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- PDB-6byg: Crystal structure of the nucleophile mutant (E575A) of the GH2 ex... -

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Basic information

Entry
Database: PDB / ID: 6byg
TitleCrystal structure of the nucleophile mutant (E575A) 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
beta-D-mannopyranose / Beta-mannosidase
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.999 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 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-mannosidase
B: Beta-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,0204
Polymers193,6602
Non-polymers3602
Water22,0501224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint18 kcal/mol
Surface area61430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.445, 116.048, 104.936
Angle α, β, γ (deg.)90.000, 98.170, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-mannosidase /


Mass: 96830.000 Da / Num. of mol.: 2 / Mutation: E575A
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: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1224 / 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: 2.47 Å3/Da / Density % sol: 50.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 6000 Sodium acetate Magnesium chloride

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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: 1.99→43.147 Å / Num. obs: 121038 / % possible obs: 95.13 % / Redundancy: 4.6 % / Biso Wilson estimate: 28.4 Å2 / Net I/σ(I): 10.57
Reflection shell
Resolution (Å)Diffraction-ID
2.12-2.271
2.27-2.451
2.45-2.681
2.68-2.991
2.99-3.461
3.46-4.231
4.23-5.951

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementResolution: 1.999→43.147 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.64
RfactorNum. reflection% reflection
Rfree0.2154 5986 4.95 %
Rwork0.1707 --
obs0.1729 121017 95.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.03 Å2 / Biso mean: 33.07 Å2 / Biso min: 10.47 Å2
Refinement stepCycle: final / Resolution: 1.999→43.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13618 0 24 1224 14866
Biso mean--36.09 34.74 -
Num. residues----1714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114011
X-RAY DIFFRACTIONf_angle_d1.23619032
X-RAY DIFFRACTIONf_chiral_restr0.0512009
X-RAY DIFFRACTIONf_plane_restr0.0062505
X-RAY DIFFRACTIONf_dihedral_angle_d13.5365158
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9987-2.02140.31681740.28323487366187
2.0214-2.04520.32151840.26373596378089
2.0452-2.07010.33371900.25053658384891
2.0701-2.09630.31622150.23683678389392
2.0963-2.12390.26512000.23053693389394
2.1239-2.1530.26372090.22023764397393
2.153-2.18380.25752000.22353809400995
2.1838-2.21640.31771850.24583780396594
2.2164-2.2510.34282050.28223774397995
2.251-2.28790.31791980.2623790398894
2.2879-2.32730.27581730.22093845401895
2.3273-2.36970.25791930.19223848404195
2.3697-2.41520.2181940.18333813400795
2.4152-2.46450.22762230.18283835405896
2.4645-2.51810.25681730.1873881405496
2.5181-2.57670.25062050.18933819402496
2.5767-2.64110.25632160.19323876409296
2.6411-2.71250.26751900.18233866405696
2.7125-2.79230.24251900.18093902409296
2.7923-2.88240.22362060.18243883408997
2.8824-2.98540.24192320.1883878411097
2.9854-3.10490.25152040.18163883408797
3.1049-3.24620.23451960.17843917411397
3.2462-3.41730.22871770.17413974415197
3.4173-3.63130.20952330.1583897413097
3.6313-3.91150.16021910.14483958414997
3.9115-4.30480.1451770.12283955413298
4.3048-4.92690.14462370.113947418498
4.9269-6.20450.15632000.12374007420798
6.2045-43.15750.1532160.12984018423497
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.58290.0245-0.05760.3007-0.00220.29490.002-0.0773-0.03880.0395-0.0048-0.00010.0110.01090.00490.2359-0.0122-0.00570.15190.01550.2085.8079-0.570910.6085
20.64460.1021-0.00720.39590.00340.7076-0.04440.1725-0.0407-0.02650.0176-0.0605-0.01020.1730.01930.2028-0.03970.0110.30470.00630.194934.32086.6502-34.6109
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 29:883)A29 - 883
2X-RAY DIFFRACTION2(chain B and resid 29:888)B29 - 888

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