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- PDB-5xyh: Crystal Structure of catalytic domain of 1,4-beta-Cellobiosidase ... -

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Basic information

Entry
Database: PDB / ID: 5xyh
TitleCrystal Structure of catalytic domain of 1,4-beta-Cellobiosidase (CbsA) from Xanthomonas oryzae pv. oryzae
ComponentsCbsA
KeywordsHYDROLASE / exoglucanase / Xoo / cell-wall degrading enzyme / bacterial blight
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesXanthomonas oryzae pv. oryzae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.864 Å
AuthorsKumar, S. / Haque, A.S. / Nathawat, R. / Sankaranaryanan, R.
Funding support India, 1items
OrganizationGrant numberCountry
CSIR India
Citation
Journal: Mol. Plant Pathol. / Year: 2018
Title: A mutation in an exoglucanase of Xanthomonas oryzae pv. oryzae, which confers an endo mode of activity, affects bacterial virulence, but not the induction of immune responses, in rice
Authors: Tayi, L. / Kumar, S. / Nathawat, R. / Haque, A.S. / Maku, R.V. / Patel, H.K. / Sankaranarayanan, R. / Sonti, R.V.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2012
Title: Crystallization and preliminary crystallographic studies of CbsA, a secretory exoglucanase from Xanthomonas oryzae pv. oryzae.
Authors: Kumar, S. / Haque, A.S. / Jha, G. / Sonti, R.V. / Sankaranarayanan, R.
History
DepositionJul 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Database references / Structure summary
Category: citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CbsA


Theoretical massNumber of molelcules
Total (without water)45,6251
Polymers45,6251
Non-polymers00
Water7,963442
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16700 Å2
Unit cell
Length a, b, c (Å)46.142, 90.720, 99.781
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CbsA


Mass: 45624.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: culture supernatant
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (bacteria)
Strain: BXO43 / Gene: cbsA / Plasmid: pUFR034 / Details (production host): overexpression / Production host: Xanthomonas oryzae pv. oryzae (bacteria) / Strain (production host): BXO2700
References: UniProt: A0A384E106*PLUS, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: polyethylene glycol 3350 citric acid / PH range: 3.0 to 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.86→25 Å / Num. obs: 33848 / % possible obs: 93.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 31.69
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 7.75 / % possible all: 89.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B4H

4b4h


Resolution: 1.864→24.517 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2377 1628 4.84 %
Rwork0.189 --
obs0.1913 33638 94.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.864→24.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3211 0 0 442 3653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063308
X-RAY DIFFRACTIONf_angle_d0.8284522
X-RAY DIFFRACTIONf_dihedral_angle_d2.5422627
X-RAY DIFFRACTIONf_chiral_restr0.052488
X-RAY DIFFRACTIONf_plane_restr0.005593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8641-1.91890.37991290.34442640X-RAY DIFFRACTION94
1.9189-1.98080.31451460.25362734X-RAY DIFFRACTION99
1.9808-2.05160.26851430.19632771X-RAY DIFFRACTION100
2.0516-2.13370.22971490.18742807X-RAY DIFFRACTION100
2.1337-2.23070.2753980.20262124X-RAY DIFFRACTION95
2.2307-2.34820.3295960.27652150X-RAY DIFFRACTION76
2.3482-2.49520.27491450.19622820X-RAY DIFFRACTION100
2.4952-2.68770.23831280.18982842X-RAY DIFFRACTION100
2.6877-2.95770.23551430.19112825X-RAY DIFFRACTION100
2.9577-3.38480.24111610.17442849X-RAY DIFFRACTION100
3.3848-4.26080.21251280.15692430X-RAY DIFFRACTION84
4.2608-24.51910.15921620.13983018X-RAY DIFFRACTION100

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