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- PDB-7wh7: The mutant crystal structure of b-1,4-Xylanase (XynAF1_N179S) wit... -

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Basic information

Entry
Database: PDB / ID: 7wh7
TitleThe mutant crystal structure of b-1,4-Xylanase (XynAF1_N179S) with xylotetraose
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: 1.44 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) with xylotetraose
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)73,4616
Polymers70,4262
Non-polymers3,0354
Water15,745874
1
A: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7313
Polymers35,2131
Non-polymers1,5172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint24 kcal/mol
Surface area12250 Å2
MethodPISA
2
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7313
Polymers35,2131
Non-polymers1,5172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint23 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.318, 119.687, 60.906
Angle α, β, γ (deg.)90.000, 102.200, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-xylanase / 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 beta-D-xylopyranose-(1-4)-alpha-D-xylopyranose


Type: oligosaccharide / Mass: 282.245 Da / Num. of mol.: 2
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: 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
#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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
DManpa1-2DManpa1-2DManpa1-3[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_e2-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]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 874 / 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: 2.8 Å3/Da / Density % sol: 56.04 %
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: Nov 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.44→50 Å / Num. obs: 138872 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.038 / Rrim(I) all: 0.101 / Χ2: 0.963 / Net I/σ(I): 5.5 / Num. measured all: 945941
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.44-1.496.80.51138850.8950.210.5521.037100
1.49-1.556.70.398138210.9150.1650.4311.004100
1.55-1.626.40.306138650.9450.1310.3330.976100
1.62-1.716.80.249138800.9630.1030.270.996100
1.71-1.817.10.203138350.9750.0820.2190.939100
1.81-1.9570.171138990.9790.0690.1850.931100
1.95-2.156.70.127139110.9870.0530.1380.97100
2.15-2.466.70.105138640.9880.0440.1140.926100
2.46-3.17.20.077139460.9940.0310.0841.039100
3.1-506.70.057139660.9950.0240.0610.81399.3

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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: 1.44→16.96 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.924 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1715 6816 5 %RANDOM
Rwork0.1496 ---
obs0.1507 130361 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.15 Å2 / Biso mean: 13.837 Å2 / Biso min: 7.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.04 Å2
2--0.04 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.44→16.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4838 0 204 874 5916
Biso mean--22.49 27.33 -
Num. residues----638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135264
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174698
X-RAY DIFFRACTIONr_angle_refined_deg1.9061.6847235
X-RAY DIFFRACTIONr_angle_other_deg1.6341.61610891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.435657
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65825.07215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.81515745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.435156
X-RAY DIFFRACTIONr_chiral_restr0.1030.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025959
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021163
LS refinement shellResolution: 1.441→1.479 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 443 -
Rwork0.214 8751 -
all-9194 -
obs--89.44 %

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