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- PDB-6ece: Vlm2 thioesterase domain with genetically encoded 2,3-diaminoprop... -

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Basic information

Entry
Database: PDB / ID: 6ece
TitleVlm2 thioesterase domain with genetically encoded 2,3-diaminopropionic acid bound with a dodecadepsipeptide, space group H3
Components
  • Vlm2
  • dodecadepsipeptide
KeywordsHYDROLASE / thioesterase / thioesterase domain / NRPS / non-ribosomal peptide synthetase / nonribosomal peptide synthetase / valinomycin / depsipeptide / unnatural amino acid / 2 / 3-diaminopropionic acid
Function / homology
Function and homology information


: / amino acid activation for nonribosomal peptide biosynthetic process / carboxylic acid metabolic process / secondary metabolite biosynthetic process / lipid biosynthetic process / phosphopantetheine binding / antibiotic biosynthetic process / catalytic activity / cytosol
Similarity search - Function
Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / Polyketide synthase, ketoreductase domain / KR domain / ANL, N-terminal domain ...Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / Polyketide synthase, ketoreductase domain / KR domain / ANL, N-terminal domain / PKS_KR / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Biological speciesStreptomyces tsusimaensis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAlonzo, D.A. / Huguenin-Dezot, N. / Heberlig, G.W. / Mahesh, M. / Nguyen, D.P. / Dornan, M.H. / Boddy, C.N. / Chin, J.W. / Schmeing, T.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)106615 Canada
CitationJournal: Nature / Year: 2019
Title: Trapping biosynthetic acyl-enzyme intermediates with encoded 2,3-diaminopropionic acid.
Authors: Huguenin-Dezot, N. / Alonzo, D.A. / Heberlig, G.W. / Mahesh, M. / Nguyen, D.P. / Dornan, M.H. / Boddy, C.N. / Schmeing, T.M. / Chin, J.W.
History
DepositionAug 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: 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
Revision 1.5Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vlm2
B: Vlm2
C: dodecadepsipeptide
D: dodecadepsipeptide


Theoretical massNumber of molelcules
Total (without water)68,4504
Polymers68,4504
Non-polymers00
Water1,60389
1
A: Vlm2
C: dodecadepsipeptide


Theoretical massNumber of molelcules
Total (without water)34,2252
Polymers34,2252
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vlm2
D: dodecadepsipeptide


Theoretical massNumber of molelcules
Total (without water)34,2252
Polymers34,2252
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.571, 77.571, 235.151
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-2702-

HOH

21A-2749-

HOH

31B-2705-

HOH

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Components

#1: Protein Vlm2


Mass: 33095.512 Da / Num. of mol.: 2 / Fragment: thioesterase domain (UNP residues 2368-2655)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces tsusimaensis (bacteria) / Gene: vlm2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q1PSF3, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Protein/peptide dodecadepsipeptide


Mass: 1129.336 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.04 Å3/Da / Density % sol: 39.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.3 M DL-malic acid, pH 8.1, 25 mM HEPES, pH 8.0, 100 mM sodium chloride, 0.2 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 15, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→64.59 Å / Num. obs: 35685 / % possible obs: 100 % / Redundancy: 5 % / Biso Wilson estimate: 39.62 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.053 / Rrim(I) all: 0.088 / Χ2: 0.89 / Net I/σ(I): 9.8
Reflection shellResolution: 2→2.05 Å / Num. measured obs: 13233 / Num. unique obs: 2682 / CC1/2: 0.382

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6ECB

6ecb


Resolution: 2→64.59 Å / SU ML: 0.2718 / Cross valid method: FREE R-VALUE / σ(F): 2.09 / Phase error: 26.854
RfactorNum. reflection% reflection
Rfree0.2428 1784 5 %
Rwork0.2092 --
obs0.2109 35678 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 52.5 Å2
Refinement stepCycle: LAST / Resolution: 2→64.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3624 0 26 89 3739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313741
X-RAY DIFFRACTIONf_angle_d0.52735097
X-RAY DIFFRACTIONf_chiral_restr0.0404581
X-RAY DIFFRACTIONf_plane_restr0.003664
X-RAY DIFFRACTIONf_dihedral_angle_d10.00732192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.33411370.33612627X-RAY DIFFRACTION100
2.05-2.110.33141360.30092588X-RAY DIFFRACTION100
2.11-2.180.31491350.28662610X-RAY DIFFRACTION99.96
2.18-2.260.28551410.26592620X-RAY DIFFRACTION100
2.26-2.350.28661360.23832587X-RAY DIFFRACTION100
2.35-2.460.26471370.24092610X-RAY DIFFRACTION100
2.46-2.590.27891390.2332639X-RAY DIFFRACTION100
2.59-2.750.27181360.23022580X-RAY DIFFRACTION100
2.75-2.960.25651370.22972612X-RAY DIFFRACTION100
2.96-3.260.23991370.2132605X-RAY DIFFRACTION100
3.26-3.730.22651370.1872605X-RAY DIFFRACTION100
3.73-4.70.19021370.17032594X-RAY DIFFRACTION100
4.7-64.630.24311390.19242617X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: 15.5882246133 Å / Origin y: -22.9006581781 Å / Origin z: -2.6962886655 Å
111213212223313233
T0.183971871162 Å20.0188415651042 Å20.016653382934 Å2-0.259487243445 Å20.0593743700041 Å2--0.223340416974 Å2
L-0.0874392317262 °2-0.00629268386751 °20.129391468763 °2-0.211129541292 °2-0.174882060704 °2--0.0605676394601 °2
S-0.00410471514168 Å °-0.00274066053027 Å °-0.00938065874199 Å °-0.0105228778644 Å °-0.0832642236366 Å °-0.06652136028 Å °-0.0173936762871 Å °-0.0272891415555 Å °2.9748438058E-12 Å °
Refinement TLS groupSelection details: all

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