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- PDB-6t30: Streptavidin variants harbouring an artificial organocatalyst bas... -

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Basic information

Entry
Database: PDB / ID: 6t30
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: 1.8 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 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 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 1.3Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
B: Streptavidin
A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9958
Polymers32,9102
Non-polymers1,0856
Water2,054114
1
B: Streptavidin
A: Streptavidin
hetero molecules

B: Streptavidin
A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,99016
Polymers65,8204
Non-polymers2,17112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area10290 Å2
ΔGint-44 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.132, 55.132, 131.209
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-311-

HOH

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Components

#1: Protein Streptavidin


Mass: 16454.887 Da / Num. of mol.: 2
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.: 2 / 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.: 3 / 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.: 114 / 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: 1.75 Å3/Da / Density % sol: 29.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M di-Sodium hydrogen phosphate 20% PEG 3350

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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 PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→47.75 Å / Num. obs: 21936 / % possible obs: 98.89 % / Redundancy: 10.9 % / Biso Wilson estimate: 38.93 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.36
Reflection shellResolution: 1.8→1.865 Å / Num. unique obs: 2112 / CC1/2: 0.366

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Processing

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

6t1e


Resolution: 1.8→47.75 Å / SU ML: 0.2301 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.5861
RfactorNum. reflection% reflection
Rfree0.2297 1094 4.99 %
Rwork0.1863 --
obs0.1885 21916 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 50.28 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1838 0 74 114 2026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01411967
X-RAY DIFFRACTIONf_angle_d1.27372681
X-RAY DIFFRACTIONf_chiral_restr0.0837291
X-RAY DIFFRACTIONf_plane_restr0.0078338
X-RAY DIFFRACTIONf_dihedral_angle_d14.21211232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.880.38641320.36462494X-RAY DIFFRACTION97.84
1.88-1.980.3111340.28022563X-RAY DIFFRACTION98.29
1.98-2.110.25691330.23682554X-RAY DIFFRACTION98.64
2.11-2.270.25061340.20142552X-RAY DIFFRACTION98.53
2.27-2.50.29461380.20382603X-RAY DIFFRACTION99.35
2.5-2.860.24991360.19422611X-RAY DIFFRACTION99.31
2.86-3.60.21291390.17642648X-RAY DIFFRACTION99.82
3.6-47.750.20351480.16562797X-RAY DIFFRACTION99.29
Refinement TLS params.Method: refined / Origin x: 3.68936016905 Å / Origin y: -7.67456813277 Å / Origin z: -14.283079717 Å
111213212223313233
T0.311557142439 Å20.0753884247952 Å2-0.00160615969564 Å2-0.233328829656 Å20.0229270861393 Å2--0.217374103256 Å2
L1.39955277986 °2-0.036934787715 °2-0.154631225943 °2-1.58543113606 °2-0.0594050984715 °2--2.65875583489 °2
S-0.0552901722987 Å °-0.228198942607 Å °-0.198435341923 Å °0.0920069983448 Å °-0.00877210965107 Å °-0.080069805946 Å °0.148013959838 Å °0.0628791089715 Å °0.0113323545634 Å °
Refinement TLS groupSelection details: all

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