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- PDB-6ecc: Vlm2 thioesterase domain wild type structure 2 -

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Basic information

Entry
Database: PDB / ID: 6ecc
TitleVlm2 thioesterase domain wild type structure 2
ComponentsVlm2
KeywordsHYDROLASE / thioesterase / thioesterase domain / NRPS / non-ribosomal peptide synthetase / nonribosomal peptide synthetase / valinomycin / depsipeptide
Function / homology
Function and homology information


amide biosynthetic process / : / organonitrogen compound biosynthetic process / secondary metabolite biosynthetic process / carboxylic acid metabolic process / lipid biosynthetic process / phosphopantetheine binding / antibiotic biosynthetic process / catalytic activity
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 / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
Water3,081171
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 area10320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.202, 152.202, 152.202
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

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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 / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 4.44 Å3/Da / Density % sol: 72.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.65 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: Aug 8, 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: 1.8→152.2 Å / Num. obs: 55855 / % possible obs: 99.4 % / Redundancy: 12.7 % / Biso Wilson estimate: 28.31 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.023 / Rrim(I) all: 0.083 / Χ2: 0.94 / Net I/σ(I): 19
Reflection shellResolution: 1.8→1.84 Å / Num. measured obs: 19234 / Num. unique obs: 3083 / CC1/2: 0.4

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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: 1.8→87.87 Å / SU ML: 0.1973 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.34
RfactorNum. reflection% reflection
Rfree0.1898 3093 5.54 %
Rwork0.1757 --
obs0.1765 55838 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.37 Å2
Refinement stepCycle: LAST / Resolution: 1.8→87.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1742 0 0 171 1913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01871791
X-RAY DIFFRACTIONf_angle_d1.47552438
X-RAY DIFFRACTIONf_chiral_restr0.0945271
X-RAY DIFFRACTIONf_plane_restr0.0115322
X-RAY DIFFRACTIONf_dihedral_angle_d13.3381060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.33741320.3292199X-RAY DIFFRACTION92.98
1.83-1.860.27271360.28152280X-RAY DIFFRACTION95.49
1.86-1.890.2591360.24962310X-RAY DIFFRACTION97.84
1.89-1.920.25441390.23042364X-RAY DIFFRACTION99.13
1.92-1.960.21711360.21422336X-RAY DIFFRACTION99.64
1.96-20.20961390.18472373X-RAY DIFFRACTION100
2-2.050.20271390.17372375X-RAY DIFFRACTION100
2.05-2.090.1831390.16712389X-RAY DIFFRACTION100
2.09-2.150.17161390.16652367X-RAY DIFFRACTION100
2.15-2.20.17471390.15952390X-RAY DIFFRACTION100
2.2-2.270.18451410.15142396X-RAY DIFFRACTION100
2.27-2.340.14931400.15672387X-RAY DIFFRACTION100
2.34-2.420.2011400.15742398X-RAY DIFFRACTION100
2.42-2.520.16941400.16742390X-RAY DIFFRACTION100
2.52-2.640.19391410.17342411X-RAY DIFFRACTION100
2.64-2.780.20651410.18282407X-RAY DIFFRACTION100
2.78-2.950.18441410.1892428X-RAY DIFFRACTION100
2.95-3.180.19661430.16792430X-RAY DIFFRACTION100
3.18-3.50.18661430.16122438X-RAY DIFFRACTION100
3.5-40.15661460.14792487X-RAY DIFFRACTION100
4-5.040.16731460.14412501X-RAY DIFFRACTION100
5.04-87.980.21421570.22182689X-RAY DIFFRACTION99.72
Refinement TLS params.Method: refined / Origin x: 352.486685536 Å / Origin y: 131.926690914 Å / Origin z: 382.008725783 Å
111213212223313233
T0.168799007254 Å2-0.0437854024413 Å20.0087951740409 Å2-0.187739773184 Å20.0154347098075 Å2--0.239739418369 Å2
L1.26622623064 °20.19559738663 °20.0928414641124 °2-1.11105042692 °2-0.0735866831786 °2--1.30757683486 °2
S-0.017352752661 Å °-0.000440528653908 Å °-0.0492436368125 Å °0.0805722767329 Å °0.0245269143378 Å °0.164957358917 Å °0.00490800753509 Å °-0.0436679475558 Å °-9.20945923772E-6 Å °
Refinement TLS groupSelection details: all

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