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- PDB-5e4y: Orthorhombic structure of the acetyl esterase MekB -

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Basic information

Entry
Database: PDB / ID: 5e4y
TitleOrthorhombic structure of the acetyl esterase MekB
ComponentsHomoserine O-acetyltransferase
KeywordsHYDROLASE / Esterase / alpha/beta hydrolase / methyl alkyl ketone degradation pathway / transferase
Function / homology
Function and homology information


ethyl acetate hydrolase / biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / 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
Ethyl acetate hydrolase
Similarity search - Component
Biological speciesPseudomonas veronii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNiefind, K. / Toelzer, C. / Pal, S. / Watzlawick, H. / Altenbuchner, J.
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
DepositionOct 7, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 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

Downloads & links

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Assembly

Deposited unit
A: Homoserine O-acetyltransferase
B: Homoserine O-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)79,4942
Polymers79,4942
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-19 kcal/mol
Surface area25070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.346, 79.946, 142.177
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Homoserine O-acetyltransferase / hydrolase


Mass: 39746.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas veronii (bacteria) / Gene: mekB / Production host: Escherichia coli (E. coli)
References: UniProt: Q0MRG5, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, homoserine O-acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.09 Å3/Da / Density % sol: 41.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6, 5 % PEG 1000, 30 % PEG 600, 10 % Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.8→44.74 Å / Num. obs: 16961 / % possible obs: 99.74 % / Redundancy: 5.9 % / Rsym value: 0.282 / Net I/σ(I): 6.01
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.0826 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D60

5d60


Resolution: 2.8→44.736 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2367 839 4.95 %
Rwork0.1859 --
obs0.1885 16952 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→44.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5338 0 0 89 5427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025480
X-RAY DIFFRACTIONf_angle_d0.497430
X-RAY DIFFRACTIONf_dihedral_angle_d11.8391970
X-RAY DIFFRACTIONf_chiral_restr0.019802
X-RAY DIFFRACTIONf_plane_restr0.003971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.97550.29611430.24262623X-RAY DIFFRACTION100
2.9755-3.20520.28241240.23092673X-RAY DIFFRACTION100
3.2052-3.52760.26161380.19852640X-RAY DIFFRACTION100
3.5276-4.03780.23581350.17052669X-RAY DIFFRACTION100
4.0378-5.08610.21551510.15092686X-RAY DIFFRACTION100
5.0861-44.740.19421480.18122822X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°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)
15.25914.32760.40018.7741.63462.5529-0.12210.2365-0.0483-0.0760.0902-0.089-0.130.27190.04850.24120.0633-0.03940.36770.00650.15348.826829.842641.0424
24.1581-2.5028-2.09132.33822.12083.46020.0223-0.0056-0.1206-0.1797-0.0163-0.0111-0.17920.0508-0.00420.273-0.07640.00340.27670.02350.128122.173128.348138.3979
33.011-2.1011-1.91592.37741.12111.2869-0.0780.4411-0.25010.3002-0.38480.42590.2934-0.69250.50660.2533-0.0858-0.01190.3422-0.09520.29829.324422.719845.9706
43.00150.63292.36023.41921.4735.5305-0.0215-0.0036-0.1110.2440.11580.15470.3205-0.0476-0.0980.1085-0.01160.04510.19980.04290.200723.524118.401146.64
53.9806-1.7264-0.75426.30041.64680.50270.12580.26160.15170.4661-0.21060.0509-0.035-0.24840.11840.2692-0.0050.04840.4359-0.06090.14749.853838.361760.887
64.10980.4461.74760.8852-0.57681.5513-0.08790.29910.1188-0.06650.0849-0.0137-0.19290.0590.02040.29440.01280.0250.2116-0.03550.177424.400246.832956.3657
72.0764-1.73730.24642.9516-0.73290.2110.0903-0.1756-0.1602-0.165-0.02370.15310.09960.0229-0.05530.22980.00620.03860.2553-0.0150.176124.053921.971557.2717
82.32761.3366-0.24259.2844-2.33291.33910.0802-0.21510.0921-0.569-0.0692-0.5912-0.10250.256-0.03820.2622-0.04970.0490.2799-0.10380.113835.080829.110753.2431
94.05290.2140.71374.12593.73835.94620.2466-0.1902-0.2807-0.11810.0668-0.90670.20090.2343-0.240.0780.05150.04770.35730.01070.213739.021625.614144.322
103.216-1.09473.52323.41070.00034.37160.3750.08070.1059-0.0107-0.2770.30720.3233-0.2847-0.14240.1990.01470.07470.38870.01670.191824.819854.383596.2043
110.56990.1610.25120.68250.24840.8611-0.03710.0579-0.0089-0.0106-0.0094-0.0164-0.00370.00810.05280.18160.008-0.00340.2659-0.01570.173127.996647.123982.6025
120.40231.24940.59994.19710.90573.58080.09090.1573-0.01410.26410.0096-0.31870.22610.1825-0.10330.19170.1164-0.03830.34110.01440.235341.075237.611684.7626
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 99 )
3X-RAY DIFFRACTION3chain 'A' and (resid 100 through 125 )
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 169 )
5X-RAY DIFFRACTION5chain 'A' and (resid 170 through 196 )
6X-RAY DIFFRACTION6chain 'A' and (resid 197 through 250 )
7X-RAY DIFFRACTION7chain 'A' and (resid 251 through 307 )
8X-RAY DIFFRACTION8chain 'A' and (resid 308 through 329 )
9X-RAY DIFFRACTION9chain 'A' and (resid 330 through 348 )
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 48 )
11X-RAY DIFFRACTION11chain 'B' and (resid 49 through 307 )
12X-RAY DIFFRACTION12chain 'B' and (resid 308 through 348 )

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