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- PDB-5yxt: Crystal structure of reducing end xylose-releasing exo-oligoxylanase -

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Basic information

Entry
Database: PDB / ID: 5yxt
TitleCrystal structure of reducing end xylose-releasing exo-oligoxylanase
ComponentsReducing end xylose-releasing exo-oligoxylanase
KeywordsHYDROLASE
Function / homology
Function and homology information


xylan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Reducing end xylose-releasing exo-oligoxylanase
Similarity search - Component
Biological speciesPaenibacillus barengoltzii G22 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsJiang, Z.Q. / You, X. / Huang, P. / Ma, J.W.
CitationJournal: To Be Published
Title: Structure of glycoside hydrolase family 8 xylanase at 1.88 Angstroms resolution
Authors: Jiang, Z.Q. / You, X. / Huang, P. / Ma, J.W.
History
DepositionDec 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Refinement description / Structure summary
Category: database_2 / refine_hist ...database_2 / refine_hist / struct / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high / _refine_hist.d_res_low / _struct.title / _struct_keywords.text
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Reducing end xylose-releasing exo-oligoxylanase
B: Reducing end xylose-releasing exo-oligoxylanase
C: Reducing end xylose-releasing exo-oligoxylanase
D: Reducing end xylose-releasing exo-oligoxylanase


Theoretical massNumber of molelcules
Total (without water)176,3684
Polymers176,3684
Non-polymers00
Water18,6461035
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-12 kcal/mol
Surface area53680 Å2
Unit cell
Length a, b, c (Å)54.570, 78.990, 89.148
Angle α, β, γ (deg.)100.34, 95.86, 106.35
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Reducing end xylose-releasing exo-oligoxylanase


Mass: 44091.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus barengoltzii G22 (bacteria)
Gene: C812_03928 / Production host: Escherichia coli (E. coli) / References: UniProt: R9L536
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1035 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium thiocyanate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.978 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.88→22.35 Å / Num. obs: 105939 / % possible obs: 93 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 5.2
Reflection shellResolution: 1.88→1.94 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_2474: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WU4

1wu4


Resolution: 1.88→22.35 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.6 / Phase error: 50.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.289 1990 1.89 %
Rwork0.2445 --
obs0.2454 105553 93.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→22.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12155 0 0 1035 13190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712579
X-RAY DIFFRACTIONf_angle_d0.82517142
X-RAY DIFFRACTIONf_dihedral_angle_d9.0327180
X-RAY DIFFRACTIONf_chiral_restr0.0491648
X-RAY DIFFRACTIONf_plane_restr0.0062267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.92280.35171390.36247230X-RAY DIFFRACTION91
1.9228-1.97480.41711470.33257643X-RAY DIFFRACTION96
1.9748-2.03290.28561500.3067744X-RAY DIFFRACTION97
2.0329-2.09840.34021460.28077646X-RAY DIFFRACTION97
2.0984-2.17340.2991480.26617696X-RAY DIFFRACTION97
2.1734-2.26030.29131490.24647707X-RAY DIFFRACTION97
2.2603-2.36310.25751470.23947653X-RAY DIFFRACTION96
2.3631-2.48760.2891470.22747681X-RAY DIFFRACTION96
2.4876-2.64330.29421470.22097652X-RAY DIFFRACTION96
2.6433-2.84710.2141460.22277583X-RAY DIFFRACTION95
2.8471-3.1330.2631430.21057433X-RAY DIFFRACTION94
3.133-3.58510.2911370.21497141X-RAY DIFFRACTION89
3.5851-4.51190.28581220.22376379X-RAY DIFFRACTION80
4.5119-23.95630.30461220.24096375X-RAY DIFFRACTION80

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