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- PDB-4u46: Crystal structure of an avidin mutant -

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Basic information

Entry
Database: PDB / ID: 4u46
TitleCrystal structure of an avidin mutant
ComponentsAvidin
KeywordsBiotin binding protein / Avidin / Biotin / Ligand binding / Sterols
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 ...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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsAgrawal, N. / Lehtonen, S. / Kahkonen, N. / Riihimaki, T. / Hytonen, V.P. / Kulomaa, M.S. / Johnson, M.S. / Airenne, T.T.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Artificial Avidin-Based Receptors for a Panel of Small Molecules.
Authors: Lehtonen, S.I. / Tullila, A. / Agrawal, N. / Kukkurainen, S. / Kahkonen, N. / Koskinen, M. / Nevanen, T.K. / Johnson, M.S. / Airenne, T.T. / Kulomaa, M.S. / Riihimaki, T.A. / Hytonen, V.P.
History
DepositionJul 23, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Dec 20, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)32,15314
Polymers31,7282
Non-polymers42512
Water1,29772
1
A: Avidin
B: Avidin
hetero molecules

A: Avidin
B: Avidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,30628
Polymers63,4554
Non-polymers85124
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area13030 Å2
ΔGint-257 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.480, 79.800, 43.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-324-

HOH

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Components

#1: Protein Avidin


Mass: 15863.781 Da / Num. of mol.: 2 / Fragment: UNP residues 25-152
Source method: isolated from a genetically manipulated source
Details: OmpA signal was used in expression. / Source: (gene. exp.) Gallus gallus (chicken) / Gene: AVD / Plasmid: pET101/D / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): AI / References: UniProt: P02701
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: Well solution: 0.2 M sodium chloride, 0.1 M sodium cacodylate, 2.0 M ammonium sulphate
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. all: 19367 / Num. obs: 19264 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.7.0032refinement
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WBI

1wbi


Resolution: 1.95→19.34 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.038 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21402 964 5 %RANDOM
Rwork0.18203 ---
obs0.18364 18300 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.228 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å2-0 Å2-0 Å2
2--0.59 Å20 Å2
3----1.9 Å2
Refinement stepCycle: 1 / Resolution: 1.95→19.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 12 72 1942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021917
X-RAY DIFFRACTIONr_bond_other_d0.0010.021806
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.9082598
X-RAY DIFFRACTIONr_angle_other_deg0.8253.0024134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6585236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95223.40988
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.90515336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0211514
X-RAY DIFFRACTIONr_chiral_restr0.1080.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022160
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02486
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7232.839932
X-RAY DIFFRACTIONr_mcbond_other2.7142.836931
X-RAY DIFFRACTIONr_mcangle_it4.0884.2251160
X-RAY DIFFRACTIONr_mcangle_other4.0894.2271161
X-RAY DIFFRACTIONr_scbond_it3.2353.332985
X-RAY DIFFRACTIONr_scbond_other3.2343.335986
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1174.7921435
X-RAY DIFFRACTIONr_long_range_B_refined7.57423.2552097
X-RAY DIFFRACTIONr_long_range_B_other7.51123.1922090
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 70 -
Rwork0.223 1320 -
obs--99.93 %

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