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

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Basic information

Entry
Database: PDB / ID: 6ecd
TitleVlm2 thioesterase domain with genetically encoded 2,3-diaminopropionic acid bound with a tetradepsipeptide
Components
  • Vlm2
  • tetradepsipeptide
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 / secondary metabolite biosynthetic process / lipid biosynthetic process / catalytic activity / phosphopantetheine binding / antibiotic biosynthetic process / cytoplasm
Similarity search - Function
Polyketide synthase, thioesterase domain / Thioesterase / Condensation domain / Condensation domain / Amino acid adenylation domain / Thioesterase / Thioesterase domain / Polyketide synthase, ketoreductase domain / KR domain / ANL, N-terminal domain ...Polyketide synthase, thioesterase domain / Thioesterase / Condensation domain / Condensation domain / Amino acid adenylation domain / Thioesterase / Thioesterase domain / Polyketide synthase, ketoreductase domain / KR domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / AMP-binding enzyme, C-terminal domain superfamily / 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: 1.9 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 / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vlm2
B: tetradepsipeptide


Theoretical massNumber of molelcules
Total (without water)33,4842
Polymers33,4842
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-2 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.298, 152.298, 152.298
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number207
Space group name H-MP432
Space group name HallP423
Symmetry operation#1: x,y,z
#2: x,-z,y
#3: x,z,-y
#4: z,y,-x
#5: -z,y,x
#6: -y,x,z
#7: y,-x,z
#8: z,x,y
#9: y,z,x
#10: -y,-z,x
#11: z,-x,-y
#12: -y,z,-x
#13: -z,-x,y
#14: -z,x,-y
#15: y,-z,-x
#16: x,-y,-z
#17: -x,y,-z
#18: -x,-y,z
#19: y,x,-z
#20: -y,-x,-z
#21: z,-y,x
#22: -z,-y,-x
#23: -x,z,y
#24: -x,-z,-y
Components on special symmetry positions
IDModelComponents
11A-2759-

HOH

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Components

#1: Protein Vlm2


Mass: 33095.512 Da / Num. of mol.: 1 / 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 tetradepsipeptide


Mass: 388.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 4.42 Å3/Da / Density % sol: 72.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.65 M DL-malic acid, pH 8.0, 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: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 13, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→107.69 Å / Num. obs: 48063 / % possible obs: 100 % / Redundancy: 37.2 % / Biso Wilson estimate: 37.63 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.02 / Rrim(I) all: 0.124 / Net I/σ(I): 23.3
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 3071

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Processing

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

6ecb


Resolution: 1.9→107.69 Å / SU ML: 0.1974 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7972
RfactorNum. reflection% reflection
Rfree0.2141 2658 5.53 %
Rwork0.1881 --
obs0.1895 48054 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 59.42 Å2
Refinement stepCycle: LAST / Resolution: 1.9→107.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 12 106 1904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171856
X-RAY DIFFRACTIONf_angle_d1.40152529
X-RAY DIFFRACTIONf_chiral_restr0.0923285
X-RAY DIFFRACTIONf_plane_restr0.0104335
X-RAY DIFFRACTIONf_dihedral_angle_d11.33961092
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.31261380.28172356X-RAY DIFFRACTION100
1.93-1.970.26081370.24522341X-RAY DIFFRACTION99.96
1.97-2.010.23651370.22212338X-RAY DIFFRACTION100
2.01-2.060.21931380.21552344X-RAY DIFFRACTION100
2.06-2.10.231370.2042342X-RAY DIFFRACTION100
2.1-2.160.21991370.18182365X-RAY DIFFRACTION99.96
2.16-2.210.23741380.18192338X-RAY DIFFRACTION100
2.21-2.280.19591370.18262346X-RAY DIFFRACTION99.96
2.28-2.350.19991390.1852361X-RAY DIFFRACTION100
2.35-2.440.23691380.18632367X-RAY DIFFRACTION99.96
2.44-2.540.19041380.1932369X-RAY DIFFRACTION100
2.54-2.650.23091390.20332370X-RAY DIFFRACTION100
2.65-2.790.26141400.21512385X-RAY DIFFRACTION100
2.79-2.960.21971390.22242385X-RAY DIFFRACTION100
2.96-3.190.22331410.19432408X-RAY DIFFRACTION100
3.19-3.520.18751420.18132416X-RAY DIFFRACTION99.96
3.52-4.020.20571420.15872433X-RAY DIFFRACTION100
4.02-5.070.19011450.14882472X-RAY DIFFRACTION99.96
5.07-107.860.22291560.21162660X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: 351.708539507 Å / Origin y: 132.478698021 Å / Origin z: 381.98961583 Å
111213212223313233
T0.264430306598 Å2-0.0851683344578 Å20.00330180417594 Å2-0.283457118476 Å20.0397785642006 Å2--0.371808040879 Å2
L1.40649296683 °20.445982586261 °20.11125870367 °2-1.12130267716 °20.0130446160556 °2--1.62917544175 °2
S-0.0383682354524 Å °-0.0153669234738 Å °-0.105008310208 Å °0.0670211949655 Å °0.0302742716935 Å °0.192591321298 Å °0.0292006980122 Å °-0.0702798317345 Å °-0.000245106582512 Å °
Refinement TLS groupSelection details: all

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