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- PDB-7zei: Thermostable GH159 glycoside hydrolase from Caldicellulosiruptor ... -

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Basic information

Entry
Database: PDB / ID: 7zei
TitleThermostable GH159 glycoside hydrolase from Caldicellulosiruptor at 1.7 A
ComponentsCh_Gaf159A
KeywordsHYDROLASE / BETA PROPELLER / GALACTOFURANOSE / ARABINOFURANOSIDASE / CATALYSIS / EXO-HYDROLASE
Function / homologyGlycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / Uncharacterized protein
Function and homology information
Biological speciesCaldicellulosiruptor hydrothermalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBaudrexl, M. / Fida, T. / Berk, B. / Schwarz, W. / Zverlov, V.V. / Groll, M. / Liebl, W.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Communitys Seventh Framework Programme283570European Union
CitationJournal: Front Mol Biosci / Year: 2022
Title: Biochemical and Structural Characterization of Thermostable GH159 Glycoside Hydrolases Exhibiting alpha-L-Arabinofuranosidase Activity.
Authors: Baudrexl, M. / Fida, T. / Berk, B. / Schwarz, W.H. / Zverlov, V.V. / Groll, M. / Liebl, W.
History
DepositionMar 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Ch_Gaf159A
B: Ch_Gaf159A
C: Ch_Gaf159A
D: Ch_Gaf159A
E: Ch_Gaf159A
F: Ch_Gaf159A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,26436
Polymers226,0866
Non-polymers2,17730
Water37,4892081
1
A: Ch_Gaf159A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1256
Polymers37,6811
Non-polymers4445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ch_Gaf159A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9605
Polymers37,6811
Non-polymers2794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ch_Gaf159A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0226
Polymers37,6811
Non-polymers3415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ch_Gaf159A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1147
Polymers37,6811
Non-polymers4336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Ch_Gaf159A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0226
Polymers37,6811
Non-polymers3415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Ch_Gaf159A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0226
Polymers37,6811
Non-polymers3415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.090, 108.740, 251.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Ch_Gaf159A


Mass: 37681.074 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor hydrothermalis (bacteria)
Gene: Calhy_0274 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E4QB49

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Non-polymers , 6 types, 2111 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2081 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.75 Å3/Da / Density % sol: 55.31 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM MES, 30% PEG 8000, 5% GLYCEROLE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Dec 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 269815 / % possible obs: 98.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 15.5
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 42069

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
X-Areadata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ALPHAFOLD2

Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 3.291 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1534 13488 5 %RANDOM
Rwork0.1261 ---
obs0.1275 256285 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.5 Å2 / Biso mean: 22.72 Å2 / Biso min: 13.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å20 Å2
2--0.35 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15561 0 128 2088 17777
Biso mean--32.14 36.34 -
Num. residues----1857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01316228
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714071
X-RAY DIFFRACTIONr_angle_refined_deg1.21.64622057
X-RAY DIFFRACTIONr_angle_other_deg1.1971.58232633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.64551851
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.9222.181963
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.657152507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.771596
X-RAY DIFFRACTIONr_chiral_restr0.050.21911
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218210
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023885
X-RAY DIFFRACTIONr_rigid_bond_restr0.583330299
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 984 -
Rwork0.209 18706 -
all-19690 -
obs--98.48 %

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