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

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Basic information

Entry
Database: PDB / ID: 6ecf
TitleVlm2 thioesterase domain with genetically encoded 2,3-diaminopropionic acid bound with a dodecadepsipeptide, space group P1
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 / 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: 2.5 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: Vlm2
D: Vlm2
E: Vlm2
F: Vlm2
G: dodecadepsipeptide
I: dodecadepsipeptide
H: dodecadepsipeptide
K: dodecadepsipeptide
J: dodecadepsipeptide
L: dodecadepsipeptide


Theoretical massNumber of molelcules
Total (without water)205,34912
Polymers205,34912
Non-polymers00
Water3,711206
1
A: Vlm2
G: 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
I: dodecadepsipeptide


Theoretical massNumber of molelcules
Total (without water)34,2252
Polymers34,2252
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Vlm2
H: dodecadepsipeptide


Theoretical massNumber of molelcules
Total (without water)34,2252
Polymers34,2252
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Vlm2
K: dodecadepsipeptide


Theoretical massNumber of molelcules
Total (without water)34,2252
Polymers34,2252
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Vlm2
J: dodecadepsipeptide


Theoretical massNumber of molelcules
Total (without water)34,2252
Polymers34,2252
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Vlm2
L: 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)76.996, 77.129, 90.329
Angle α, β, γ (deg.)91.768, 114.886, 117.938
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Vlm2


Mass: 33095.512 Da / Num. of mol.: 6 / 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.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.06 Å3/Da / Density % sol: 40.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.4 M DL-malic acid, 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: Dec 3, 2017
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: 2.5→78.55 Å / Num. obs: 53945 / % possible obs: 97.6 % / Redundancy: 1.7 % / Biso Wilson estimate: 41.08 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.071 / Rrim(I) all: 0.1 / Χ2: 0.55 / Net I/σ(I): 4.1
Reflection shellResolution: 2.5→2.58 Å / Num. measured obs: 9480 / Num. unique obs: 5422 / CC1/2: 0.706

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Processing

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

6ecb


Resolution: 2.5→78.55 Å / SU ML: 0.329 / Cross valid method: FREE R-VALUE / σ(F): 2.08 / Phase error: 26.508
RfactorNum. reflection% reflection
Rfree0.2489 2683 4.97 %
Rwork0.1969 --
obs0.1995 53933 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 48.32 Å2
Refinement stepCycle: LAST / Resolution: 2.5→78.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11451 0 93 206 11750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002411837
X-RAY DIFFRACTIONf_angle_d0.557916106
X-RAY DIFFRACTIONf_chiral_restr0.04041817
X-RAY DIFFRACTIONf_plane_restr0.00282110
X-RAY DIFFRACTIONf_dihedral_angle_d11.3556960
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.550.29921590.24232661X-RAY DIFFRACTION97.01
2.55-2.590.30441270.24182711X-RAY DIFFRACTION97.19
2.59-2.650.26351430.2392735X-RAY DIFFRACTION97.3
2.65-2.710.29031350.23452588X-RAY DIFFRACTION96.63
2.71-2.770.34451260.24972739X-RAY DIFFRACTION96.82
2.77-2.840.29831200.24042754X-RAY DIFFRACTION97.32
2.84-2.910.30611660.23622611X-RAY DIFFRACTION97.17
2.91-30.28451690.22052692X-RAY DIFFRACTION97.48
3-3.10.30611210.22182706X-RAY DIFFRACTION97.68
3.1-3.210.2771060.21812748X-RAY DIFFRACTION97.47
3.21-3.340.2661260.22282687X-RAY DIFFRACTION97.54
3.34-3.490.28981300.19422732X-RAY DIFFRACTION98.08
3.49-3.670.21721140.18082731X-RAY DIFFRACTION97.57
3.67-3.90.18591550.17242675X-RAY DIFFRACTION97.82
3.9-4.20.24371190.17022698X-RAY DIFFRACTION97.68
4.2-4.630.19371830.15832675X-RAY DIFFRACTION98.28
4.63-5.290.19731520.15452724X-RAY DIFFRACTION98.43
5.29-6.670.26731740.212657X-RAY DIFFRACTION97.99
6.67-78.590.26351580.19732726X-RAY DIFFRACTION98.67

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