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- PDB-6a6o: Crystal structure of acetyl ester-xyloside bifunctional hydrolase... -

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Basic information

Entry
Database: PDB / ID: 6a6o
TitleCrystal structure of acetyl ester-xyloside bifunctional hydrolase from Caldicellulosiruptor lactoaceticus
ComponentsEsterase/lipase-like protein
KeywordsHYDROLASE / Bifunctional Hydrolase / Acetyl Esterase Activty / 1 / 4-Beta-xylosidase Activity / Hydrolase.
Function / homology: / BD-FAE / lipase activity / : / alpha/beta hydrolase fold / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold / Esterase/lipase-like protein
Function and homology information
Biological speciesCaldicellulosiruptor lactoaceticus 6A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCao, H. / Huang, Y. / Sun, L.C. / Liu, X. / Liu, T.F. / Wang, F.Z. / Xin, F.J.
Funding support China, 2items
OrganizationGrant numberCountry
2017YFD0400200 China
2018M630230 China
CitationJournal: Acs Catalysis / Year: 2019
Title: Structural Insights into the Dual-Substrate Recognition and Catalytic Mechanisms of a Bifunctional Acetyl Ester-Xyloside Hydrolase from Caldicellulosiruptor lactoaceticus.
Authors: Cao, H. / Sun, L.C. / Huang, Y. / Liu, X. / Yang, D. / Liu, T.F. / Jia, X.J. / Wen, B.T. / Gu, T. / Wang, F.Z. / Xin, F.J.
History
DepositionJun 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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: Esterase/lipase-like protein


Theoretical massNumber of molelcules
Total (without water)31,5151
Polymers31,5151
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.180, 68.180, 140.173
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Esterase/lipase-like protein


Mass: 31515.123 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor lactoaceticus 6A (bacteria)
Gene: Calla_1993
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: G2PVG6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.8 M potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 31576 / % possible obs: 100 % / Redundancy: 25.3 % / Biso Wilson estimate: 29.19 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.017 / Rrim(I) all: 0.086 / Χ2: 1.082 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8625.50.4730860.9740.0940.480.496100
1.86-1.9424.20.41430930.9810.0850.4230.772100
1.94-2.0326.60.23930850.9930.0470.2430.614100
2.03-2.1326.10.17831100.9960.0350.1810.7100
2.13-2.2724.80.16631200.9950.0340.1691.045100
2.27-2.4425.40.11531180.9970.0230.1180.935100
2.44-2.6926.20.09931500.9980.020.11.072100
2.69-3.0824.70.08431620.9980.0170.0851.33100
3.08-3.8826.20.07632210.9990.0150.0771.829100
3.88-5023.40.06934310.9990.0150.071.97599.9

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data collection
PDB_EXTRACT3.24data extraction
PHASERphasing
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HXK

3hxk


Resolution: 1.8→39.721 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.03
RfactorNum. reflection% reflection
Rfree0.1903 1558 4.95 %
Rwork0.1654 --
obs0.1667 31446 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.89 Å2 / Biso mean: 31.5866 Å2 / Biso min: 18.67 Å2
Refinement stepCycle: final / Resolution: 1.8→39.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2134 0 0 206 2340
Biso mean---41.13 -
Num. residues----272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062212
X-RAY DIFFRACTIONf_angle_d0.8223018
X-RAY DIFFRACTIONf_chiral_restr0.059328
X-RAY DIFFRACTIONf_plane_restr0.006388
X-RAY DIFFRACTIONf_dihedral_angle_d2.5241816
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7991-1.85720.23251350.1926462781100
1.8572-1.92350.31291290.24412643277299
1.9235-2.00060.2271380.18326702808100
2.0006-2.09160.20321390.168326742813100
2.0916-2.20190.22431260.169927032829100
2.2019-2.33980.19881320.18626912823100
2.3398-2.52040.20281420.177127042846100
2.5204-2.7740.20061480.178627132861100
2.774-3.17530.19171500.176227332883100
3.1753-3.99990.1841550.15827802935100
3.9999-39.73030.16421640.14129313095100

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