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- PDB-1ave: CRYSTAL STRUCTURE OF HEN EGG-WHITE APO-AVIDIN IN RELATION TO ITS ... -

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Entry
Database: PDB / ID: 1ave
TitleCRYSTAL STRUCTURE OF HEN EGG-WHITE APO-AVIDIN IN RELATION TO ITS THERMAL STABILITY PROPERTIES
ComponentsAVIDIN
KeywordsBIOTIN-BINDING PROTEIN
Function / homologyAvidin/streptavidin / Avidin / Avidin-like, conserved site / Avidin-like superfamily / Avidin family / Avidin-like domain signature. / Avidin-like domain profile. / biotin binding / antibacterial humoral response / extracellular region / Avidin
Function and homology information
Specimen sourceGallus gallus (chicken)
MethodX-RAY DIFFRACTION / 2.8 Å resolution
AuthorsPugliese, L. / Coda, A. / Malcovati, M. / Bolognesi, M.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Crystal structure of apo-avidin from hen egg-white.
Authors: Pugliese, L. / Malcovati, M. / Coda, A. / Bolognesi, M.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Three-Dimensional Structure of the Tetragonal Crystal Form of Egg-White Avidin in its Functional Complex with Biotin at 2.7 Angstroms Resolution
Authors: Pugliese, L. / Coda, A. / Malcovati, M. / Bolognesi, M.
#2: Journal: J.Mol.Biol. / Year: 1984
Title: Crystallization of Hen Egg-White Avidin in a Tetragonal Form
Authors: Gatti, G. / Bolognesi, M. / Coda, A. / Chiolerio, F. / Filippini, E. / Malcovati, M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 5, 1993 / Release: Jan 31, 1994
RevisionDateData content typeGroupProviderType
1.0Jan 31, 1994Structure modelrepositoryInitial release
1.1Mar 3, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance
Remark 700SHEET THE SHEET PRESENTED AS *CH1* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *CH1* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: AVIDIN
B: AVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1434
Polyers28,7002
Non-polymers4422
Water37821
1
A: AVIDIN
B: AVIDIN
hetero molecules

A: AVIDIN
B: AVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2858
Polyers57,4004
Non-polymers8854
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area (Å2)11040
ΔGint (kcal/M)-40
Surface area (Å2)21760
MethodPISA,PQS
Unit cell
γ
α
β
Length a, b, c (Å)80.150, 80.150, 85.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP 42 21 2
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

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Components

#1: Protein/peptide AVIDIN /


Mass: 14350.081 Da / Num. of mol.: 2 / Source: (gene. exp.) Gallus gallus (chicken) / Genus: Gallus / References: UniProt: P02701
#2: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 2 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Formula: H2O / Water
Sequence detailsPOSITION 34 SHOWS RESIDUE MICROHETEROGENEITY (THR OR ILE), AS DETERMINED FROM AMINO ACID SEQUENCING. ...POSITION 34 SHOWS RESIDUE MICROHETEROGENEITY (THR OR ILE), AS DETERMINED FROM AMINO ACID SEQUENCING. THE ELECTRON DENSITY HAS BEEN INTERPRETED AS THR, ALTHOUGH THE PRESENCE OF A MINOR ILE COMPONENT IN THE CRYSTAL CANNOT BE EXCLUDED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 / Density percent sol: 48.44 %
Crystal grow
*PLUS
pH: 5.7 / Method: vapor diffusion, hanging drop
Details: referred to 'Pugliese, L.', (1993) J.Mol.Biol., 231, 698-710
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
110 mg/mlprotein1drop
20.05 Mphosphate1drop
32.0 Mammonium sulfate1drop
42.5 Mammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
D resolution high: 2.8 Å / D resolution low: 1 Å / Number obs: 6390 / Number measured all: 29082 / Rmerge I obs: 0.09

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Processing

SoftwareName: TNT / Classification: refinement
Least-squares processR factor obs: 0.166 / Highest resolution: 2.8 Å
Refine hist #LASTHighest resolution: 2.8 Å
Number of atoms included #LASTProtein: 1928 / Nucleic acid: 0 / Ligand: 28 / Solvent: 21 / Total: 1977
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.020
X-RAY DIFFRACTIONt_angle_deg2.86
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Least-squares process
*PLUS
R factor obs: 0.166 / Highest resolution: 2.8 Å / Lowest resolution: 1 Å / Number reflection obs: 6390
Refine LS restraints
*PLUS
Refine IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg

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