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- PDB-6thu: Crystal structure of the SVS_A2 protein (A224I mutant) from ances... -

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Basic information

Entry
Database: PDB / ID: 6thu
TitleCrystal structure of the SVS_A2 protein (A224I mutant) from ancestral sequence reconstruction at 2.6 A resolution
ComponentsSVS_AS10 variant
KeywordsBIOSYNTHETIC PROTEIN / Crystal structure of the design protein SVS_AS10 variant at 2.6 A resolution BIOSYNTHETIC PROTEIN
Biological speciesStreptomyces sp. CWA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRudraraju, R. / Schnell, R. / Schneider, G.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Engineering of Ancestors as a Tool to Elucidate Structure, Mechanism, and Specificity of Extant Terpene Cyclase.
Authors: Schriever, K. / Saenz-Mendez, P. / Rudraraju, R.S. / Hendrikse, N.M. / Hudson, E.P. / Biundo, A. / Schnell, R. / Syren, P.O.
History
DepositionNov 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 31, 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

Downloads & links

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Assembly

Deposited unit
A: SVS_AS10 variant
B: SVS_AS10 variant


Theoretical massNumber of molelcules
Total (without water)81,0362
Polymers81,0362
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, The dimerization mode observed here is common in the protein family (EC:4.2.3.158)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-16 kcal/mol
Surface area25250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.910, 105.094, 108.253
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 SVS_AS10 variant


Mass: 40517.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Artificial design protein. / Source: (gene. exp.) Streptomyces sp. CWA1 (bacteria) / Production host: Escherichia coli (E. coli) / References: EC: 4.2.3.158
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 53 % / Description: rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Na phosphate 0.1M Bis-Tris-Propane pH 6.5 12% PEG 3350 Cryoprotection 0.2M Na phosphate 0.1M Bis-Tris-Propane pH 6.5 20% PEG 3350 5mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.91842 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 28, 2019
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91842 Å / Relative weight: 1
ReflectionResolution: 2.6→43.02 Å / Num. obs: 26961 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.033 / Net I/σ(I): 15.1
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.7 / Num. unique obs: 3237 / CC1/2: 0.801 / Rpim(I) all: 0.312 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OKZ

4okz


Resolution: 2.6→43 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.38 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.534 / ESU R Free: 0.259
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1367 5.1 %RANDOM
Rwork0.1897 ---
obs0.1911 25441 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 166.11 Å2 / Biso mean: 61.674 Å2 / Biso min: 37.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å2-0 Å2-0 Å2
2---1.12 Å2-0 Å2
3---2.02 Å2
Refinement stepCycle: final / Resolution: 2.6→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5161 0 0 45 5206
Biso mean---55.46 -
Num. residues----652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135299
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174846
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.6397200
X-RAY DIFFRACTIONr_angle_other_deg1.2951.57411135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4165644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.05519.517331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.99115818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0461566
X-RAY DIFFRACTIONr_chiral_restr0.070.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026039
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021279
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 88 -
Rwork0.267 1862 -
all-1950 -
obs--99.44 %

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