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- PDB-3t2x: Structure of shwanavidin low affinity mutant (F43A) -

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Basic information

Entry
Database: PDB / ID: 3t2x
TitleStructure of shwanavidin low affinity mutant (F43A)
ComponentsAvidin/streptavidin
KeywordsBiotin-binding protein / avidin / biotin / streptavidin / shwanavidin / high affinity systems
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
Biological speciesShewanella denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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 1.3Nov 6, 2024Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Avidin/streptavidin
B: Avidin/streptavidin
C: Avidin/streptavidin
D: Avidin/streptavidin


Theoretical massNumber of molelcules
Total (without water)51,8414
Polymers51,8414
Non-polymers00
Water9,836546
1
A: Avidin/streptavidin
B: Avidin/streptavidin


Theoretical massNumber of molelcules
Total (without water)25,9212
Polymers25,9212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-22 kcal/mol
Surface area10120 Å2
MethodPISA
2
C: Avidin/streptavidin
D: Avidin/streptavidin


Theoretical massNumber of molelcules
Total (without water)25,9212
Polymers25,9212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-21 kcal/mol
Surface area9800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.933, 113.933, 83.431
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Avidin/streptavidin


Mass: 12960.279 Da / Num. of mol.: 4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / 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: 2.01 Å3/Da / Density % sol: 38.81 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5
Details: 1.1M Sodium Formate, 0.05M sodium acetate, 50mM bis tris, pH 6.5, 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: 1.15→50 Å / Num. all: 142657 / Num. obs: 142657 / % possible obs: 99.7 % / 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: 1.15→50 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.101 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1707 7147 5 %RANDOM
Rwork0.14466 ---
obs0.14596 135363 99.57 %-
all-142657 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.217 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å20 Å2
2---0.18 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3554 0 0 546 4100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223779
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.9125195
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9925519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40626.078153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75915582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.8154
X-RAY DIFFRACTIONr_chiral_restr0.1140.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022896
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.21701
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22646
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2394
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.2130
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.251
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4841.52469
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.12123910
X-RAY DIFFRACTIONr_scbond_it2.71831568
X-RAY DIFFRACTIONr_scangle_it3.4334.51262
X-RAY DIFFRACTIONr_rigid_bond_restr1.47734037
X-RAY DIFFRACTIONr_sphericity_free6.0533546
X-RAY DIFFRACTIONr_sphericity_bonded4.51233668
LS refinement shellResolution: 1.15→1.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 497 -
Rwork0.249 10056 -
obs--99.58 %

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