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- PDB-1aov: APO DUCK OVOTRANSFERRIN -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1aov
TitleAPO DUCK OVOTRANSFERRIN
ComponentsAPO-OVOTRANSFERRIN
KeywordsTRANSFERRIN / IRON UPTAKE / PROTEIN CRYSTALLOGRAPHY / MOLECULAR REPLACEMENT
Function / homology
Function and homology information


recycling endosome / iron ion transport / 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-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 speciesAnas platyrhynchos (mallard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsRawas, A. / Muirhead, H.
CitationJournal: J.Mol.Biol. / Year: 1989
Title: Preliminary crystallographic studies on duck ovotransferrin.
Authors: Rawas, A. / Moreton, K. / Muirhead, H. / Williams, J.
History
DepositionDec 11, 1996Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: 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

Downloads & links

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Assembly

Deposited unit
A: APO-OVOTRANSFERRIN


Theoretical massNumber of molelcules
Total (without water)75,7321
Polymers75,7321
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)77.620, 98.740, 126.960
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 APO-OVOTRANSFERRIN


Mass: 75731.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Anas platyrhynchos (mallard) / Cell: EGG / References: UniProt: P56410

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 60 % / Description: DATA WERE COLLECTED USING ROTATION CAMERA.
Crystal growpH: 6
Details: PROTEIN WAS CRYSTALLIZED FROM 15 - 30% PEG 6000, PH 6., pH 6.0
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.01 Msodium acetate1reservoir
215-30 %PEG60001reservoir
330 mg/mlprotein1drop
40.01 Msodium acetate1drop
517 %PEG60001drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: FILM / Detector: FILM / Date: May 1, 1989 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 4→15 Å / Num. obs: 7487 / % possible obs: 92.8 % / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Rmerge(I) obs: 0.09 / Rsym value: 0.05 / Net I/σ(I): 10.2
Reflection shellResolution: 4→4.2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 3 / Rsym value: 0.18 / % possible all: 50

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4SCALING PROGRAMdata reduction
X-PLOR3model building
X-PLOR3refinement
CCP4data scaling
X-PLOR3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DOT

1dot


Resolution: 4→10 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: N / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.32 754 10 %RANDOM
Rwork0.21 ---
obs0.21 7487 92.8 %-
Displacement parametersBiso mean: 38 Å2
Refinement stepCycle: LAST / Resolution: 4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5300 0 0 0 5300
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg3.881
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.742
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.742

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