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- PDB-3t2w: Crystal structure of shwanavidin (F43A) - biotin complex -

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Basic information

Entry
Database: PDB / ID: 3t2w
TitleCrystal structure of shwanavidin (F43A) - biotin complex
ComponentsAvidin/streptavidin
KeywordsBiotin-binding protein / avidin / streptavidin / biotin / high affinity systems / shwanavidin
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BIOTIN / Avidin/streptavidin
Similarity search - Component
Biological speciesShewanella denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLivnah, O. / Meir, A.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Adaptation of a Thermostable Biotin-binding Protein in a Psychrophilic Environment.
Authors: Meir, A. / Bayer, E.A. / Livnah, O.
History
DepositionJul 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Jun 13, 2012Group: Database references
Revision 1.3Oct 12, 2016Group: Advisory
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Avidin/streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2052
Polymers12,9601
Non-polymers2441
Water1,964109
1
A: Avidin/streptavidin
hetero molecules

A: Avidin/streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4094
Polymers25,9212
Non-polymers4892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3460 Å2
ΔGint-21 kcal/mol
Surface area10220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.212, 63.212, 65.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-124-

HOH

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Components

#1: Protein Avidin/streptavidin


Mass: 12960.279 Da / Num. of mol.: 1 / Mutation: F43A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella denitrificans (bacteria) / Strain: OS217 / ATCC BAA-1090 / DSM 15013 / Gene: Sden_0912 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12QS6
#2: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.3
Details: 1.5M Ammonium Sulfate, 50mM tris, pH 8.3, microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9736 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2010
RadiationMonochromator: optical hutch / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9736 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 21787 / Num. obs: 21787 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.897 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20762 1111 5.1 %RANDOM
Rwork0.17687 ---
obs0.17841 20652 99.07 %-
all-21787 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.663 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2---0.63 Å20 Å2
3---1.26 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms867 0 16 109 992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022925
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.931265
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.525119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.3725.64139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.65215139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1.514152
X-RAY DIFFRACTIONr_chiral_restr0.1070.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02700
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.2406
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2621
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3871.5590
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0072922
X-RAY DIFFRACTIONr_scbond_it3.0733402
X-RAY DIFFRACTIONr_scangle_it3.4864.5340
X-RAY DIFFRACTIONr_rigid_bond_restr2.5113992
X-RAY DIFFRACTIONr_sphericity_free5.9273109
X-RAY DIFFRACTIONr_sphericity_bonded5.3573901
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 69 -
Rwork0.237 1500 -
obs--99.49 %

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