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- PDB-8bbi: Crystal structure of Xyn11 double mutant L271S, K275H from Psedot... -

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Basic information

Entry
Database: PDB / ID: 8bbi
TitleCrystal structure of Xyn11 double mutant L271S, K275H from Psedothermotoga thermarum
ComponentsBeta-xylanase
KeywordsHYDROLASE / xylanase / ester-hydrolase
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
1-methylethyl 1-thio-beta-D-galactopyranoside / Beta-xylanase
Similarity search - Component
Biological speciesPseudothermotoga thermarum DSM 5069 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCea-Rama, I. / Sanz-Aparicio, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-105838RB-C33 Spain
CitationJournal: To be published
Title: Crystal structure of Xyn11 double mutant L271S, K275H from Pseudothermotoga thermarum
Authors: Cea-Rama, I. / Sanz Aparicio, J.
History
DepositionOct 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-xylanase
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,45310
Polymers86,4242
Non-polymers1,0298
Water4,954275
1
A: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7275
Polymers43,2121
Non-polymers5154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7275
Polymers43,2121
Non-polymers5154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.324, 95.549, 101.344
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 8 - 340 / Label seq-ID: 24 - 356

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Beta-xylanase


Mass: 43212.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudothermotoga thermarum DSM 5069 (bacteria)
Gene: Theth_1636 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: F7YXD6, endo-1,4-beta-xylanase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Sugar ChemComp-IPT / 1-methylethyl 1-thio-beta-D-galactopyranoside / ISOPROPYL-1-BETA-D-THIOGALACTOSIDE / 1-(ISOPROPYLTHIO)-BETA-GALACTOPYRANSIDE / 1-methylethyl 1-thio-beta-D-galactoside / 1-methylethyl 1-thio-D-galactoside / 1-methylethyl 1-thio-galactoside


Type: D-saccharide / Mass: 238.301 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H18O5S
IdentifierTypeProgram
isopropyl-1-b-D-thiogalactosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.53 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 3350, 0.1M Bis-Tris pH 8.5, 0.2M Na formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979185 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 5, 2021 / Details: KB focusing mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979185 Å / Relative weight: 1
ReflectionResolution: 2.1→47.77 Å / Num. obs: 51806 / % possible obs: 99.9 % / Redundancy: 5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.031 / Net I/σ(I): 15.8
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4197 / CC1/2: 0.781 / Rpim(I) all: 0.29 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
MOLREP11.5.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NL2

7nl2


Resolution: 2.1→44.81 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.194 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.196 2674 5.2 %RANDOM
Rwork0.161 ---
obs0.1627 49073 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110.09 Å2 / Biso mean: 35.547 Å2 / Biso min: 21.07 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å2-0 Å2
2---0.27 Å20 Å2
3----1.48 Å2
Refinement stepCycle: final / Resolution: 2.1→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5602 0 66 275 5943
Biso mean--74.39 41.14 -
Num. residues----669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135866
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175451
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.6477947
X-RAY DIFFRACTIONr_angle_other_deg1.3381.58912553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2495681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.18421.871342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57815998
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3391540
X-RAY DIFFRACTIONr_chiral_restr0.0790.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026542
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021458
Refine LS restraints NCS

Ens-ID: 1 / Number: 12041 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 206 -
Rwork0.239 3600 -
all-3806 -
obs--99.79 %

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