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- PDB-6vjk: Streptavidin mutant M88 (N49C/A86C) -

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Basic information

Entry
Database: PDB / ID: 6vjk
TitleStreptavidin mutant M88 (N49C/A86C)
ComponentsStreptavidin
KeywordsBiotin-binding protein / ANTIMICROBIAL PROTEIN
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like, conserved site / Avidin-like domain signature. / Avidin / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile.
Similarity search - Domain/homology
BIOTIN / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 (NSERC, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Streptavidin
B: Streptavidin
C: Streptavidin
D: Streptavidin
E: Streptavidin
F: Streptavidin
G: Streptavidin
H: Streptavidin
I: Streptavidin
J: Streptavidin
K: Streptavidin
L: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,53224
Polymers157,60012
Non-polymers2,93212
Water30,0311667
1
A: Streptavidin
B: Streptavidin
hetero molecules

E: Streptavidin
F: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5118
Polymers52,5334
Non-polymers9774
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Buried area11580 Å2
ΔGint-41 kcal/mol
Surface area19220 Å2
MethodPISA
2
C: Streptavidin
D: Streptavidin
I: Streptavidin
J: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5118
Polymers52,5334
Non-polymers9774
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11590 Å2
ΔGint-40 kcal/mol
Surface area19100 Å2
MethodPISA
3
G: Streptavidin
H: Streptavidin
hetero molecules

K: Streptavidin
L: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5118
Polymers52,5334
Non-polymers9774
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area11590 Å2
ΔGint-40 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.260, 79.549, 281.549
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Streptavidin /


Mass: 13133.327 Da / Num. of mol.: 12 / Mutation: N49C, A86C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: pET29B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22629
#2: Chemical
ChemComp-BTN / BIOTIN / Biotin


Mass: 244.311 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1667 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 21% PEG 3350, 8% glycerol, 100 mM Bis-Tris-Cl pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Apr 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→50.0005 Å / Num. obs: 176700 / % possible obs: 98.7 % / Redundancy: 8.1 % / Biso Wilson estimate: 16.2 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.048 / Rrim(I) all: 0.142 / Rsym value: 0.133 / Net I/σ(I): 13
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 5.4 / Num. unique obs: 25745 / CC1/2: 0.814 / Rpim(I) all: 0.262 / Rrim(I) all: 0.793 / Rsym value: 0.747 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135 2015/10/01refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SWE

1swe


Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.644 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.099 / ESU R Free: 0.097
RfactorNum. reflection% reflection
Rfree0.2153 8889 -
Rwork0.1841 --
all0.186 --
obs-176551 98.462 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 20.982 Å2
Baniso -1Baniso -2Baniso -3
1--0.333 Å20 Å20 Å2
2--0.885 Å20 Å2
3----0.552 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10826 0 192 1667 12685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211313
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.91215481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4351440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.72223.571448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.601151505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1581548
X-RAY DIFFRACTIONr_chiral_restr0.0760.21727
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028608
X-RAY DIFFRACTIONr_nbd_refined0.1490.213338
X-RAY DIFFRACTIONr_nbtor_refined0.2820.215002
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0650.21172
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1640.2392
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1230.218
X-RAY DIFFRACTIONr_mcbond_it1.6412.4495796
X-RAY DIFFRACTIONr_mcangle_it2.5453.4317224
X-RAY DIFFRACTIONr_scbond_it2.1962.6045517
X-RAY DIFFRACTIONr_scangle_it3.3043.5628257
X-RAY DIFFRACTIONr_lrange_it5.7339.19519023
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
1.6-1.6420.2536310.215123871311799.24530.215
1.642-1.6860.2246080.203120341278698.87380.203
1.686-1.7350.246070.208116661240998.9040.208
1.735-1.7890.2276080.199113921208699.28840.199
1.789-1.8470.2325840.198109401173898.17690.198
1.847-1.9120.2325530.205103021131095.9770.205
1.912-1.9840.2165480.197103221096499.14260.197
1.984-2.0650.2245160.19699461054799.19410.196
2.065-2.1570.2154990.19296341019699.38210.192
2.157-2.2620.235120.1959082967399.18330.195
2.262-2.3840.2374690.2028367924995.53470.202
2.384-2.5280.2364370.1938212877098.62030.193
2.528-2.7020.2364170.1917811825199.72120.191
2.702-2.9180.2223750.1787283770499.40290.178
2.918-3.1950.2163510.1716735713899.27150.171
3.195-3.570.1933300.1665768647594.17760.166
3.57-4.1190.1752910.1555430573999.68640.155
4.119-5.0360.1822480.1494665492599.75630.149
5.036-7.0870.1731860.1813457386994.15870.181
7.087-50.0050.2391120.1892192230899.82670.189

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