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- PDB-1tfa: OVOTRANSFERRIN, N-TERMINAL LOBE, APO FORM -

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Basic information

Entry
Database: PDB / ID: 1tfa
TitleOVOTRANSFERRIN, N-TERMINAL LOBE, APO FORM
ComponentsPROTEIN (OVOTRANSFERRIN)
KeywordsTRANSPORT PROTEIN / TRANSFERRIN / OVOTRANSFERRIN / IRON BINDING PROTEIN
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 / response to lipopolysaccharide / antibacterial humoral response ...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 / response to lipopolysaccharide / antibacterial humoral response / early endosome / iron ion binding / response to xenobiotic stimulus => GO:0009410 / extracellular space / plasma membrane
Similarity search - Function
Transferrin-like domain signature 2. / Transferrin-like domain signature 3. / Transferrin-like domain signature 1. / Transferrin family, iron binding site / Transferrin-like domain profile. / Transferrin / Transferrin / Transferrin / Transferrin-like domain / Periplasmic binding protein-like II ...Transferrin-like domain signature 2. / Transferrin-like domain signature 3. / Transferrin-like domain signature 1. / Transferrin family, iron binding site / Transferrin-like domain profile. / Transferrin / Transferrin / Transferrin / Transferrin-like domain / 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 / MIR / Resolution: 1.9 Å
AuthorsMizutani, K. / Yamashita, H. / Mikami, B. / Hirose, M.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: Alternative structural state of transferrin. The crystallographic analysis of iron-loaded but domain-opened ovotransferrin N-lobe.
Authors: Mizutani, K. / Yamashita, H. / Kurokawa, H. / Mikami, B. / Hirose, M.
History
DepositionJan 7, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (OVOTRANSFERRIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6335
Polymers36,2491
Non-polymers3844
Water4,594255
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)125.170, 125.170, 87.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein PROTEIN (OVOTRANSFERRIN)


Mass: 36248.980 Da / Num. of mol.: 1 / Fragment: N-TERMINAL LOBE / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cell: EGG / References: UniProt: P02789
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.79 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
144.4 mg/mlprotein1drop
20.05 MBis Tris-HCl1drop
30.05 MBis-Tris1reservoir
452 %ammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jul 15, 1997
RadiationMonochromator: CARBON MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.83→30 Å / Num. obs: 194748 / % possible obs: 95.5 % / Observed criterion σ(I): 1 / Redundancy: 5.62 % / Rsym value: 0.063

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Processing

Software
NameVersionClassification
SAINTdata scaling
SAINTdata reduction
PHASESphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MIR / Resolution: 1.9→7 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.243 -10 %RANDOM
Rwork0.187 ---
obs0.187 27751 88.1 %-
Displacement parametersBiso mean: 22.8 Å2
Refinement stepCycle: LAST / Resolution: 1.9→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2569 0 20 255 2844
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.88
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.12
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.98 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2939 -10 %
Rwork0.2745 2715 -
obs--77.9 %
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 7 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.12
LS refinement shell
*PLUS
% reflection Rfree: 10 %

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