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- PDB-1ij8: CRYSTAL STRUCTURE OF LITE AVIDIN-BNI COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1ij8
TitleCRYSTAL STRUCTURE OF LITE AVIDIN-BNI COMPLEX
ComponentsAVIDIN
KeywordsUNKNOWN FUNCTION / avidin / streptavidin / pseudo enzymatic activity
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 / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsLivnah, O. / Huberman, T.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Chicken avidin exhibits pseudo-catalytic properties. Biochemical, structural, and electrostatic consequences.
Authors: Huberman, T. / Eisenberg-Domovich, Y. / Gitlin, G. / Kulik, T. / Bayer, E.A. / Wilchek, M. / Livnah, O.
History
DepositionApr 25, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)29,8716
Polymers28,7002
Non-polymers1,1714
Water1,47782
1
A: AVIDIN
B: AVIDIN
hetero molecules

A: AVIDIN
B: AVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,74312
Polymers57,4004
Non-polymers2,3438
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area13880 Å2
ΔGint-6 kcal/mol
Surface area20220 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.269, 80.362, 43.402
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 to for the avidin tetramer is generated by the two fold axis -x, -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: EGG WHITE / References: UniProt: P02701
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


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-BNI / 5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC ACID (4-NITRO-PHENYL)-AMIDE / BIOTINYL P-NITROANILINE


Mass: 364.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20N4O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 12% PEG2000, 0.1M imidazole malate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14.2 mg/mlprotein1drop
215 %PEG20001reservoir
30.1 Mphosphate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 18, 2000 / Details: Max-Flux
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 17510 / Num. obs: 17510 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 30.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.279 / % possible all: 98.1
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 98.1 % / Mean I/σ(I) obs: 4.6

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Processing

Software
NameClassification
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2AVI

2avi


Resolution: 2→50 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1568 5 %random
Rwork0.204 ---
all0.206 33015 --
obs0.206 31543 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.258 Å20 Å20 Å2
2--0.36 Å20 Å2
3---1.898 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1867 0 78 82 2027
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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