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- PDB-6t32: Streptavidin variants harbouring an artificial organocatalyst bas... -

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Basic information

Entry
Database: PDB / ID: 6t32
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: 1.75 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
A: Streptavidin
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8694
Polymers33,0622
Non-polymers8072
Water3,459192
1
A: Streptavidin
B: Streptavidin
hetero molecules

A: Streptavidin
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7388
Polymers66,1244
Non-polymers1,6144
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area9090 Å2
ΔGint-56 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.330, 85.085, 99.444
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-307-

HOH

21A-348-

HOH

31B-374-

HOH

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Components

#1: Protein Streptavidin /


Mass: 16530.982 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 1.83 Å3/Da / Density % sol: 32.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: CHES 0.1 M pH 9.5 30% PEG 3000

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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: Jun 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.745→42.89 Å / Num. obs: 24739 / % possible obs: 98.47 % / Redundancy: 4.8 % / Biso Wilson estimate: 27.85 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.05
Reflection shellResolution: 1.745→1.807 Å / Num. unique obs: 2318 / CC1/2: 0.556

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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: 1.75→42.89 Å / SU ML: 0.2213 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.5114
RfactorNum. reflection% reflection
Rfree0.1909 1237 5 %
Rwork0.1619 --
obs0.1633 24732 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.23 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 56 192 2050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01151969
X-RAY DIFFRACTIONf_angle_d1.18652707
X-RAY DIFFRACTIONf_chiral_restr0.0742297
X-RAY DIFFRACTIONf_plane_restr0.0068342
X-RAY DIFFRACTIONf_dihedral_angle_d12.68581386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.810.3681300.33292472X-RAY DIFFRACTION94.76
1.81-1.90.26661360.24692581X-RAY DIFFRACTION98.58
1.9-20.24061360.19132589X-RAY DIFFRACTION99.02
2-2.120.21031370.17522597X-RAY DIFFRACTION98.95
2.12-2.290.21451360.1592581X-RAY DIFFRACTION98.34
2.29-2.520.1811380.15432631X-RAY DIFFRACTION99.68
2.52-2.880.19681400.16082655X-RAY DIFFRACTION99.5
2.88-3.630.19521380.15362633X-RAY DIFFRACTION98.54
3.63-42.890.1531460.14232756X-RAY DIFFRACTION98.88
Refinement TLS params.Method: refined / Origin x: -5.01338499361 Å / Origin y: -27.1559097273 Å / Origin z: -19.3421619355 Å
111213212223313233
T0.173016903607 Å20.00147931812759 Å20.0472970128158 Å2-0.181133118399 Å2-0.0143893967449 Å2--0.194227083052 Å2
L1.31111650572 °2-0.148072623799 °20.710173887548 °2-1.38595951071 °2-0.0779133912077 °2--1.95322536607 °2
S-0.0453762377243 Å °-0.147869854476 Å °0.0360253526428 Å °0.110394066029 Å °-0.031322340639 Å °0.132156603258 Å °-0.0700047776828 Å °-0.182049640185 Å °0.0700114215234 Å °
Refinement TLS groupSelection details: all

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