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- PDB-6ecb: Vlm2 thioesterase domain wild type structure 1 -

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Basic information

Entry
Database: PDB / ID: 6ecb
TitleVlm2 thioesterase domain wild type structure 1
ComponentsVlm2
KeywordsHYDROLASE / thioesterase / thioesterase domain / NRPS / non-ribosomal peptide synthetase / nonribosomal peptide synthetase / valinomycin / depsipeptide
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAlonzo, D.A. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vlm2


Theoretical massNumber of molelcules
Total (without water)33,0961
Polymers33,0961
Non-polymers00
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.399, 151.399, 151.399
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-2838-

HOH

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Components

#1: Protein Vlm2


Mass: 33096.496 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 4.37 Å3/Da / Density % sol: 71.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 1.65 M DL-malic acid, pH 9.5, 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: Aug 9, 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: 1.7→151.4 Å / Num. obs: 64289 / % possible obs: 98.3 % / Redundancy: 12.3 % / Biso Wilson estimate: 23.86 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.018 / Rrim(I) all: 0.066 / Χ2: 0.95 / Net I/σ(I): 21.8
Reflection shellResolution: 1.7→1.73 Å / Num. measured obs: 13565 / Num. unique obs: 3000 / CC1/2: 0.502

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
Cootmodel building
PHASERphasing
Aimlessdata scaling
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2VSQ

2vsq


Resolution: 1.7→87.41 Å / SU ML: 0.1896 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.4826
RfactorNum. reflection% reflectionSelection details
Rfree0.1877 3561 5.54 %Random selection
Rwork0.1723 ---
obs0.1732 64287 98.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.31 Å2
Refinement stepCycle: LAST / Resolution: 1.7→87.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1981 0 0 204 2185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092032
X-RAY DIFFRACTIONf_angle_d1.01132761
X-RAY DIFFRACTIONf_chiral_restr0.0587307
X-RAY DIFFRACTIONf_plane_restr0.0067364
X-RAY DIFFRACTIONf_dihedral_angle_d11.86291210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.35681250.32652114X-RAY DIFFRACTION87.56
1.72-1.750.33311290.29362146X-RAY DIFFRACTION88.73
1.75-1.770.29411300.25752204X-RAY DIFFRACTION90.36
1.77-1.80.25391320.2612252X-RAY DIFFRACTION92.33
1.8-1.830.26461380.22432348X-RAY DIFFRACTION96.84
1.83-1.860.2071430.20622427X-RAY DIFFRACTION99.54
1.86-1.90.20911420.19532418X-RAY DIFFRACTION100
1.9-1.930.20211410.18692429X-RAY DIFFRACTION99.73
1.93-1.970.1811430.16792440X-RAY DIFFRACTION100
1.97-2.020.18391430.16332459X-RAY DIFFRACTION100
2.02-2.060.16831430.16152427X-RAY DIFFRACTION100
2.06-2.110.17281440.16042449X-RAY DIFFRACTION100
2.11-2.170.16461430.15742437X-RAY DIFFRACTION100
2.17-2.240.16281440.14942460X-RAY DIFFRACTION100
2.24-2.310.16351430.14882450X-RAY DIFFRACTION100
2.31-2.390.18051440.15592467X-RAY DIFFRACTION100
2.39-2.490.16441450.16242464X-RAY DIFFRACTION100
2.49-2.60.17521440.172474X-RAY DIFFRACTION100
2.6-2.740.20241450.17662478X-RAY DIFFRACTION99.96
2.74-2.910.1961460.17772492X-RAY DIFFRACTION100
2.91-3.130.20221460.17612495X-RAY DIFFRACTION100
3.13-3.450.17591480.16142521X-RAY DIFFRACTION100
3.45-3.950.16981480.14852536X-RAY DIFFRACTION100
3.95-4.970.15471510.13952578X-RAY DIFFRACTION100
4.97-87.530.2161610.20982761X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: 347.85511523 Å / Origin y: 132.125905029 Å / Origin z: 378.959027135 Å
111213212223313233
T0.150215759234 Å2-0.0384762321274 Å2-0.0069519404475 Å2-0.158545542577 Å20.00930410102757 Å2--0.212354105593 Å2
L1.78207211198 °20.180562005129 °2-0.0738919572796 °2-1.42310626666 °2-0.0351199978704 °2--1.32889298224 °2
S0.0023652451436 Å °0.0680519056791 Å °0.0338545283182 Å °-0.0236362734825 Å °0.00573348952668 Å °0.2541853642 Å °-0.013485371318 Å °-0.0533489937213 Å °-0.0152806166512 Å °
Refinement TLS groupSelection details: all

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