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- PDB-6t1e: Streptavidin variants harbouring an artificial organocatalyst bas... -

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Basic information

Entry
Database: PDB / ID: 6t1e
TitleStreptavidin variants harbouring an artificial organocatalyst based cofactor
ComponentsStreptavidin
KeywordsBiotin-binding protein / artificial cofactor / streptavidin / catalyst
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
ACETATE ION / Chem-HL9 / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsLechner, H. / Hocker, B.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundJ 3994 Austria
CitationJournal: Chembiochem / Year: 2021
Title: An Artificial Cofactor Catalyzing the Baylis-Hillman Reaction with Designed Streptavidin as Protein Host*.
Authors: Lechner, H. / Emann, V.R. / Breuning, M. / Hocker, B.
History
DepositionOct 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3727
Polymers16,5981
Non-polymers7746
Water2,054114
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,48928
Polymers66,3924
Non-polymers3,09724
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 area12370 Å2
ΔGint-77 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.511, 57.511, 174.663
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-523-

HOH

21A-608-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Streptavidin


Mass: 16598.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629

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Non-polymers , 5 types, 120 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-HL9 / 5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-(1-pyridin-4-ylpiperidin-4-yl)pentanamide


Mass: 403.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29N5O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: (NH4)2SO4 1.8 M, NaCH3COO 0.1 M, pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.3→29.76 Å / Num. obs: 36595 / % possible obs: 99.92 % / Redundancy: 14.4 % / Biso Wilson estimate: 17 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08801 / Rpim(I) all: 0.02393 / Rrim(I) all: 0.09129 / Net I/σ(I): 18.71
Reflection shellResolution: 1.3→1.346 Å / Num. unique obs: 3573 / CC1/2: 0.398

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→29.76 Å / SU ML: 0.1288 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.1802
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1579 1830 5 %
Rwork0.1289 34765 -
obs0.1303 36595 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.68 Å2
Refinement stepCycle: LAST / Resolution: 1.3→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms937 0 51 114 1102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01671100
X-RAY DIFFRACTIONf_angle_d1.40741510
X-RAY DIFFRACTIONf_chiral_restr0.3649160
X-RAY DIFFRACTIONf_plane_restr0.0102197
X-RAY DIFFRACTIONf_dihedral_angle_d12.7065696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.29571382608X-RAY DIFFRACTION99.35
1.33-1.370.29361380.26372629X-RAY DIFFRACTION100
1.37-1.420.28811380.23122627X-RAY DIFFRACTION100
1.42-1.470.21231390.19142632X-RAY DIFFRACTION99.96
1.47-1.530.17821390.16132647X-RAY DIFFRACTION100
1.53-1.60.181390.13342650X-RAY DIFFRACTION99.93
1.6-1.680.15691400.11242650X-RAY DIFFRACTION100
1.68-1.790.11861402656X-RAY DIFFRACTION100
1.79-1.930.11211412674X-RAY DIFFRACTION99.93
1.93-2.120.1161402668X-RAY DIFFRACTION100
2.12-2.430.12881432710X-RAY DIFFRACTION99.96
2.43-3.050.14491430.11992735X-RAY DIFFRACTION99.97
3.05-29.760.17311520.14632879X-RAY DIFFRACTION99.54

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