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- PDB-6tiv: Crystal structure of the SVS_A2 protein (205-DREMH-209 /205-AQDLE... -

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Basic information

Entry
Database: PDB / ID: 6tiv
TitleCrystal structure of the SVS_A2 protein (205-DREMH-209 /205-AQDLE-209 mutant) from ancestral sequence reconstruction at 2.38 A resolution
ComponentsSVS variant AT2
KeywordsBIOSYNTHETIC PROTEIN / SVS_variant_AT2 BIOSYNTHETIC PROTEIN
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesStreptomyces sp. CWA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 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 22, 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

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Assembly

Deposited unit
A: SVS variant AT2
B: SVS variant AT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,14715
Polymers80,7232
Non-polymers1,42413
Water5,260292
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 area8140 Å2
ΔGint43 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.079, 104.250, 108.189
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 AT2


Mass: 40361.613 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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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 % / 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 20% PEG 3350

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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 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91842 Å / Relative weight: 1
ReflectionResolution: 2.38→29.66 Å / Num. obs: 34458 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 26 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.057 / Net I/σ(I): 7.7
Reflection shellResolution: 2.38→2.48 Å / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 3 / Num. unique obs: 4109 / CC1/2: 0.855 / Rpim(I) all: 0.234 / % possible all: 98.8

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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: 2.38→29 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.052 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.332 / ESU R Free: 0.211
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 1745 5.1 %RANDOM
Rwork0.1864 ---
obs0.1877 32477 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 112.95 Å2 / Biso mean: 29.722 Å2 / Biso min: 11.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å2-0 Å2-0 Å2
2---1.63 Å20 Å2
3---1.47 Å2
Refinement stepCycle: final / Resolution: 2.38→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5159 0 94 292 5545
Biso mean--45.52 32.41 -
Num. residues----654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135378
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174954
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.647274
X-RAY DIFFRACTIONr_angle_other_deg1.3681.5711401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1445647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.61219.787328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.80515810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2991564
X-RAY DIFFRACTIONr_chiral_restr0.0850.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026046
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021262
LS refinement shellResolution: 2.38→2.441 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 130 -
Rwork0.284 2334 -
all-2464 -
obs--99.96 %

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