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- PDB-6tja: Crystal structure of the SVS_A2 protein (W79F,G83L mutant) from a... -

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Basic information

Entry
Database: PDB / ID: 6tja
TitleCrystal structure of the SVS_A2 protein (W79F,G83L mutant) from ancestral sequence reconstruction at 2.27 A resolution
ComponentsSVS_variant_AS1
KeywordsBIOSYNTHETIC PROTEIN / Terpene cyclase / engineered enzyme
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesStreptomyces sp. CWA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 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 1.3Oct 4, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SVS_variant_AS1
B: SVS_variant_AS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3045
Polymers80,9862
Non-polymers3183
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&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 area4700 Å2
ΔGint-1 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.754, 104.928, 108.694
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_variant_AS1


Mass: 40492.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: artificial protein / Source: (gene. exp.) Streptomyces sp. CWA1 (bacteria) / Production host: Escherichia coli (E. coli) / References: EC: 4.2.3.158
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 53.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.2M Na phosphate 0.1M Bis-Tris-Propane pH 7.2 12% PEG 3350 Cryoprotection: 0.2M Na phosphate 0.1M Bis-Tris-Propane pH 7.2 20% PEG 3350 5mM MgCl2 FPP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.91841 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 28, 2019 / Details: KB mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.27→29.43 Å / Num. obs: 40139 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 30 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.05 / Net I/σ(I): 9.7
Reflection shellResolution: 2.27→2.34 Å / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3637 / CC1/2: 0.853 / Rpim(I) all: 0.264 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OKZ

4okz


Resolution: 2.27→29.43 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.785 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.191
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2013 5 %RANDOM
Rwork0.1824 ---
obs0.1844 38033 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 131.69 Å2 / Biso mean: 35.637 Å2 / Biso min: 18.36 Å2
Baniso -1Baniso -2Baniso -3
1-1.95 Å20 Å20 Å2
2---0.51 Å20 Å2
3----1.43 Å2
Refinement stepCycle: final / Resolution: 2.27→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5121 0 21 218 5360
Biso mean--40.86 35.72 -
Num. residues----648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135274
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174833
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.647159
X-RAY DIFFRACTIONr_angle_other_deg1.3651.57211108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9495641
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.20619.604328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05315810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6671565
X-RAY DIFFRACTIONr_chiral_restr0.0810.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025998
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021265
LS refinement shellResolution: 2.27→2.329 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 140 -
Rwork0.243 2761 -
all-2901 -
obs--99.55 %

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