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- PDB-6t2l: Streptavidin variants harbouring an artificial organocatalyst bas... -

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Basic information

Entry
Database: PDB / ID: 6t2l
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
Chem-HL9 / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 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 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 1.3Jan 24, 2024Group: 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

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Assembly

Deposited unit
A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9974
Polymers16,4391
Non-polymers5583
Water3,189177
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,98616
Polymers65,7564
Non-polymers2,23112
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 area10630 Å2
ΔGint-47 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.215, 57.215, 174.866
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-301-

HOH

21A-302-

HOH

31A-325-

HOH

41A-451-

HOH

51A-455-

HOH

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Components

#1: Protein Streptavidin


Mass: 16438.887 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
#2: 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
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.18 Å3/Da / Density % sol: 43.48 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop
Details: 0.17M Na-acetate, 0.085M TRIS-HCl, pH 8.5, 25.5% PEG 4000, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1→43.72 Å / Num. obs: 78168 / % possible obs: 99.45 % / Redundancy: 8.5 % / Biso Wilson estimate: 9.19 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.49
Reflection shellResolution: 1→1.036 Å / Num. unique obs: 7610 / CC1/2: 0.356

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Processing

Software
NameVersionClassification
Coot1.16_3549model building
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6t1e

6t1e


Resolution: 1→43.72 Å / SU ML: 0.0948 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 14.5247
RfactorNum. reflection% reflection
Rfree0.1342 2101 2.69 %
Rwork0.1231 --
obs0.1235 78155 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.73 Å2
Refinement stepCycle: LAST / Resolution: 1→43.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms894 0 38 177 1109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081085
X-RAY DIFFRACTIONf_angle_d1.1021499
X-RAY DIFFRACTIONf_chiral_restr0.3458161
X-RAY DIFFRACTIONf_plane_restr0.0065196
X-RAY DIFFRACTIONf_dihedral_angle_d14.9787629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.020.32091370.34274935X-RAY DIFFRACTION98.22
1.02-1.050.30881360.2954952X-RAY DIFFRACTION98.59
1.05-1.080.2951370.27214951X-RAY DIFFRACTION98.78
1.08-1.110.23661370.20624975X-RAY DIFFRACTION98.99
1.11-1.140.17481390.16855020X-RAY DIFFRACTION99.27
1.14-1.190.15651390.14475013X-RAY DIFFRACTION99.38
1.19-1.230.15181380.14235023X-RAY DIFFRACTION99.38
1.23-1.290.15921400.12835049X-RAY DIFFRACTION99.67
1.29-1.360.1411390.11765050X-RAY DIFFRACTION99.75
1.36-1.440.11041400.10735070X-RAY DIFFRACTION99.94
1.44-1.550.11671410.09285110X-RAY DIFFRACTION99.9
1.55-1.710.11131410.08845097X-RAY DIFFRACTION99.96
1.71-1.960.09491420.09155152X-RAY DIFFRACTION99.96
1.96-2.470.10011440.09785219X-RAY DIFFRACTION99.98
2.47-43.720.1321510.11925438X-RAY DIFFRACTION99.93

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