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- PDB-6nps: Crystal structure of GH115 enzyme AxyAgu115A from Amphibacillus x... -

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Basic information

Entry
Database: PDB / ID: 6nps
TitleCrystal structure of GH115 enzyme AxyAgu115A from Amphibacillus xylanus
ComponentsAxyAgu115A
KeywordsHYDROLASE / gylcosyl hydrolase family 115 / GH115 / hemicellulase / arabinoglucuronoxylan / sugar binding protein / GLUCURONIDASE / GLUCURONIC ACID
Function / homology
Function and homology information


Glycosyl hydrolase family 115 / Glycosyl hydrolase family 115 / Gylcosyl hydrolase 115 C-terminal domain / Glycosyl hydrolase 115 superfamily / Glycosyl hydrolase family 115 / Gylcosyl hydrolase family 115 C-terminal domain / Bacteroidetes-Associated Carbohydrate-binding Often N-terminal / Beta-hexosaminidase-like, domain 2 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
GH115_C domain-containing protein
Similarity search - Component
Biological speciesAmphibacillus xylanus NBRC 15112 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsStogios, P.J. / Skarina, T. / Di Leo, R. / Yan, R. / Master, E. / Savchenko, A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)Industrial Biocatalysis Network Canada
CitationJournal: N Biotechnol / Year: 2021
Title: Structural characterization of the family GH115 alpha-glucuronidase from Amphibacillus xylanus yields insight into its coordinated action with alpha-arabinofuranosidases.
Authors: Yan, R. / Wang, W. / Vuong, T.V. / Xiu, Y. / Skarina, T. / Di Leo, R. / Gatenholm, P. / Toriz, G. / Tenkanen, M. / Stogios, P.J. / Master, E.R.
History
DepositionJan 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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: AxyAgu115A
B: AxyAgu115A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,04124
Polymers220,1852
Non-polymers1,85622
Water33,0941837
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-50 kcal/mol
Surface area72200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.080, 96.210, 111.750
Angle α, β, γ (deg.)84.37, 78.37, 83.32
Int Tables number1
Space group name H-MP1

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Components

#1: Protein AxyAgu115A


Mass: 110092.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amphibacillus xylanus NBRC 15112 (bacteria)
Strain: ATCC 51415 / DSM 6626 / JCM 7361 / LMG 17667 / NBRC 15112 / Ep01
Gene: AXY_23000 / Plasmid: p15Tv lic / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: K0J4X5
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1837 / 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: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20 mg/mL protein solution with 0.5 microL of reservoir solution 20% (w/v) PEG 3350, 0.2 M diammonium hydrogen citrate and 10 mM D-glucuronic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97913 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 1.99→47.64 Å / Num. obs: 165501 / % possible obs: 94.6 % / Redundancy: 11.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.042 / Net I/σ(I): 14.1
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 11805 / CC1/2: 0.82 / Rpim(I) all: 0.534 / % possible all: 90.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
X-Areadata reduction
Aimlessdata scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZMH, 4C90

4zmh

4c90


Resolution: 1.99→47.638 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.94
RfactorNum. reflection% reflectionSelection details
Rfree0.1896 8156 4.93 %RANDOM
Rwork0.1475 ---
obs0.1496 165435 94.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.99→47.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15470 0 117 1837 17424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01216022
X-RAY DIFFRACTIONf_angle_d1.13321740
X-RAY DIFFRACTIONf_dihedral_angle_d20.5185851
X-RAY DIFFRACTIONf_chiral_restr0.0752320
X-RAY DIFFRACTIONf_plane_restr0.0072828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.01260.26622700.24485092X-RAY DIFFRACTION91
2.0126-2.03630.27652440.24445058X-RAY DIFFRACTION91
2.0363-2.06110.24982450.21724942X-RAY DIFFRACTION91
2.0611-2.08720.25263000.20125055X-RAY DIFFRACTION91
2.0872-2.11470.24082590.18684964X-RAY DIFFRACTION90
2.1147-2.14370.24552850.18664907X-RAY DIFFRACTION90
2.1437-2.17430.23422600.17814967X-RAY DIFFRACTION88
2.1743-2.20670.232620.17894768X-RAY DIFFRACTION87
2.2067-2.24120.23372690.17445111X-RAY DIFFRACTION91
2.2412-2.2780.2332250.17444784X-RAY DIFFRACTION87
2.278-2.31720.19912570.1674810X-RAY DIFFRACTION87
2.3172-2.35940.22542940.16215406X-RAY DIFFRACTION98
2.3594-2.40480.20962780.15345464X-RAY DIFFRACTION99
2.4048-2.45380.20382870.15925419X-RAY DIFFRACTION98
2.4538-2.50720.24092600.15515480X-RAY DIFFRACTION99
2.5072-2.56550.2012740.15595466X-RAY DIFFRACTION99
2.5655-2.62970.2263080.16035493X-RAY DIFFRACTION99
2.6297-2.70080.20632640.15815421X-RAY DIFFRACTION99
2.7008-2.78020.21752820.15585518X-RAY DIFFRACTION99
2.7802-2.870.19982740.15115512X-RAY DIFFRACTION99
2.87-2.97250.20622930.15425416X-RAY DIFFRACTION99
2.9725-3.09150.19482700.1555504X-RAY DIFFRACTION99
3.0915-3.23220.19512800.15195422X-RAY DIFFRACTION98
3.2322-3.40250.19452730.14245498X-RAY DIFFRACTION98
3.4025-3.61570.17552870.13495406X-RAY DIFFRACTION98
3.6157-3.89470.1632730.12635408X-RAY DIFFRACTION97
3.8947-4.28640.15962590.12194879X-RAY DIFFRACTION89
4.2864-4.90610.13272680.11215147X-RAY DIFFRACTION93
4.9061-6.17910.1692750.12935556X-RAY DIFFRACTION100
6.1791-47.65120.17942810.15675406X-RAY DIFFRACTION98
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)
11.482-0.4069-0.4162.16780.93081.67140.19270.1230.0688-0.0583-0.2057-0.126-0.18150.07030.02540.40420.0399-0.01870.26670.06910.273893.4419121.850158.6138
20.4075-0.1150.11480.8375-0.24250.70060.03280.0332-0.01010.0156-0.04670.15360.0108-0.05810.01310.3169-0.0052-0.02140.2536-0.04650.255683.53793.596181.2184
31.93620.50470.64381.62870.18531.35980.0899-0.1436-0.14950.0282-0.1221-0.15830.10050.14520.01430.20790.01720.04480.22490.06910.2499106.107661.6543151.417
47.0443-1.18540.12933.870.77782.42960.11470.2058-0.0963-0.4557-0.2290.9309-0.0388-0.44930.03990.2848-0.0271-0.05330.3073-0.05180.420776.695559.7868143.309
50.27040.1319-0.07610.929-0.31440.7386-0.0123-0.02330.0722-0.028-0.00390.123-0.1301-0.00810.01440.22160.0066-0.02780.2148-0.02940.241295.398795.7152130.1332
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 314 )
2X-RAY DIFFRACTION2chain 'A' and (resid 315 through 966 )
3X-RAY DIFFRACTION3chain 'B' and (resid -1 through 289 )
4X-RAY DIFFRACTION4chain 'B' and (resid 290 through 381 )
5X-RAY DIFFRACTION5chain 'B' and (resid 382 through 966 )

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