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- PDB-1rav: RECOMBINANT AVIDIN -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1rav
TitleRECOMBINANT AVIDIN
ComponentsAVIDIN
KeywordsGLYCOPROTEIN / AVIDIN / BIOTIN BINDING PROTEIN / CALYCINS / UP-AND-DOWN BETA BARREL
Function / homology
Function and homology information


biotin binding / antibacterial humoral response / extracellular region
Similarity search - Function
Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin ...Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRosano, C. / Arosio, P. / Bolognesi, M.
Citation
Journal: Eur.J.Biochem. / Year: 1998
Title: Biochemical characterization and crystal structure of a recombinant hen avidin and its acidic mutant expressed in Escherichia coli.
Authors: Nardone, E. / Rosano, C. / Santambrogio, P. / Curnis, F. / Corti, A. / Magni, F. / Siccardi, A.G. / Paganelli, G. / Losso, R. / Apreda, B. / Bolognesi, M. / Sidoli, A. / Arosio, P.
#1: 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.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Three-Dimensional Structures of Avidin and the Avidin-Biotin Complex
Authors: Livnah, O. / Bayer, E.A. / Wilchek, M. / Sussman, J.L.
#3: 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 A Resolution
Authors: Pugliese, L. / Coda, A. / Malcovati, M. / Bolognesi, M.
History
DepositionMar 27, 1998Processing site: BNL
Revision 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AVIDIN
B: AVIDIN


Theoretical massNumber of molelcules
Total (without water)28,5822
Polymers28,5822
Non-polymers00
Water1,44180
1
A: AVIDIN
B: AVIDIN

A: AVIDIN
B: AVIDIN


Theoretical massNumber of molelcules
Total (without water)57,1644
Polymers57,1644
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area10210 Å2
ΔGint-49 kcal/mol
Surface area21920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.690, 80.790, 43.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein AVIDIN


Mass: 14291.058 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Cell: EGG / Cell line: BL21 / Cellular location: CYTOPLASM (WHITE) / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P02701
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 58.7 %
Crystal growMethod: vapor diffusion / pH: 7.2
Details: RECOMBINANT AVIDIN WAS CRYSTALLIZED FROM 9% W/V PEG 8000. PH 7.2 0.05 M TRIS BUFFER AT 22 C BY VAPOUR DIFFUSION TECHNIQUES., vapor diffusion
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
29 %mass/vPEG80001drop
30.05 MTris-HCl1droppH7.2
42.0 Mammonium sulfate1reservoir
50.05 Msodium phosphate1reservoirpH5.7

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20.5 Å / Num. obs: 13827 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 15
Reflection shellResolution: 2.2→2.7 Å / % possible all: 93.1
Reflection
*PLUS
Num. measured all: 48932

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data reduction
AMoREphasing
TNT5Erefinement
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AVE

1ave


Resolution: 2.2→20.2 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
all0.17 13480 -
obs-13480 95 %
Solvent computationSolvent model: TNT / Bsol: 150 Å2 / ksol: 0.77 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→20.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 0 80 2032
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01619944.5
X-RAY DIFFRACTIONt_angle_deg2.61126967.5
X-RAY DIFFRACTIONt_dihedral_angle_d20.53811940
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.017485.5
X-RAY DIFFRACTIONt_gen_planes0.01828821.9
X-RAY DIFFRACTIONt_it3.466199417
X-RAY DIFFRACTIONt_nbd0.0624112
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20.5380
X-RAY DIFFRACTIONt_planar_d0.0175.5
X-RAY DIFFRACTIONt_plane_restr0.01821.9

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