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- PDB-8slj: K164A mutant of a chlorogenic acid esterase from Lactobacillus he... -

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Basic information

Entry
Database: PDB / ID: 8slj
TitleK164A mutant of a chlorogenic acid esterase from Lactobacillus helveticus
ComponentsAlpha/beta hydrolase
KeywordsHYDROLASE / Chlorogenic acid / esterase / ferulic acid esterase / insertion domain
Function / homologySerine aminopeptidase, S33 / Serine aminopeptidase, S33 / aminopeptidase activity / Alpha/Beta hydrolase fold / Alpha/beta hydrolase
Function and homology information
Biological speciesLactobacillus helveticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsOwens, C.P. / Omori, K.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institute of Food and Agriculture (NIFA, United States)2020-67018-31261 United States
National Science Foundation (NSF, United States)1905399 United States
CitationJournal: Febs Lett. / Year: 2023
Title: The structure of a Lactobacillus helveticus chlorogenic acid esterase and the dynamics of its insertion domain provide insights into substrate binding.
Authors: Omori, K.K. / Drucker, C.T. / Okumura, T.L.S. / Carl, N.B. / Dinn, B.T. / Ly, D. / Sacapano, K.N. / Tajii, A. / Owens, C.P.
History
DepositionApr 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha/beta hydrolase
B: Alpha/beta hydrolase
C: Alpha/beta hydrolase


Theoretical massNumber of molelcules
Total (without water)83,4673
Polymers83,4673
Non-polymers00
Water13,385743
1
A: Alpha/beta hydrolase

A: Alpha/beta hydrolase


Theoretical massNumber of molelcules
Total (without water)55,6452
Polymers55,6452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2
B: Alpha/beta hydrolase
C: Alpha/beta hydrolase


Theoretical massNumber of molelcules
Total (without water)55,6452
Polymers55,6452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.606, 111.829, 75.930
Angle α, β, γ (deg.)90.00, 111.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-458-

HOH

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Components

#1: Protein Alpha/beta hydrolase


Mass: 27822.365 Da / Num. of mol.: 3 / Mutation: K164A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus helveticus (bacteria) / Gene: BCM45_08315 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0D5MKR6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / 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: 4.25 Å3/Da / Density % sol: 71.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: citric acid, PEG 6000, zinc chloride, lithium chloride

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.101→67.48 Å / Num. obs: 80226 / % possible obs: 98.55 % / Redundancy: 6.7 % / Biso Wilson estimate: 32.67 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08979 / Rpim(I) all: 0.03709 / Net I/σ(I): 10.76
Reflection shellResolution: 2.101→2.176 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.4666 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 7915 / CC1/2: 0.882 / CC star: 0.968 / Rpim(I) all: 0.1952 / % possible all: 97.79

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.101→67.48 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.202 4016 5.01 %
Rwork0.1755 --
obs0.1768 80084 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.101→67.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5867 0 0 743 6610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.846
X-RAY DIFFRACTIONf_dihedral_angle_d5.364824
X-RAY DIFFRACTIONf_chiral_restr0.054900
X-RAY DIFFRACTIONf_plane_restr0.0081085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.101-2.130.35651320.29622493X-RAY DIFFRACTION95
2.13-2.150.3171620.27162642X-RAY DIFFRACTION99
2.15-2.180.28751440.25742609X-RAY DIFFRACTION99
2.18-2.210.30021200.24792641X-RAY DIFFRACTION99
2.21-2.240.2531410.23242659X-RAY DIFFRACTION99
2.24-2.270.28371350.22512576X-RAY DIFFRACTION99
2.27-2.30.2361600.22482604X-RAY DIFFRACTION99
2.3-2.340.2511160.22222633X-RAY DIFFRACTION99
2.34-2.380.25561400.21292630X-RAY DIFFRACTION99
2.38-2.420.2421440.20652587X-RAY DIFFRACTION98
2.42-2.460.2331090.19342645X-RAY DIFFRACTION98
2.46-2.510.23821300.18782583X-RAY DIFFRACTION97
2.51-2.560.21821390.18092545X-RAY DIFFRACTION97
2.56-2.620.20561360.1842655X-RAY DIFFRACTION99
2.62-2.680.21811290.17762634X-RAY DIFFRACTION99
2.68-2.750.19211700.18712631X-RAY DIFFRACTION99
2.75-2.820.21321310.1812643X-RAY DIFFRACTION100
2.82-2.90.21731470.18032605X-RAY DIFFRACTION99
2.9-30.21781420.17922637X-RAY DIFFRACTION99
3-3.10.21991400.17852622X-RAY DIFFRACTION98
3.1-3.230.17761370.17632602X-RAY DIFFRACTION98
3.23-3.370.21591190.17162615X-RAY DIFFRACTION97
3.37-3.550.2021220.17062668X-RAY DIFFRACTION100
3.55-3.780.19421420.1552670X-RAY DIFFRACTION100
3.78-4.070.13831472617X-RAY DIFFRACTION99
4.07-4.480.1821450.13852664X-RAY DIFFRACTION99
4.48-5.120.17561370.13622603X-RAY DIFFRACTION97
5.12-6.450.1671442690X-RAY DIFFRACTION100
6.45-67.480.17021560.16192665X-RAY DIFFRACTION98

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