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- PDB-8skm: Wild type chlorogenic acid esterase from Lactobacillus helveticus -

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Basic information

Entry
Database: PDB / ID: 8skm
TitleWild type chlorogenic acid esterase from Lactobacillus helveticus
ComponentsChlorogenic acid esterase
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: 2.2 Å
AuthorsOwens, C.P. / Okumura, T.L.S.
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 20, 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: Chlorogenic acid esterase
B: Chlorogenic acid esterase
C: Chlorogenic acid esterase


Theoretical massNumber of molelcules
Total (without water)83,6413
Polymers83,6413
Non-polymers00
Water8,143452
1
A: Chlorogenic acid esterase
B: Chlorogenic acid esterase


Theoretical massNumber of molelcules
Total (without water)55,7612
Polymers55,7612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Chlorogenic acid esterase

C: Chlorogenic acid esterase


Theoretical massNumber of molelcules
Total (without water)55,7612
Polymers55,7612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)180.549, 110.292, 75.979
Angle α, β, γ (deg.)90.00, 111.49, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-393-

HOH

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Components

#1: Protein Chlorogenic acid esterase


Mass: 27880.467 Da / Num. of mol.: 3
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.: 452 / 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: 4.21 Å3/Da / Density % sol: 70.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: citric acid, PEG 6000, lithium chloride

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→37.92 Å / Num. obs: 649288 / % possible obs: 99.04 % / Redundancy: 9.3 % / Biso Wilson estimate: 26.68 Å2 / CC1/2: 0.926 / Rmerge(I) obs: 0.5713 / Rpim(I) all: 0.196 / Net I/σ(I): 7.54
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 9.5 % / Rmerge(I) obs: 1.645 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 6651 / CC1/2: 0.339 / CC star: 0.712 / Rpim(I) all: 0.559 / % possible all: 94.97

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→35.91 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 2015 2.9 %
Rwork0.1765 --
obs0.1774 69602 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→35.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5871 0 0 452 6323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086006
X-RAY DIFFRACTIONf_angle_d0.9568153
X-RAY DIFFRACTIONf_dihedral_angle_d6.148833
X-RAY DIFFRACTIONf_chiral_restr0.058905
X-RAY DIFFRACTIONf_plane_restr0.0091089
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.3041410.27074554X-RAY DIFFRACTION94
2.26-2.320.28831390.25694768X-RAY DIFFRACTION98
2.32-2.380.28431460.2444806X-RAY DIFFRACTION99
2.38-2.460.27191340.23044833X-RAY DIFFRACTION100
2.46-2.550.26351510.2254813X-RAY DIFFRACTION99
2.55-2.650.26141400.20374833X-RAY DIFFRACTION99
2.65-2.770.24371420.1984839X-RAY DIFFRACTION100
2.77-2.920.2111570.1864859X-RAY DIFFRACTION100
2.92-3.10.21561370.17744844X-RAY DIFFRACTION100
3.1-3.340.21991430.17064855X-RAY DIFFRACTION100
3.34-3.680.17741470.15164871X-RAY DIFFRACTION100
3.68-4.210.14591430.12824906X-RAY DIFFRACTION100
4.21-5.30.16481440.13534867X-RAY DIFFRACTION99
5.3-35.910.18831510.1674939X-RAY DIFFRACTION99

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