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- PDB-6byc: Crystal structure of the GH2 exo-beta-mannanase from Xanthomonas ... -

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Basic information

Entry
Database: PDB / ID: 6byc
TitleCrystal structure of the GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri
ComponentsBeta-mannosidase
KeywordsHYDROLASE/CARBOHYDRATE / CARBOHYDRATE / HYDROLASE-CARBOHYDRATE complex
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / extracellular region
Similarity search - Function
Mannosidase Ig/CBM-like domain / Beta-mannosidase, Ig-fold domain / Ig-fold domain / Mannosidase Ig/CBM-like domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily ...Mannosidase Ig/CBM-like domain / Beta-mannosidase, Ig-fold domain / Ig-fold domain / Mannosidase Ig/CBM-like domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Beta-mannosidase
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.897 Å
AuthorsDomingues, M.N. / Vieira, P.S. / Morais, M.A.B. / Murakami, M.T.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis of exo-beta-mannanase activity in the GH2 family.
Authors: Domingues, M.N. / Souza, F.H.M. / Vieira, P.S. / de Morais, M.A.B. / Zanphorlin, L.M. / Dos Santos, C.R. / Pirolla, R.A.S. / Honorato, R.V. / de Oliveira, P.S.L. / Gozzo, F.C. / Murakami, M.T.
History
DepositionDec 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,14713
Polymers97,1131
Non-polymers1,03412
Water10,323573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint4 kcal/mol
Surface area32730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.502, 68.575, 79.021
Angle α, β, γ (deg.)90.000, 95.160, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1094-

HOH

21A-1125-

HOH

31A-1477-

HOH

41A-1491-

HOH

51A-1549-

HOH

61A-1555-

HOH

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Components

#1: Protein Beta-mannosidase


Mass: 97113.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (strain 306) (bacteria)
Strain: 306 / Gene: XAC3075 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PI23
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Ammonium acetate Bis-Tris pH 5.5 PEG 10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.897→19.978 Å / Num. obs: 71912 / % possible obs: 94.91 % / Redundancy: 4.6 % / Biso Wilson estimate: 25.35 Å2 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Diffraction-ID
1.9-2.011
2.01-2.151
2.15-2.321
2.32-2.541
2.54-2.841
2.84-3.281
3.28-4.011
4.01-5.641

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JE8

2je8


Resolution: 1.897→19.978 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.44
RfactorNum. reflection% reflection
Rfree0.2165 3658 5.09 %
Rwork0.1745 --
obs0.1766 71908 94.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.42 Å2 / Biso mean: 27.0768 Å2 / Biso min: 12.75 Å2
Refinement stepCycle: final / Resolution: 1.897→19.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6841 0 68 573 7482
Biso mean--37.08 29.94 -
Num. residues----861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117071
X-RAY DIFFRACTIONf_angle_d1.2639582
X-RAY DIFFRACTIONf_chiral_restr0.0571002
X-RAY DIFFRACTIONf_plane_restr0.0061260
X-RAY DIFFRACTIONf_dihedral_angle_d13.5492599
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.897-1.9220.36131000.29442250235081
1.922-1.94830.2571410.20382531267293
1.9483-1.97610.27191310.19612575270693
1.9761-2.00550.2781520.20642533268593
2.0055-2.03680.24151430.18972547269093
2.0368-2.07020.22481460.18132550269694
2.0702-2.10590.25981560.1862560271693
2.1059-2.14410.27261330.18672631276494
2.1441-2.18530.22381460.18072553269994
2.1853-2.22990.24061470.18622617276494
2.2299-2.27830.25681550.17642569272494
2.2783-2.33120.22961350.18222631276695
2.3312-2.38940.24981420.18722597273995
2.3894-2.45390.25311110.18172658276995
2.4539-2.5260.2411270.18742659278696
2.526-2.60730.22681540.18272637279196
2.6073-2.70030.25391290.1912650277996
2.7003-2.80810.25811470.19472650279796
2.8081-2.93560.24461500.19092677282797
2.9356-3.08980.22891210.18862716283797
3.0898-3.28260.22131650.19082687285297
3.2826-3.53480.20541260.17212688281498
3.5348-3.88810.19771470.15562737288498
3.8881-4.44530.16141490.14362739288898
4.4453-5.58040.16281450.14192784292999
5.5804-19.9790.17761600.16352824298499

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