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- PDB-4ekv: Streptavidin 8-aa-loop H127C mutein with reversible biotin binding -

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Basic information

Entry
Database: PDB / ID: 4ekv
TitleStreptavidin 8-aa-loop H127C mutein with reversible biotin binding
ComponentsStreptavidin
Keywordsbiotin-binding protein / Beta-barrel / Binding protein / Biotin-binding
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 ...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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsBarrette-Ng, I.H. / Honetschlaeger, C. / Wong, S.L. / Ng, K.K.S.
CitationJournal: Plos One / Year: 2012
Title: Development of a tetrameric streptavidin mutein with reversible biotin binding capability: engineering a mobile loop as an exit door for biotin.
Authors: O'Sullivan, V.J. / Barrette-Ng, I. / Hommema, E. / Hermanson, G.T. / Schofield, M. / Wu, S.C. / Honetschlaeger, C. / Ng, K.K. / Wong, S.L.
History
DepositionApr 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5663
Polymers16,2861
Non-polymers2802
Water1,26170
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,26512
Polymers65,1464
Non-polymers1,1198
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area9110 Å2
ΔGint-74 kcal/mol
Surface area20570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.066, 57.066, 70.186
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

DetailsThe homotetramer is generated from the single protomer in the asymmetric unit using the four-fold crystallographic symmetry operators.

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Components

#1: Protein Streptavidin


Mass: 16286.493 Da / Num. of mol.: 1 / Mutation: H151C
Source method: isolated from a genetically manipulated source
Details: Synthetic gene / Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: pSSAV / Production host: Bacillus subtilis (bacteria) / Strain (production host): WB800 / References: UniProt: P22629
#2: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S
#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.: 70 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsthe 8-residue loop region was modified from TTEANAWK to DSSNGSDG

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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: 1.75 Å3/Da / Density % sol: 29.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50% Tacsimate, 10% glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 7, 2010 / Details: Osmic multilayer
RadiationMonochromator: Osmic multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 8958 / Num. obs: 8607 / % possible obs: 96.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 28.4
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.8 / Num. unique all: 776 / Rsym value: 0.0496 / % possible all: 88

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1SWE

1swe


Resolution: 2→19.39 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2252 / WRfactor Rwork: 0.1882 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8437 / SU B: 4.098 / SU ML: 0.114 / SU R Cruickshank DPI: 0.1995 / SU Rfree: 0.1652 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: REFINED INDIVIDUALLY. THE SF DATA DO NOT HAVE FREE SET MARKER.
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 394 4.9 %RANDOM
Rwork0.1882 ---
all0.1902 7585 --
obs0.1902 7585 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 83.47 Å2 / Biso mean: 37.5624 Å2 / Biso min: 21.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20 Å2
2---0.98 Å20 Å2
3---1.96 Å2
Refinement stepCycle: LAST / Resolution: 2→19.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms898 0 17 70 985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021936
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9231280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3635121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.78323.88936
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.97415122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.614154
X-RAY DIFFRACTIONr_chiral_restr0.0790.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02710
X-RAY DIFFRACTIONr_mcbond_it2.0482601
X-RAY DIFFRACTIONr_mcangle_it3.2042.5950
X-RAY DIFFRACTIONr_scbond_it4.2633.5335
X-RAY DIFFRACTIONr_scangle_it5.7674.5330
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 23 -
Rwork0.281 404 -
all-427 -
obs--100 %

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