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- PDB-6tjz: Crystal structure of the SVS_A2 protein (W156Y mutant) from ances... -

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Basic information

Entry
Database: PDB / ID: 6tjz
TitleCrystal structure of the SVS_A2 protein (W156Y mutant) from ancestral sequence reconstruction at 2.4 A resolution
ComponentsSVS_variant_AS3
KeywordsBIOSYNTHETIC PROTEIN / Terpene cyclase / engineered enzyme
Biological speciesStreptomyces sp. CWA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 27, 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 1.3Jan 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: SVS_variant_AS3
B: SVS_variant_AS3


Theoretical massNumber of molelcules
Total (without water)80,9052
Polymers80,9052
Non-polymers00
Water1,06359
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 area3780 Å2
ΔGint-14 kcal/mol
Surface area24720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.882, 104.583, 109.240
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_AS3


Mass: 40452.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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.: 59 / 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: 53.05 % / Description: rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 0.2M Na phosphate 0.1M Bis-Tris-Propane pH 6.3 18% PEG 3350 Cryoprotection: 0.2M Na phosphate 0.1M Bis-Tris-Propane pH 6.3 24% PEG 3350 5mM MgCl2 5 mM 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: 2.4→40.66 Å / Num. obs: 34301 / % possible obs: 100 % / Redundancy: 5.6 % / Biso Wilson estimate: 61.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.031 / Net I/σ(I): 10.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3555 / CC1/2: 0.739 / Rpim(I) all: 0.353 / % possible all: 99.9

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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: 2.4→25 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 8.128 / SU ML: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.301 / ESU R Free: 0.218
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2208 1735 5.1 %RANDOM
Rwork0.1799 ---
obs0.1821 32300 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 156.37 Å2 / Biso mean: 63.92 Å2 / Biso min: 43.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2---1.82 Å20 Å2
3---1.81 Å2
Refinement stepCycle: final / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5206 0 0 59 5265
Biso mean---59.43 -
Num. residues----659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135345
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174867
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.6417265
X-RAY DIFFRACTIONr_angle_other_deg1.3181.57311189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2435652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.94419.585337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18615819
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4191567
X-RAY DIFFRACTIONr_chiral_restr0.0720.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026115
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021286
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 122 -
Rwork0.292 2311 -
all-2433 -
obs--98.74 %

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