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- PDB-7wwh: Crystal structure of the Geobacillus thermoglucosidasius feruloyl... -

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Basic information

Entry
Database: PDB / ID: 7wwh
TitleCrystal structure of the Geobacillus thermoglucosidasius feruloyl esterase GthFAE
ComponentsAlpha/beta hydrolase
KeywordsHYDROLASE / Alpha/beta hydrolase / Feruloyl esterase
Function / homologySerine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold / hydrolase activity / Alpha/beta hydrolase
Function and homology information
Biological speciesParageobacillus thermoglucosidasius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsYang, W. / Wu, Y.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Structure-guided rational design of the Geobacillus thermoglucosidasius feruloyl esterase GthFAE to improve its thermostability.
Authors: Yang, W. / Sun, L. / Dong, P. / Chen, Y. / Zhang, H. / Huang, X. / Wu, L. / Chen, L. / Jing, D. / Wu, Y.
History
DepositionFeb 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)56,3502
Polymers56,3502
Non-polymers00
Water7,512417
1
A: Alpha/beta hydrolase


Theoretical massNumber of molelcules
Total (without water)28,1751
Polymers28,1751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha/beta hydrolase


Theoretical massNumber of molelcules
Total (without water)28,1751
Polymers28,1751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.038, 87.410, 69.456
Angle α, β, γ (deg.)90.000, 95.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha/beta hydrolase


Mass: 28175.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parageobacillus thermoglucosidasius (bacteria)
Gene: DV712_01095 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A369WTY0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.51 Å3/Da / Density % sol: 45.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Tris-HCl pH 7.0, 20% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 41148 / % possible obs: 98.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.03 / Rrim(I) all: 0.079 / Χ2: 0.583 / Net I/σ(I): 5.6 / Num. measured all: 277606
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.91-1.946.20.50519380.9050.220.5520.50494.6
1.94-1.986.50.48320340.9250.2060.5260.5195.6
1.98-2.026.60.37420090.9560.1570.4060.51797.8
2.02-2.066.70.34320230.9620.1420.3720.53798.4
2.06-2.16.80.29820530.970.1240.3230.54899.2
2.1-2.156.90.24720780.9850.1020.2680.57899.6
2.15-2.26.80.21520570.9830.0880.2320.58499.8
2.2-2.266.80.18720790.9860.0770.2030.6299.6
2.26-2.336.70.16320620.9880.0680.1770.59999.4
2.33-2.416.10.13720460.990.060.150.59197.6
2.41-2.496.70.13120500.9910.0550.1420.61799.6
2.49-2.597.20.11820690.9930.0470.1270.61599.9
2.59-2.717.10.10121040.9940.0410.1090.61799.8
2.71-2.857.10.08720850.9950.0350.0940.62299.8
2.85-3.0370.07620450.9960.0310.0820.63999.4
3.03-3.276.80.06320830.9960.0260.0680.62499.3
3.27-3.596.10.05220070.9980.0230.0570.6396.6
3.59-4.117.20.04520940.9980.0180.0490.60899.7
4.11-5.187.10.0420980.9980.0160.0430.57799.8
5.18-506.60.03821340.9990.0150.0410.50199.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PF8

3pf8


Resolution: 1.92→26.29 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 21.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2034 2035 4.95 %
Rwork0.1743 39063 -
obs0.1758 41098 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.89 Å2 / Biso mean: 32.6405 Å2 / Biso min: 12.82 Å2
Refinement stepCycle: final / Resolution: 1.92→26.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3948 0 0 417 4365
Biso mean---36.61 -
Num. residues----502
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.92-1.960.25571190.20992225234486
1.96-2.010.25391280.20672580270897
2.01-2.070.25041280.20062595272398
2.07-2.130.25931400.19062623276399
2.13-2.20.22671380.17626532791100
2.2-2.270.21121540.177826012755100
2.27-2.360.21581250.17912622274799
2.36-2.470.24211340.17762639277398
2.47-2.60.22621390.185126392778100
2.6-2.770.19971450.186626242769100
2.77-2.980.22641460.175326282774100
2.98-3.280.22731400.17892674281499
3.28-3.750.16641390.16532568270797
3.75-4.720.1581310.146626752806100
4.72-26.290.19161290.17612717284699

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