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- PDB-1lel: The avidin BCAP complex -

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Basic information

Entry
Database: PDB / ID: 1lel
TitleThe avidin BCAP complex
ComponentsAvidin
KeywordsUNKNOWN FUNCTION / avidin / streptavidin / biotin / ligand exchange
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
E-AMINO BIOTINYL CAPROIC ACID / Avidin
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPazy, Y. / Kulik, T. / Bayer, E.A. / Wilchek, M. / Livnah, O.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Ligand exchange between proteins: exchange of biotin and biotin derivatives between avidin and streptavidin
Authors: Pazy, Y. / Kulik, T. / Bayer, E.A. / Wilchek, M. / Livnah, O.
History
DepositionApr 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / 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_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _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

Downloads & links

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Assembly

Deposited unit
A: Avidin
B: Avidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8586
Polymers28,7002
Non-polymers1,1574
Water0
1
A: Avidin
B: Avidin
hetero molecules

A: Avidin
B: Avidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,71512
Polymers57,4004
Non-polymers2,3158
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area13820 Å2
ΔGint-38 kcal/mol
Surface area19180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.963, 80.692, 43.074
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe second part of the biological assembly is generated by the two fold axis: -x+1, -y+1, z.

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Components

#1: Protein Avidin /


Mass: 14350.081 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue fraction: egg white / References: UniProt: P02701
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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-BH7 / E-AMINO BIOTINYL CAPROIC ACID / 6-[5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-4-YL)-PENTANOYLAMINO]-HEXANOIC ACID


Mass: 357.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H27N3O4S

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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: 2.15 Å3/Da / Density % sol: 42.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 12% PEG 1000, 0.1M immidazole malate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14.2 mg/mlprotein1drop
212 %PEG10001reservoir
30.1 Mimidazole-malate1reservoirpH5.8

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 20, 2001 / Details: MAX FLUX
RadiationMonochromator: MAX FLUX optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 5785 / % possible obs: 95.8 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.9→3 Å / % possible all: 97.8
Reflection
*PLUS
Lowest resolution: 40 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.114
Reflection shell
*PLUS
% possible obs: 97.8 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 3.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→40 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.284 784 RANDOM
Rwork0.204 --
all-16261 -
obs-15477 -
Refinement stepCycle: LAST / Resolution: 2.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1795 0 76 0 1871
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.012
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.8

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