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- PDB-3wzn: Crystal structure of the core streptavidin mutant V21 (Y22S/N23D/... -

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Basic information

Entry
Database: PDB / ID: 3wzn
TitleCrystal structure of the core streptavidin mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) complexed with biotin at 1.3 A resolution
ComponentsStreptavidin
KeywordsBIOTIN BINDING PROTEIN / beta-barrel
Function / homology
Function and homology information


biotin binding / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BIOTIN / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKawato, T. / Mizohata, E. / Shimizu, Y. / Meshizuka, T. / Yamamoto, T. / Takasu, N. / Matsuoka, M. / Matsumura, H. / Tsumoto, K. / Kodama, T. ...Kawato, T. / Mizohata, E. / Shimizu, Y. / Meshizuka, T. / Yamamoto, T. / Takasu, N. / Matsuoka, M. / Matsumura, H. / Tsumoto, K. / Kodama, T. / Kanai, M. / Doi, H. / Inoue, T. / Sugiyama, A.
CitationJournal: J.Biochem. / Year: 2015
Title: Structure-based design of a streptavidin mutant specific for an artificial biotin analogue.
Authors: Kawato, T. / Mizohata, E. / Shimizu, Y. / Meshizuka, T. / Yamamoto, T. / Takasu, N. / Matsuoka, M. / Matsumura, H. / Kodama, T. / Kanai, M. / Doi, H. / Inoue, T. / Sugiyama, A.
History
DepositionOct 1, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _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
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Streptavidin
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0395
Polymers26,4542
Non-polymers5853
Water3,999222
1
A: Streptavidin
B: Streptavidin
hetero molecules

A: Streptavidin
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,07810
Polymers52,9094
Non-polymers1,1696
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area12020 Å2
ΔGint-63 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.677, 54.344, 60.064
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Streptavidin /


Mass: 13227.240 Da / Num. of mol.: 2 / Fragment: UNP residues 37-163 / Mutation: Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: pCold TF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3) / References: UniProt: P22629
#2: Chemical ChemComp-BTN / BIOTIN / Biotin


Mass: 244.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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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: 41.08 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 100 mM sodium acetate trihydrate, 2.0 M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 55326 / Num. obs: 54829 / % possible obs: 99.1 % / Redundancy: 7.5 % / Rsym value: 0.072 / Net I/σ(I): 26.8
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 3.95 / Num. unique all: 54829 / Rsym value: 0.406 / % possible all: 99.1

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WYQ

3wyq


Resolution: 1.3→15 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.288 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20658 2761 5.1 %RANDOM
Rwork0.15995 ---
obs0.16239 51662 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---0.65 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1801 0 37 222 2060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0211929
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3281.9162656
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1965263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.96325.275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6115260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.876154
X-RAY DIFFRACTIONr_chiral_restr0.3250.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021476
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.7671.51230
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.82421961
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.3413699
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.1124.5686
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.71931929
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 206 -
Rwork0.323 3744 -
obs--98.55 %

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