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- PDB-5d7b: Trigonal Crystal Structure of an acetylester hydrolase from Coryn... -

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Basic information

Entry
Database: PDB / ID: 5d7b
TitleTrigonal Crystal Structure of an acetylester hydrolase from Corynebacterium glutamicum
ComponentsHomoserine O-acetyltransferase
KeywordsHYDROLASE / Acetylester hydrolase / Alpha/Beta-Hydrolase
Function / homology
Function and homology information


homoserine O-acetyltransferase activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / biosynthetic process / hydrolase activity
Similarity search - Function
Homoserine/serine acetyltransferase MetX-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable esterase Cgl0839
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsNiefind, K. / Toelzer, C. / Pal, S. / Altenbuchner, J. / Watzlawick, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB 635 Germany
CitationJournal: Febs Lett. / Year: 2016
Title: A novel esterase subfamily with alpha / beta-hydrolase fold suggested by structures of two bacterial enzymes homologous to l-homoserine O-acetyl transferases.
Authors: Tolzer, C. / Pal, S. / Watzlawick, H. / Altenbuchner, J. / Niefind, K.
History
DepositionAug 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: 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: Homoserine O-acetyltransferase
B: Homoserine O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,12217
Polymers77,7402
Non-polymers1,38115
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-21 kcal/mol
Surface area24240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.393, 143.393, 197.783
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-510-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 1:349 )
211chain 'B' and (resseq 1:349 )

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Components

#1: Protein Homoserine O-acetyltransferase / Acetyl ester hydrolase


Mass: 38870.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: cg0961, Cgl0839 / Plasmid: pHWG771 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: Q8NS43, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, homoserine O-acetyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 7.52 Å3/Da / Density % sol: 83.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Reservoir: 25.5 %(w/v) polyethylenglycol 4000, 15 %(v/v) glycerol, 0.17 M Lithium sulfate, 85 mM Tris/HCl, pH 8.5 Drop: 0.4 microliter reservoir solution plut 0.8 microliter protein solution ...Details: Reservoir: 25.5 %(w/v) polyethylenglycol 4000, 15 %(v/v) glycerol, 0.17 M Lithium sulfate, 85 mM Tris/HCl, pH 8.5 Drop: 0.4 microliter reservoir solution plut 0.8 microliter protein solution with 5 mg/ml protein concentration

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3.2→48.6 Å / Num. obs: 39336 / % possible obs: 99.93 % / Redundancy: 9.5 % / Rsym value: 0.245 / Net I/σ(I): 24.66
Reflection shellResolution: 3.2→3.314 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 2.66 / % possible all: 99.95

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B61

2b61


Resolution: 3.2→48.529 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1120 2.85 %Random selection
Rwork0.1868 ---
obs0.1872 39329 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→48.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5484 0 90 17 5591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025726
X-RAY DIFFRACTIONf_angle_d0.6037758
X-RAY DIFFRACTIONf_dihedral_angle_d11.5822050
X-RAY DIFFRACTIONf_chiral_restr0.021822
X-RAY DIFFRACTIONf_plane_restr0.0031016
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2753X-RAY DIFFRACTIONPOSITIONAL
12B2753X-RAY DIFFRACTIONPOSITIONAL0.034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.34570.2651500.26764707X-RAY DIFFRACTION100
3.3457-3.5220.27191410.23554681X-RAY DIFFRACTION100
3.522-3.74260.221420.21784725X-RAY DIFFRACTION100
3.7426-4.03140.18721410.18894738X-RAY DIFFRACTION100
4.0314-4.43690.18391300.15854752X-RAY DIFFRACTION100
4.4369-5.07830.15731390.15154791X-RAY DIFFRACTION100
5.0783-6.39580.19641450.17964806X-RAY DIFFRACTION100
6.3958-48.53490.20371320.18675009X-RAY DIFFRACTION100
Refinement TLS params.

L12: -0.8488 °2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.75740.54862.1951-0.74241.71860.26340.1492-0.3007-0.0257-0.08740.26270.29430.2266-0.14280.8890.0888-0.01560.3014-0.11830.593376.3272-12.930749.4163
21.82290.5732.3467-1.07832.00620.3170.35-0.4316-0.4947-0.16090.58150.1506-0.233-0.12350.96220.2328-0.1990.531-0.17980.815252.19285.284923.5326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'

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