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- PDB-8gkd: Crystal structure of the peptidoglycan O-acetylesterase Ape1 (ami... -

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Basic information

Entry
Database: PDB / ID: 8gkd
TitleCrystal structure of the peptidoglycan O-acetylesterase Ape1 (amino acids 41-392) from Campylobacter jejuni
ComponentsSGNH hydrolase-type esterase domain-containing protein
KeywordsHYDROLASE / Peptidoglycan O-acetylesterase / SGNH hydrolase / CBM35 / product bound complex
Function / homologySGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / ACETATE ION / SGNH hydrolase-type esterase domain-containing protein
Function and homology information
Biological speciesCampylobacter jejuni subsp. jejuni 81-176 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsLin, C.S. / Murphy, M.E.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-142176 Canada
CitationJournal: To be published
Title: Mechanism of the CBM35 domain in assisting catalysis by Ape1, a Campylobacter jejuni O-acetyl esterase
Authors: Lin, C.S. / Yen, I.Y. / Chan, A.C. / Murphy, M.E.
History
DepositionMar 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SGNH hydrolase-type esterase domain-containing protein
B: SGNH hydrolase-type esterase domain-containing protein
C: SGNH hydrolase-type esterase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,2146
Polymers123,0373
Non-polymers1773
Water11,133618
1
A: SGNH hydrolase-type esterase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0712
Polymers41,0121
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SGNH hydrolase-type esterase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0712
Polymers41,0121
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SGNH hydrolase-type esterase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0712
Polymers41,0121
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.905, 94.905, 102.741
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein SGNH hydrolase-type esterase domain-containing protein


Mass: 41012.312 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni 81-176 (Campylobacter)
Strain: 81-176 / Gene: CJJ81176_0638 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3PJ52
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 618 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.35 % / Description: rod-shaped crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100 mM CAPS pH 10.5, 200 mM NaCl, 16% (w/v) PEG8000, 2.5% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 95429 / % possible obs: 99.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.045 / Rrim(I) all: 0.11 / Χ2: 0.921 / Net I/σ(I): 5.5 / Num. measured all: 546678
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.835.10.79848030.810.3860.890.47599.7
1.83-1.865.90.70347750.8720.3140.7710.47199.8
1.86-1.95.80.61347770.8920.2750.6730.51299.9
1.9-1.945.80.56547970.8710.2530.620.64399.9
1.94-1.985.80.42147250.9440.190.4620.52999.9
1.98-2.035.80.36148300.950.1630.3970.52399.8
2.03-2.085.60.31347550.9440.1440.3450.66699.6
2.08-2.135.60.24947330.9670.1150.2750.56199.4
2.13-2.25.10.247450.9740.0970.2230.61199.4
2.2-2.275.90.21347940.9760.0950.2340.79899.6
2.27-2.355.90.16647740.9860.0740.1820.65499.7
2.35-2.445.90.13947990.990.0630.1530.65999.8
2.44-2.555.90.12147480.9920.0540.1330.75299.8
2.55-2.695.80.11248150.9920.0510.1230.87599.9
2.69-2.865.30.09547500.9910.0450.1061.01399.1
2.86-3.086.10.08447470.9930.0370.0921.18199.9
3.08-3.3960.07348180.9950.0320.081.49899.8
3.39-3.885.80.06447680.9960.0290.071.80499.9
3.88-4.885.70.05647220.9970.0250.0622.02499
4.88-505.90.05747540.9970.0260.0632.05998.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.21 Å34.86 Å
Translation4.21 Å34.86 Å

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
SCALEPACKdata scaling
PHASER2.8.2phasing
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→34.86 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1875 2038 2.1 %
Rwork0.1656 --
obs-95393 99.6 %
Displacement parametersBiso max: 146.07 Å2 / Biso mean: 27.5055 Å2 / Biso min: 13.31 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8503 0 12 618 9133
LS refinement shellResolution: 1.8→1.87 Å
RfactorNum. reflection% reflection
Rfree0.3058 206 -
Rwork0.2762 --
obs-9580 99.5 %

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