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- PDB-7whe: The mutant crystal structure of b-1,4-Xylanase (XynAF1_R246K) wit... -

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Basic information

Entry
Database: PDB / ID: 7whe
TitleThe mutant crystal structure of b-1,4-Xylanase (XynAF1_R246K) with xylobiose
ComponentsBeta-xylanaseXylanase
KeywordsHYDROLASE / GH10 family xylanase
Function / homology
Function and homology information


cellulose binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region
Similarity search - Function
CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 ...CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLi, G.Q. / Zhang, R.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The mutant crystal structure of b-1,4-Xylanase (XynAF1_R246K) with xylobiose
Authors: Li, G.Q. / Zhang, R.F.
History
DepositionDec 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: 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: Beta-xylanase
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3889
Polymers70,4242
Non-polymers9647
Water8,647480
1
A: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8026
Polymers35,2121
Non-polymers5905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint1 kcal/mol
Surface area11960 Å2
MethodPISA
2
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5873
Polymers35,2121
Non-polymers3742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.056, 85.854, 97.701
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Beta-xylanase / Xylanase


Mass: 35212.184 Da / Num. of mol.: 2 / Mutation: R246K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: CDV57_00377 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A229WLM4, endo-1,4-beta-xylanase
#2: Polysaccharide beta-D-xylopyranose-(1-4)-alpha-D-xylopyranose


Type: oligosaccharide / Mass: 282.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-4DXylpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a212h-1a_1-5][a212h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Xylp]{[(4+1)][b-D-Xylp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.03 Å3/Da / Density % sol: 39.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium formate, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97914 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 58475 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.043 / Rrim(I) all: 0.154 / Χ2: 0.995 / Net I/σ(I): 6 / Num. measured all: 764269
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.8112.70.4757470.9420.1370.491.027100
1.81-1.8913.40.40357870.9570.1150.421.095100
1.89-1.9713.60.33557640.9680.0950.3481.1100
1.97-2.0713.30.27957840.9750.080.291.083100
2.07-2.212.50.2358200.9790.0680.240.99100
2.2-2.3813.60.258070.9850.0570.2080.902100
2.38-2.6113.40.17258280.9860.0490.1790.794100
2.61-2.9912.80.14458690.9910.0420.151.029100
2.99-3.7713.30.11759250.9940.0340.1220.845100
3.77-5012.10.08461440.9960.0250.0871.09599.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JDT

6jdt


Resolution: 1.75→30.11 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.994 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1845 2873 4.9 %RANDOM
Rwork0.1515 ---
obs0.1531 55433 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.44 Å2 / Biso mean: 18.305 Å2 / Biso min: 10.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å20 Å2
2--0.05 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.75→30.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4838 0 63 480 5381
Biso mean--30.34 28.39 -
Num. residues----638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0125037
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.636882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0845640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21625.377212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0315738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.646154
X-RAY DIFFRACTIONr_chiral_restr0.1120.2676
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023829
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 241 -
Rwork0.183 3990 -
all-4231 -
obs--99.32 %

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