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- PDB-8xzy: Structure of a xylanase Xyl-1 M4 mutant E175A -

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Basic information

Entry
Database: PDB / ID: 8xzy
TitleStructure of a xylanase Xyl-1 M4 mutant E175A
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
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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

Downloads & links

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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)86,46911
Polymers86,0114
Non-polymers4587
Water12,556697
1
A: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6343
Polymers21,5031
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-27 kcal/mol
Surface area8180 Å2
MethodPISA
2
B: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6343
Polymers21,5031
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-24 kcal/mol
Surface area8110 Å2
MethodPISA
3
C: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5682
Polymers21,5031
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-23 kcal/mol
Surface area8180 Å2
MethodPISA
4
D: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6343
Polymers21,5031
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-26 kcal/mol
Surface area8250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.231, 137.536, 52.857
Angle α, β, γ (deg.)90.00, 97.66, 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 (strain NIH 2624 / FGSC A1156) (mold)
Gene: ATEG_04943 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0CMZ1, endo-1,4-beta-xylanase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 697 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 43.77 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 6.5
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 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.75→25 Å / Num. obs: 70638 / % possible obs: 95.8 % / Redundancy: 3.8 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.026 / Rrim(I) all: 0.05 / Χ2: 1.363 / Net I/σ(I): 26 / Num. measured all: 266971
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.75-1.814.10.12366640.9880.9970.0650.141.3890.4
1.81-1.8940.09967730.9920.9980.0540.1141.42292.2
1.89-1.973.80.07669260.9950.9990.0430.0881.47694.4
1.97-2.073.60.06170200.9950.9990.0360.0711.3695.3
2.07-2.23.70.05371420.9960.9990.0310.0621.38297
2.2-2.373.70.04972230.9960.9990.0290.0571.33798
2.37-2.614.10.04873090.9970.9990.0260.0551.29599.1
2.61-2.9940.04373050.9970.9990.0240.0491.34299.1
2.99-3.773.50.03671810.9970.9990.0220.0431.35796.9
3.77-253.10.03670950.9960.9990.0250.0441.26595.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→23.29 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.914 / SU B: 2.227 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 3368 4.8 %RANDOM
Rwork0.18071 ---
obs0.18301 67221 95.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.855 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å2-0 Å2-0.44 Å2
2---0.05 Å2-0 Å2
3----0.91 Å2
Refinement stepCycle: 1 / Resolution: 1.75→23.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5852 0 7 716 6575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0126024
X-RAY DIFFRACTIONr_bond_other_d0.0010.0184768
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.658248
X-RAY DIFFRACTIONr_angle_other_deg1.5531.56211132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.385752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.72524.557316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87515800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.851512
X-RAY DIFFRACTIONr_chiral_restr0.0840.2788
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027036
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021336
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_it1.8991.9193020
X-RAY DIFFRACTIONr_mcbond_other1.8951.9193019
X-RAY DIFFRACTIONr_mcangle_it2.6372.8693768
X-RAY DIFFRACTIONr_mcangle_other2.6372.873769
X-RAY DIFFRACTIONr_scbond_it2.9812.2313004
X-RAY DIFFRACTIONr_scbond_other2.982.2293002
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4383.2394480
X-RAY DIFFRACTIONr_long_range_B_refined6.04923.8267053
X-RAY DIFFRACTIONr_long_range_B_other5.91823.1616887
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.752→1.798 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 212 -
Rwork0.167 4525 -
obs--86.69 %

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