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- PDB-6vjl: Streptavidin mutant M112 (G26C/A46C) -

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Basic information

Entry
Database: PDB / ID: 6vjl
TitleStreptavidin mutant M112 (G26C/A46C)
ComponentsStreptavidin
KeywordsBiotin-binding protein
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMarangoni, J.M. / Wu, S.C. / Fogen, D. / Wong, S.L. / Ng, K.K.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (Canada)05728 Canada
CitationJournal: Sci Rep / Year: 2020
Title: Engineering a disulfide-gated switch in streptavidin enables reversible binding without sacrificing binding affinity.
Authors: Marangoni, J.M. / Wu, S.C. / Fogen, D. / Wong, S.L. / Ng, K.K.S.
History
DepositionJan 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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 / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9592
Polymers16,7141
Non-polymers2441
Water2,810156
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8348
Polymers66,8574
Non-polymers9774
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_555y,x,-z1
Buried area11550 Å2
ΔGint-39 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.772, 57.772, 184.419
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-524-

HOH

21A-629-

HOH

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Components

#1: Protein Streptavidin


Mass: 16714.205 Da / Num. of mol.: 1 / Mutation: G26C, A46C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22629
#2: Chemical ChemComp-BTN / BIOTIN


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


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28% PEG 4000, 0.15 M ammonium sulfate, 50 mM Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 39166 / % possible obs: 99.9 % / Redundancy: 11 % / CC1/2: 1 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.076 / Rsym value: 0.073 / Net I/σ(I): 19.6
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.0101 / Num. unique obs: 2809 / CC1/2: 0.577 / Rrim(I) all: 1.11 / Rsym value: 0.0101 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135 2015/10/01refinement
XDS20161205data reduction
XSCALE20161205data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SWE

1swe


Resolution: 1.3→37.35 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 0.625 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.046
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2009 2002 -
Rwork0.19 --
all0.191 --
obs-38946 99.872 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 19.813 Å2
Baniso -1Baniso -2Baniso -3
1-0.231 Å20 Å20 Å2
2--0.231 Å20 Å2
3----0.462 Å2
Refinement stepCycle: LAST / Resolution: 1.3→37.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms918 0 16 156 1090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02968
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9091329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5935126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.80523.84639
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.93215130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.378154
X-RAY DIFFRACTIONr_chiral_restr0.0830.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02738
X-RAY DIFFRACTIONr_nbd_refined0.150.21050
X-RAY DIFFRACTIONr_nbtor_refined0.2840.21294
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0610.272
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1510.2134
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0720.26
X-RAY DIFFRACTIONr_mcbond_it1.9112.146495
X-RAY DIFFRACTIONr_mcangle_it2.923.01618
X-RAY DIFFRACTIONr_scbond_it2.7622.396470
X-RAY DIFFRACTIONr_scangle_it4.1683.24707
X-RAY DIFFRACTIONr_lrange_it7.3338.4441572
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
1.3-1.3340.2891390.2782671284598.76980.278
1.334-1.370.2811170.2522642276299.89140.252
1.37-1.410.2331240.2272566269199.96280.227
1.41-1.4530.1811460.202244325891000.202
1.453-1.5010.2111420.1912388253199.96050.191
1.501-1.5530.211300.1792326245799.95930.179
1.553-1.6120.1831340.183224823821000.183
1.612-1.6780.2061150.1752168228499.95620.175
1.678-1.7520.2181090.184209422031000.184
1.752-1.8370.176980.185199620941000.185
1.837-1.9370.2011120.18191020221000.18
1.937-2.0540.193960.185182119171000.185
2.054-2.1950.187780.18171417921000.18
2.195-2.370.213920.1941578167199.94020.194
2.37-2.5950.234910.199148215731000.199
2.595-2.90.173760.1871340141799.92940.187
2.9-3.3450.204730.187118912621000.187
3.345-4.0890.162590.1691033109399.90850.169
4.089-5.7480.193340.16783386899.88480.167
5.748-37.350.216370.2345025391000.234

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