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- PDB-8y00: Structure of a xylanase Xyl-1 M4 mutant E175A in complex with xyl... -

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Basic information

Entry
Database: PDB / ID: 8y00
TitleStructure of a xylanase Xyl-1 M4 mutant E175A in complex with xylotriose
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / Evolutionarily conserved mutations / Xylanase robustness / Non-loop region / Substrate binding patterns / Conformational dynamics
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
beta-D-xylopyranose / Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesAspergillus terreus NIH2624 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsXiang, W.L. / Huang, J.-W. / Yang, Y. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Agric.Food Chem. / Year: 2024
Title: Unleashing the Power of Evolution in Xylanase Engineering: Investigating the Role of Distal Mutation Regulation.
Authors: Wu, Y. / Yang, Y. / Lu, G. / Xiang, W.L. / Sun, T.Y. / Chen, K.W. / Lv, X. / Gui, Y.F. / Zeng, R.Q. / Du, Y.K. / Fu, C.H. / Huang, J.W. / Chen, C.C. / Guo, R.T. / Yu, L.J.
History
DepositionJan 21, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase
B: Endo-1,4-beta-xylanase
C: Endo-1,4-beta-xylanase
D: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,09716
Polymers86,0114
Non-polymers2,08612
Water12,611700
1
A: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0665
Polymers21,5031
Non-polymers5634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-26 kcal/mol
Surface area8520 Å2
MethodPISA
2
B: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0484
Polymers21,5031
Non-polymers5453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-26 kcal/mol
Surface area8190 Å2
MethodPISA
3
C: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0484
Polymers21,5031
Non-polymers5453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-26 kcal/mol
Surface area8220 Å2
MethodPISA
4
D: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9353
Polymers21,5031
Non-polymers4322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.192, 137.834, 52.822
Angle α, β, γ (deg.)90.00, 97.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Endo-1,4-beta-xylanase / xylotriose


Mass: 21502.773 Da / Num. of mol.: 4 / Mutation: E176A,D31P,A34Q,K118Q,A168H
Source method: isolated from a genetically manipulated source
Details: The GenBank ID is MZ569606.1 / Source: (gene. exp.) Aspergillus terreus NIH2624 (mold) / Gene: ATEG_04943 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0CMZ1, endo-1,4-beta-xylanase

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Sugars , 3 types, 6 molecules

#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 282.245 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a212h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 414.360 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a212h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 706 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 700 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 295 K / Method: evaporation
Details: 0.2 M sodium formate, 0.1 M Bis-Tris propane 6.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99987 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.71→25 Å / Num. obs: 76502 / % possible obs: 96.6 % / Redundancy: 6.4 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.027 / Rrim(I) all: 0.067 / Χ2: 1.424 / Net I/σ(I): 16.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.72-1.785.90.25974240.9730.9930.1160.2851.14893.9
1.78-1.856.60.276540.9840.9960.0840.2171.42497.1
1.85-1.947.20.15477570.9890.9970.0620.1671.53897.9
1.94-2.0470.1276780.9930.9980.0490.131.52397.2
2.04-2.176.80.09776390.9940.9980.0410.1061.46996.9
2.17-2.336.30.08175500.9950.9990.0350.0881.46595.6
2.33-2.576.50.07676100.9950.9990.0320.0831.51996
2.57-2.946.40.06575890.9960.9990.0280.0711.44595.7
2.94-3.76.10.05477090.9970.9990.0240.0591.34397
3.7-255.10.04578920.9970.9990.0220.051.26798.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→24.47 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.506 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22895 3773 4.9 %RANDOM
Rwork0.1822 ---
obs0.18455 72686 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.741 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å2-0 Å2-0.8 Å2
2--0.7 Å20 Å2
3----1.31 Å2
Refinement stepCycle: 1 / Resolution: 1.71→24.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5891 0 118 711 6720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0126175
X-RAY DIFFRACTIONr_bond_other_d0.0010.0184884
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.6538451
X-RAY DIFFRACTIONr_angle_other_deg1.5311.56411418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3545760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.7924.557316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42615803
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1061512
X-RAY DIFFRACTIONr_chiral_restr0.0930.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027092
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021344
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7652.0643052
X-RAY DIFFRACTIONr_mcbond_other1.7632.0633051
X-RAY DIFFRACTIONr_mcangle_it2.4573.0913808
X-RAY DIFFRACTIONr_mcangle_other2.4573.0913809
X-RAY DIFFRACTIONr_scbond_it2.8412.3183123
X-RAY DIFFRACTIONr_scbond_other2.8412.3183124
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1653.3884644
X-RAY DIFFRACTIONr_long_range_B_refined5.44925.2617223
X-RAY DIFFRACTIONr_long_range_B_other5.44925.2637224
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.71→1.754 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 219 -
Rwork0.218 4926 -
obs--87.4 %

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