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- PDB-1aiv: APO OVOTRANSFERRIN -

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Basic information

Entry
Database: PDB / ID: 1aiv
TitleAPO OVOTRANSFERRIN
ComponentsOVOTRANSFERRINConalbumin
KeywordsIRON TRANSPORT PROTEIN
Function / homologyTransferrin-like domain signature 2. / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain profile. / Transferrin-like domain / Transferrin / Transferrin family, iron binding site / Transferrin / extracellular sequestering of iron ion / organomineral extracellular matrix ...Transferrin-like domain signature 2. / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain profile. / Transferrin-like domain / Transferrin / Transferrin family, iron binding site / Transferrin / extracellular sequestering of iron ion / organomineral extracellular matrix / intracellular sequestering of iron ion / antimicrobial humoral response / ferric iron binding / acute-phase response / cell / iron ion transport / response to lipopolysaccharide / response to drug / iron ion binding / extracellular space / Ovotransferrin
Function and homology information
Specimen sourceGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 3 Å resolution
AuthorsKurokawa, H. / Dewan, J.C. / Mikami, B. / Sacchettini, J.C. / Hirose, M.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: Crystal structure of hen apo-ovotransferrin. Both lobes adopt an open conformation upon loss of iron
Authors: Kurokawa, H. / Dewan, J.C. / Mikami, B. / Sacchettini, J.C. / Hirose, M.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Crystal Structure of Diferric Hen Ovotransferrin at 2.4 A Resolution
Authors: Kurokawa, H. / Mikami, B. / Hirose, M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 28, 1997 / Release: Apr 29, 1998
RevisionDateData content typeGroupProviderType
1.0Apr 29, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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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)76,3713
Polyers75,9291
Non-polymers4422
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)92.260, 92.260, 178.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP 43 21 2

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Components

#1: Protein/peptide OVOTRANSFERRIN / Conalbumin / CONALBUMIN


Mass: 75929.008 Da / Num. of mol.: 1 / Details: APO FORM / Source: (natural) Gallus gallus (chicken) / Genus: Gallus / References: UniProt: P02789
#2: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 1 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Chemical ChemComp-NDG / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Mass: 221.208 Da / Num. of mol.: 1 / Formula: C8H15NO6
Sequence detailsINTRASPECIFIC AND INTRA-INDIVIDUAL HETEROGENEITY OF OVOTRANSFERRIN HAS BEEN KNOWN FROM ...INTRASPECIFIC AND INTRA-INDIVIDUAL HETEROGENEITY OF OVOTRANSFERRIN HAS BEEN KNOWN FROM ELECTROPHORESIS STUDIES. THE DEPOSITORS' SEQUENCING STUDIES OF TRYPTIC FRAGMENTS OF OVOTRANSFERRIN USED FOR CRYSTALLOGRAPHIC STUDIES, SHOWED THAT RESIDUE 33 (29 IN ABOVE) IS SER OR ALA, THE RESIDUES 220 (216) AND 221 ARE GLN AND LEU, RESPECTIVELY, AND THE RESIDUE 135 IS ARG. THESE ARE CONSISTENT WITH THE SEQUENCE REPORTED BY JELTSCH, J. ET AL. (1987) NUCLEIC ACIDS RESEARCH 15, 7643-7645. THUS, THE DEPOSITORS DECIDED TO USE THE SEQUENCE. NO NEGATIVE OR POSITIVE FEATURE AROUND THE VARIABLE RESIDUES LISTED ABOVE CAN BE SEEN.

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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: 2.5 / Density percent sol: 50.72 %
Crystal growpH: 5.9 / Details: pH 5.9
Crystal grow
*PLUS
Temp: 4 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
142.5 mg/mlprotein1drop
20.02 Macetate1drop
32-3 %PEG60001drop
44-6 %PEG60001reservoir
50.02 Macetate1reservoir

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Data collection

DiffractionMean temperature: 123 kelvins
SourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Collection date: Dec 20, 1996
RadiationMonochromator: COLLIMATOR / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 3 Å / D resolution low: 2 Å / Number obs: 12920 / Observed criterion sigma I: 1 / Rsym value: 0.069 / NetI over sigmaI: 6.5 / Percent possible obs: 80.27
Reflection
*PLUS
Number measured all: 31370 / Rmerge I obs: 0.069

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Processing

Software
NameVersionClassification
SAINTdata scaling
SAINTdata reduction
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OVT
R Free selection details: RANDOM / Data cutoff high absF: 1 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / Sigma F: 2
Least-squares processR factor R free: 0.265 / R factor R work: 0.231 / R factor obs: 0.231 / Highest resolution: 3 Å / Lowest resolution: 2 Å / Number reflection obs: 11989 / Percent reflection obs: 74.9
Refine hist #LASTHighest resolution: 3 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 5312 / Nucleic acid: 0 / Ligand: 28 / Solvent: 0 / Total: 5340
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.010
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_deg1.690
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.41
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.385
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 DIFFRACTION1PARHCSDX.PROTOPH3.CHO
X-RAY DIFFRACTION2TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.413
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.385

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