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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
Revision 2.0Nov 6, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / cell / chem_comp / chem_comp_atom / chem_comp_bond / database_PDB_caveat / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conf / struct_conn / struct_conn_type / struct_sheet_range / symmetry
Item: _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[3][3] ..._atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[3][3] / _cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _entity_src_gen.gene_src_common_name / _pdbx_contact_author.id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_protein_modification / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.overall_SU_ML / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_residues_total / _software.classification / _software.name / _software.version / _struct_asym.entity_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _symmetry.space_group_name_Hall
Description: Model completeness
Details: Add water molecules to the model box as specified in the original PDB file, and remove the hydrogen atoms from the model.
Provider: author / Type: Coordinate replacement

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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)59,0348
Polymers57,4004
Non-polymers1,6344
Water4,792266
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10260 Å2
ΔGint-62 kcal/mol
Surface area18600 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
Space group name HallP2yb

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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: 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: isolated from a genetically manipulated source
Formula: C18H24N4O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.31 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
PHENIX1.21.1_5286refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AVI

2avi


Resolution: 1.58→44.84 Å / SU ML: 0.2356 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8925
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2365 1987 2.78 %
Rwork0.2087 69475 -
obs0.2094 71463 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.65 Å2
Refinement stepCycle: LAST / Resolution: 1.58→44.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3784 0 112 266 4162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.620.36211440.354928X-RAY DIFFRACTION99.47
1.62-1.660.36381510.32854926X-RAY DIFFRACTION99.84
1.66-1.710.3161330.34936X-RAY DIFFRACTION99.98
1.71-1.770.35381420.29094951X-RAY DIFFRACTION99.96
1.77-1.830.31621430.27874951X-RAY DIFFRACTION99.96
1.83-1.90.28231310.24874975X-RAY DIFFRACTION99.96
1.9-1.990.30151420.22564923X-RAY DIFFRACTION99.98
1.99-2.10.22881510.21694961X-RAY DIFFRACTION99.92
2.1-2.230.22141420.21254965X-RAY DIFFRACTION100
2.23-2.40.26971330.21144984X-RAY DIFFRACTION99.96
2.4-2.640.24291440.2134962X-RAY DIFFRACTION99.94
2.64-3.020.22471440.20254953X-RAY DIFFRACTION99.9
3.02-3.810.2261410.18955010X-RAY DIFFRACTION99.92

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