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- PDB-7wh6: The mutant crystal structure of b-1,4-Xylanase (XynAF1_N179S) -

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Basic information

Entry
Database: PDB / ID: 7wh6
TitleThe mutant crystal structure of b-1,4-Xylanase (XynAF1_N179S)
ComponentsBeta-xylanase
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 / 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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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_N179S)
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 1.2Oct 30, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,7566
Polymers70,4262
Non-polymers2,3304
Water14,898827
1
A: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5403
Polymers35,2131
Non-polymers1,3272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint23 kcal/mol
Surface area12350 Å2
MethodPISA
2
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2163
Polymers35,2131
Non-polymers1,0032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint15 kcal/mol
Surface area12120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.297, 119.139, 60.828
Angle α, β, γ (deg.)90.000, 102.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-xylanase


Mass: 35213.172 Da / Num. of mol.: 2 / Mutation: N179S
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 alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2[DManpa1-6]DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_d6-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 827 / 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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M BIS-TRIS pH 6.5, 25% 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: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 104905 / % possible obs: 99.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.056 / Rrim(I) all: 0.136 / Χ2: 0.99 / Net I/σ(I): 4.2 / Num. measured all: 613650
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.58-1.645.90.498104910.7710.220.5450.985100
1.64-1.75.90.426104470.8750.1870.4661.01100
1.7-1.785.90.357105300.9040.1590.3911.031100
1.78-1.875.80.288104120.9190.130.3171.037100
1.87-1.995.60.227104690.940.1050.251.044100
1.99-2.146.10.182105120.8780.0790.1991.073100
2.14-2.366.10.155104690.8830.0680.171.034100
2.36-2.75.70.125105090.9720.0580.1380.95100
2.7-3.460.093105380.9910.0410.1020.871100
3.4-505.60.07105280.9910.0320.0770.8699

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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: 1.58→19.8 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.575 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1809 5147 4.9 %RANDOM
Rwork0.1548 ---
obs0.1561 99306 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.78 Å2 / Biso mean: 14.926 Å2 / Biso min: 8.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å2-0.05 Å2
2--0.18 Å20 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 1.58→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4838 0 156 827 5821
Biso mean--24.78 27.93 -
Num. residues----638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135210
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174672
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.6767151
X-RAY DIFFRACTIONr_angle_other_deg1.5971.61310811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.525657
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41725.07215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88915745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.813156
X-RAY DIFFRACTIONr_chiral_restr0.0930.2731
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025959
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021163
LS refinement shellResolution: 1.58→1.62 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.226 342 -
Rwork0.217 6933 -
obs--93.68 %

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