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- PDB-8xzz: Structure of a xylanase Xyl-1 M4 E175A in complex with xylobiose -

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Basic information

Entry
Database: PDB / ID: 8xzz
TitleStructure of a xylanase Xyl-1 M4 E175A in complex with xylobiose
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 / metal ion binding
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
4beta-beta-xylobiose / beta-D-xylopyranose / Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesAspergillus terreus NIH2624 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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)87,58717
Polymers86,0114
Non-polymers1,57513
Water13,331740
1
A: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9164
Polymers21,5031
Non-polymers4133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9345
Polymers21,5031
Non-polymers4314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8033
Polymers21,5031
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9345
Polymers21,5031
Non-polymers4314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.074, 137.540, 52.848
Angle α, β, γ (deg.)90.00, 97.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 21502.773 Da / Num. of mol.: 4 / Mutation: E176A,D31P,A34Q,K118Q,A168H
Source method: isolated from a genetically manipulated source
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
#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 282.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligosaccharide / References: 4beta-beta-xylobiose
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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Sugar
ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 6 / Source method: isolated from a natural source / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 740 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 295 K / Method: evaporation
Details: 0.2 M sodium formate, 0.1 M Bis-Tris propane, pH 6.5, and 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: 1.72→24.27 Å / Num. obs: 73843 / % possible obs: 95.5 % / Redundancy: 3.9 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.031 / Rrim(I) all: 0.06 / Χ2: 1.369 / Net I/σ(I): 21.3
Reflection shellResolution: 1.72→1.78 Å / Redundancy: 4 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 13.45 / Num. unique obs: 6968 / % possible all: 90.6

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-2000data scaling
DENZOdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WP4

3wp4


Resolution: 1.72→24.27 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 19.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1917 2006 2.72 %RANDOM
Rwork0.1608 ---
obs0.1617 73804 95.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.72→24.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5903 0 82 740 6725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066151
X-RAY DIFFRACTIONf_angle_d0.8978418
X-RAY DIFFRACTIONf_dihedral_angle_d7.387877
X-RAY DIFFRACTIONf_chiral_restr0.06886
X-RAY DIFFRACTIONf_plane_restr0.0041089
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.760.24761290.18894483X-RAY DIFFRACTION84
1.76-1.810.21181380.18145007X-RAY DIFFRACTION93
1.81-1.870.25441400.17115107X-RAY DIFFRACTION94
1.87-1.930.21811510.16555102X-RAY DIFFRACTION95
1.93-1.990.21450.16345136X-RAY DIFFRACTION96
1.99-2.070.22211420.16235205X-RAY DIFFRACTION96
2.07-2.170.19741410.16315187X-RAY DIFFRACTION96
2.17-2.280.18451420.15915165X-RAY DIFFRACTION96
2.28-2.430.20781500.16915210X-RAY DIFFRACTION97
2.43-2.610.21621460.17245282X-RAY DIFFRACTION97
2.61-2.880.19571440.17345278X-RAY DIFFRACTION98
2.88-3.290.18261510.15815292X-RAY DIFFRACTION98
3.29-4.140.15971440.14375143X-RAY DIFFRACTION95
4.14-24.270.16991430.15265201X-RAY DIFFRACTION95

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