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- PDB-7eo6: X-ray structure analysis of xylanase -

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Basic information

Entry
Database: PDB / ID: 7eo6
TitleX-ray structure analysis of xylanase
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / Xylanase
Function / homology
Function and homology information


polysaccharide binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / 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 ...Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / 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 / CBM2/CBM3, carbohydrate-binding domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
IODIDE ION / Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesActinobacteria bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWan, Q. / Yi, Y. / Xu, S.
Funding support1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2021
Title: Characterization and structural analysis of a thermophilic GH11 xylanase from compost metatranscriptome.
Authors: Yi, Y. / Xu, S. / Kovalevsky, A. / Zhang, X. / Liu, D. / Wan, Q.
History
DepositionApr 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 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: Endo-1,4-beta-xylanase
B: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2944
Polymers43,0402
Non-polymers2542
Water3,873215
1
A: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6472
Polymers21,5201
Non-polymers1271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-0 kcal/mol
Surface area7960 Å2
MethodPISA
2
B: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6472
Polymers21,5201
Non-polymers1271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-0 kcal/mol
Surface area7910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.800, 42.476, 59.734
Angle α, β, γ (deg.)74.320, 87.400, 86.110
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 21520.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacteria bacterium (bacteria) / Gene: DIU60_09020 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2W4QIY3, endo-1,4-beta-xylanase
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.06 Å3/Da / Density % sol: 40.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 15% PEG 8000, 0.2M NaI, 0.1M MES, pH6.0

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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, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→38.52 Å / Num. obs: 25769 / % possible obs: 96.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 9.68 Å2 / CC1/2: 0.969 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.07 / Rrim(I) all: 0.125 / Net I/σ(I): 7.5 / Num. measured all: 82664 / Scaling rejects: 638
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.942.90.21475216450.760.1540.2624.395.3
9.11-38.523.60.088372320.9190.0550.09812.296.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M4W

1m4w


Resolution: 1.9→30.72 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 2.06 / Phase error: 20.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 1211 4.7 %
Rwork0.1919 24540 -
obs0.193 25751 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 48.81 Å2 / Biso mean: 11.1415 Å2 / Biso min: 4.65 Å2
Refinement stepCycle: final / Resolution: 1.9→30.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2999 0 2 215 3216
Biso mean--34.43 15.32 -
Num. residues----381
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9001-1.97620.24721640.2147268995
1.9762-2.06610.21351390.2073268796
2.0661-2.1750.22551210.2026269296
2.175-2.31130.2251130.206274596
2.3113-2.48960.2461480.2162273597
2.4896-2.740.22661360.2038273597
2.74-3.13620.19791560.1884270897
3.1362-3.94990.20721080.1697278498
3.9499-4.06340.19651260.1719276598
Refinement TLS params.Method: refined / Origin x: 4.9268 Å / Origin y: -13.5061 Å / Origin z: -14.0617 Å
111213212223313233
T0.0487 Å2-0.0006 Å2-0.0109 Å2-0.0676 Å20.0076 Å2--0.0589 Å2
L0.0913 °2-0.1253 °2-0.2012 °2-0.243 °20.2261 °2--0.2757 °2
S0.0051 Å °0.0331 Å °0.0151 Å °0.0014 Å °-0.0085 Å °0.0107 Å °-0.0077 Å °-0.0131 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 192
2X-RAY DIFFRACTION1allB3 - 192
3X-RAY DIFFRACTION1allD2 - 259
4X-RAY DIFFRACTION1allC1 - 2

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