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- PDB-8keu: Crystal Structures of Endo-beta-1,4-xylanase II mutant T2CT28C -

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Basic information

Entry
Database: PDB / ID: 8keu
TitleCrystal Structures of Endo-beta-1,4-xylanase II mutant T2CT28C
ComponentsEndo-1,4-beta-xylanase II
KeywordsHYDROLASE / Endo-beta-1 / 4-xylanase
Function / homology
Function and homology information


endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process
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
IODIDE ION / Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesTrichoderma reesei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsLi, Z.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: To Be Published
Title: High resolution crystal structure of xylanase T2CT28C
Authors: Li, Z.
History
DepositionAug 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 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 II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5906
Polymers20,8181
Non-polymers7715
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-1 kcal/mol
Surface area7960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.119, 59.298, 69.782
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 20818.492 Da / Num. of mol.: 1 / Mutation: T2C,T28C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoderma reesei (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: B2CZF9
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20% PEG 8000, 0.2M NaI, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→17.06 Å / Num. obs: 78472 / % possible obs: 98.12 % / Redundancy: 11.7 % / Biso Wilson estimate: 11.76 Å2 / Rsym value: 0.127 / Net I/σ(I): 23.857
Reflection shellResolution: 1.1→1.139 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2 / Num. unique obs: 6874 / Rsym value: 0.661 / % possible all: 87.11

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→17.06 Å / SU ML: 0.0911 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 14.1579 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1493 3966 5.05 %
Rwork0.1352 74499 -
obs0.136 78465 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.83 Å2
Refinement stepCycle: LAST / Resolution: 1.1→17.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 27 241 1744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00461612
X-RAY DIFFRACTIONf_angle_d1.02232217
X-RAY DIFFRACTIONf_chiral_restr0.0892219
X-RAY DIFFRACTIONf_plane_restr0.0053290
X-RAY DIFFRACTIONf_dihedral_angle_d7.711141
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.26611080.25012160X-RAY DIFFRACTION80.63
1.11-1.130.25281370.23022367X-RAY DIFFRACTION88.89
1.13-1.140.22331390.21392493X-RAY DIFFRACTION92.97
1.14-1.160.24611360.19512542X-RAY DIFFRACTION95.13
1.16-1.170.22211540.18542593X-RAY DIFFRACTION97.17
1.17-1.190.20471310.17372630X-RAY DIFFRACTION98.96
1.19-1.210.2011430.16722683X-RAY DIFFRACTION99.02
1.21-1.230.17281350.15852636X-RAY DIFFRACTION99.07
1.23-1.250.17731540.15132682X-RAY DIFFRACTION99.37
1.25-1.270.16141310.1482693X-RAY DIFFRACTION99.23
1.27-1.30.15441290.14012645X-RAY DIFFRACTION99.46
1.3-1.330.14621300.13612701X-RAY DIFFRACTION99.65
1.33-1.350.18511460.13152685X-RAY DIFFRACTION99.58
1.35-1.390.14341400.1242686X-RAY DIFFRACTION99.65
1.39-1.420.13611600.12282657X-RAY DIFFRACTION99.82
1.42-1.460.14381330.11532717X-RAY DIFFRACTION99.82
1.46-1.50.13431390.11012703X-RAY DIFFRACTION99.93
1.5-1.550.12771480.10812698X-RAY DIFFRACTION99.93
1.55-1.610.11871450.10242695X-RAY DIFFRACTION99.96
1.61-1.670.12171660.10652681X-RAY DIFFRACTION100
1.67-1.750.13261500.10862737X-RAY DIFFRACTION100
1.75-1.840.13131430.11442714X-RAY DIFFRACTION99.97
1.84-1.950.13861190.1182744X-RAY DIFFRACTION100
1.95-2.10.12951560.11922739X-RAY DIFFRACTION100
2.1-2.310.15771560.12682717X-RAY DIFFRACTION100
2.31-2.650.16191470.1412774X-RAY DIFFRACTION100
2.65-3.330.14561350.13952806X-RAY DIFFRACTION100
3.33-17.060.14371560.15172921X-RAY DIFFRACTION99.9

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