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- PDB-6xnd: Avidin-Biotin-Phenol -

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Basic information

Entry
Database: PDB / ID: 6xnd
TitleAvidin-Biotin-Phenol
ComponentsAvidin
KeywordsSTRUCTURAL PROTEIN / the complex of Avidin and Biotin-Phenol / Structural Genomics / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


biotin binding / antibacterial humoral response / extracellular region
Similarity search - Function
Avidin-like, conserved site / Avidin-like domain signature. / Avidin / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile.
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsAhmadvand, P. / Kang, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE 1804699 United States
CitationJournal: Chemmedchem / Year: 2020
Title: A Ligand-Directed Nitrophenol Carbonate for Transient in situ Bioconjugation and Drug Delivery
Authors: Burt, A.J. / Ahmadvand, P. / Opp, L.K. / Ryan, A.T. / Kang, C. / Mancini, R.J.
History
DepositionJul 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Avidin
B: Avidin
C: Avidin
D: Avidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,91912
Polymers57,4004
Non-polymers2,5198
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11450 Å2
ΔGint-43 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.526, 79.254, 74.683
Angle α, β, γ (deg.)90.000, 105.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Avidin


Mass: 14350.081 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: AVD / Production host: Gallus gallus (chicken) / 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.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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-V8M / N-[2-(2-hydroxy-5-nitrophenyl)ethyl]-5-[(3aS,4S,6aS)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide


Mass: 408.472 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H24N4O5S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Tris, pH 7.0, and 25% (w/v) PEG 1500 / PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→44.843 Å / Num. obs: 71463 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Net I/σ(I): 10.23
Reflection shellResolution: 1.58→1.64 Å / Num. unique obs: 6991 / CC1/2: 0.462

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AVI

2avi


Resolution: 1.58→44.843 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2718 1987 2.78 %
Rwork0.2341 69476 -
obs0.2351 71463 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.63 Å2 / Biso mean: 34.3868 Å2 / Biso min: 15.58 Å2
Refinement stepCycle: final / Resolution: 1.58→44.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3784 0 208 0 3992
Biso mean--39.5 --
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124032
X-RAY DIFFRACTIONf_angle_d1.5255464
X-RAY DIFFRACTIONf_dihedral_angle_d9.9812316
X-RAY DIFFRACTIONf_chiral_restr0.443632
X-RAY DIFFRACTIONf_plane_restr0.007676
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.58-1.61950.40081440.3494492999
1.6195-1.66330.3621510.32744925100
1.6633-1.71230.30971330.30454937100
1.7123-1.76750.35871420.28744951100
1.7675-1.83070.30881430.27944950100
1.8307-1.9040.30491310.26294977100
1.904-1.99070.33611420.24684921100
1.9907-2.09560.28091510.24324962100
2.0956-2.22690.28981420.24774966100
2.2269-2.39880.28131330.25094983100
2.3988-2.64020.29591440.25144961100
2.6402-3.02220.26811440.24424954100
3.0222-3.80730.25991410.22345010100
3.8073-4.6460.22321460.1885050100

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