome / response to xenobiotic stimulus / iron ion binding / extracellular space / 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-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin / Periplasmic binding protein-like II ...Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsDattagupta, J.K. / Thakurta, P.G. / Choudhury, D. / Dasgupta, R.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: Tertiary structural changes associated with iron binding and release in hen serum transferrin: a crystallographic and spectroscopic study
Authors: Thakurta, P.G. / Choudhury, D. / Dasgupta, R. / Dattagupta, J.K.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2003
Title: Structure of Diferric hen Serum Transferrin at 2.8 A Resolution
Authors: Guha Thakurta, P. / Choudhury, D. / Dasgupta, R. / Dattagupta, J.K.
History
DepositionDec 23, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ovotransferrin


Theoretical massNumber of molelcules
Total (without water)75,9291
Polymers75,9291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.295, 90.295, 177.666
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Ovotransferrin / Conalbumin / Allergen Gal d 3 / Gal d III / Serum transferrin


Mass: 75929.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: hen serum / References: UniProt: P02789

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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: 2.78 Å3/Da / Density % sol: 55.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 18-23% PEG 6000 in 0.02M sodium acetate buffer, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2002 / Details: Osmic MaxFlux Confocal Optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.4→20 Å / Num. all: 55815 / Num. obs: 10753 / Redundancy: 5.2 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.102
Reflection shellResolution: 3.4→3.48 Å / Rmerge(I) obs: 0.453

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AIV

1aiv


Resolution: 3.5→19.69 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 4475883.76 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THE RESIDUES WHOSE SIDE CHAINS COULD NOT BE LOCATED IN THE ELECTRON DENSITY MAP WERE KEPT AS ALANINE, HOWEVER, THE RESIDUE NAMES REMAIN UNALTERED IN THIS PDB FILE.
RfactorNum. reflection% reflectionSelection details
Rfree0.341 444 5.2 %RANDOM
Rwork0.283 ---
obs0.283 8604 88.3 %-
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.89 Å20 Å20 Å2
2--2.89 Å20 Å2
3----5.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.75 Å0.58 Å
Luzzati d res low-20 Å
Luzzati sigma a0.66 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 3.5→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4657 0 0 0 4657
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d1.29
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.441 75 5.3 %
Rwork0.342 1340 -
obs--90.5 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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