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- PDB-2avi: THREE-DIMENSIONAL STRUCTURES OF AVIDIN AND THE AVIDIN-BIOTIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2avi
TitleTHREE-DIMENSIONAL STRUCTURES OF AVIDIN AND THE AVIDIN-BIOTIN COMPLEX
ComponentsAVIDIN
KeywordsBIOTIN BINDING PROTEIN
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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsLivnah, O. / Sussman, J.
CitationJournal: 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.
History
DepositionApr 23, 1993Processing site: BNL
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_comp_id_1 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AVIDIN
B: AVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6316
Polymers28,7002
Non-polymers9314
Water1,33374
1
A: AVIDIN
B: AVIDIN
hetero molecules

A: AVIDIN
B: AVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,26212
Polymers57,4004
Non-polymers1,8628
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area13850 Å2
ΔGint-14 kcal/mol
Surface area18670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.150, 80.370, 43.540
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: 14350.081 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P02701
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE 34 OF EACH CHAIN EXISTS IN TWO FORMS - THR OR ILE. IN THIS ENTRY IT IS PRESENTED AS THR.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein solution1drop
223 %PEG10001reservoir
320 mMcitrate1reservoir

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.151 / Highest resolution: 3 Å
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1892 0 60 74 2026
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.83
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 8 Å / Num. reflection obs: 4984 / Rfactor obs: 0.151
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg

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