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- PDB-5lur: An avidin mutant -

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Basic information

Entry
Database: PDB / ID: 5lur
TitleAn avidin mutant
ComponentsAvidin
Keywordsbiotin binding protein / Avidin / antidins / steroids / progesterone / Steroid-binding
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
PROGESTERONE / Avidin
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAgrawal, N. / Lehtonen, S.I. / Riihimaki, T.A. / Kulomaa, M.S. / Hytonen, V.P. / Johnson, M.S. / Airenne, T.T.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland257814,272283,136288,290506 Finland
CitationJournal: TO BE PUBLISHED
Title: An avidin mutant
Authors: Agrawal, N. / Lehtonen, S.I. / Riihimaki, T.A. / Kulomaa, M.S. / Hytonen, V.P. / Johnson, M.S. / Airenne, T.T.
History
DepositionSep 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)32,3925
Polymers31,7282
Non-polymers6643
Water46826
1
A: Avidin
B: Avidin
hetero molecules

A: Avidin
B: Avidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,78410
Polymers63,4554
Non-polymers1,3296
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area13510 Å2
ΔGint-62 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.130, 80.350, 43.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
Helical symmetry: (Num. of operations: 2 / Rise per n subunits: 1 Å / Rotation per n subunits: 180 °)

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Components

#1: Protein Avidin / Antidin


Mass: 15863.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: AVD / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): A1 / References: UniProt: P02701
#2: Chemical ChemComp-STR / PROGESTERONE


Mass: 314.462 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: Drop size: 150 nl of protein-ligand solution and well solution. Protein-ligand solution: 1.8 mg/ml of protein solution (20 mM sodium phosphate, 1M sodium chloride, 20mM imidazole, pH 7.4) ...Details: Drop size: 150 nl of protein-ligand solution and well solution. Protein-ligand solution: 1.8 mg/ml of protein solution (20 mM sodium phosphate, 1M sodium chloride, 20mM imidazole, pH 7.4) and 50 mM ligand solution (1.57 mg in 100 microL of water) were mixed in 10:1 (v/v) ratio. Well solution: 0.18 M sodium chloride, 0.09 M sodium cacodylate (pH 6.5) and 1.8 M ammonium sulfate.
Temp details: Temperature-controlled incubator was used.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.7→19.56 Å / Num. obs: 7458 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.37
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.11 / CC1/2: 0.7 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSVERSION Oct 15, 2015 BUILT=20151231data reduction
XSCALEVERSION Oct 15, 2015 BUILT=20151231data scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U46

4u46


Resolution: 2.7→19.56 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.895 / SU B: 13.075 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R Free: 0.349 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23995 370 5 %RANDOM
Rwork0.17662 ---
obs0.17971 7073 96.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.703 Å2
Baniso -1Baniso -2Baniso -3
1-2.05 Å20 Å20 Å2
2--0.56 Å2-0 Å2
3----2.61 Å2
Refinement stepCycle: 1 / Resolution: 2.7→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 47 26 1931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021949
X-RAY DIFFRACTIONr_bond_other_d0.0020.021844
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.9432645
X-RAY DIFFRACTIONr_angle_other_deg0.96534225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.475227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89823.40988
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.24415332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9971514
X-RAY DIFFRACTIONr_chiral_restr0.0990.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022155
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02487
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_it2.2883.355923
X-RAY DIFFRACTIONr_mcbond_other2.2873.352922
X-RAY DIFFRACTIONr_mcangle_it3.8624.9941145
X-RAY DIFFRACTIONr_mcangle_other3.8624.9981146
X-RAY DIFFRACTIONr_scbond_it2.7513.8321026
X-RAY DIFFRACTIONr_scbond_other2.7493.8341027
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6025.6111501
X-RAY DIFFRACTIONr_long_range_B_refined6.8938.3712072
X-RAY DIFFRACTIONr_long_range_B_other6.8938.3682072
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 27 -
Rwork0.257 504 -
obs--97.97 %

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