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

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Basic information

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


cellulose binding / endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / 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 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / 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 / 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
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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)
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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)70,9226
Polymers70,4242
Non-polymers4974
Water7,656425
1
A: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6184
Polymers35,2121
Non-polymers4053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint2 kcal/mol
Surface area11950 Å2
MethodPISA
2
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3042
Polymers35,2121
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.165, 85.939, 97.831
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


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: 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


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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 39.54 %
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 PILATUS 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: 1.83→50 Å / Num. obs: 51300 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.03 / Rrim(I) all: 0.109 / Χ2: 0.997 / Net I/σ(I): 8 / Num. measured all: 676674
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.83-1.9130.4850320.9580.1380.50.942100
1.9-1.9713.30.38250560.9740.1080.3971.029100
1.97-2.0613.70.29650700.9820.0830.3071.035100
2.06-2.1713.40.23550800.9860.0660.2441.084100
2.17-2.3112.80.18650650.9920.0540.1941.11100
2.31-2.4813.70.15551120.9930.0430.1611.007100
2.48-2.7313.30.12451210.9950.0350.1291.027100
2.73-3.1313.20.09451510.9970.0270.0980.929100
3.13-3.94130.06852050.9980.020.0710.861100
3.94-5012.50.0554080.9990.0150.0530.94599.8

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Processing

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

6jdt


Resolution: 1.83→32.3 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.196 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1831 2359 4.6 %RANDOM
Rwork0.1539 ---
obs0.1552 48893 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.21 Å2 / Biso mean: 19.592 Å2 / Biso min: 10.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0 Å2
2---0.09 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 1.83→32.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4838 0 32 425 5295
Biso mean--27.37 28.62 -
Num. residues----638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124996
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.636825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2415636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40325.377212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84415736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.664154
X-RAY DIFFRACTIONr_chiral_restr0.1120.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023817
LS refinement shellResolution: 1.83→1.877 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.185 138 -
Rwork0.158 3444 -
all-3582 -
obs--96.5 %

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