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- PDB-6ms2: Crystal structure of the GH43 BlXynB protein from Bacillus lichen... -

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Basic information

Entry
Database: PDB / ID: 6ms2
TitleCrystal structure of the GH43 BlXynB protein from Bacillus licheniformis
ComponentsGlycoside Hydrolase Family 43
KeywordsHYDROLASE / glycoside hydrolase / GH43 / Bacillus lincheniformis
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / Beta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
Glycoside Hydrolase Family 43
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.494 Å
AuthorsZanphorlin, L.M. / Morais, M.A.B. / Diogo, J.A. / Murakami, M.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)15/26982-0 Brazil
CitationJournal: Biotechnol. Bioeng. / Year: 2019
Title: Structure-guided design combined with evolutionary diversity led to the discovery of the xylose-releasing exo-xylanase activity in the glycoside hydrolase family 43.
Authors: Zanphorlin, L.M. / de Morais, M.A.B. / Diogo, J.A. / Domingues, M.N. / de Souza, F.H.M. / Ruller, R. / Murakami, M.T.
History
DepositionOct 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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

Downloads & links

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Assembly

Deposited unit
A: Glycoside Hydrolase Family 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5092
Polymers60,4691
Non-polymers401
Water1,04558
1
A: Glycoside Hydrolase Family 43
hetero molecules

A: Glycoside Hydrolase Family 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,0194
Polymers120,9392
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2410 Å2
ΔGint-33 kcal/mol
Surface area35310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.858, 41.902, 71.805
Angle α, β, γ (deg.)90.000, 91.700, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glycoside Hydrolase Family 43


Mass: 60469.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 / NCIMB 9375 / NRRL NRS-1264 / Gibson 46) (bacteria)
Strain: ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 / NCIMB 9375 / NRRL NRS-1264 / Gibson 46
Gene: xynB, BL03023 / Production host: Escherichia coli (E. coli) / References: UniProt: Q65MB6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 1.9 Å3/Da / Density % sol: 35.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 36% (v/v) 2-methyl-2,4-pentanediol, 5% (w/v) polyethelyne glycol 8,000 and 0.1 M sodium cacodylate pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.49→40.41 Å / Num. obs: 15465 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 33.78 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.109 / Χ2: 0.884 / Net I/σ(I): 9.58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.49-2.640.5541.8122090.7080.71585.3
2.64-2.830.2723.2123290.8970.34395.8
2.83-3.050.2034.7421690.940.25196.2
3.05-3.340.138.319920.9770.15794.9
3.34-3.730.09111.9618160.9840.11295.4
3.73-4.30.0715.6215920.9910.08594.8
4.3-5.250.04919.4914150.9960.05997.6
5.25-7.370.05516.7510800.9940.06795.7
7.37-40.410.03823.796570.9960.04696.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.10_2148refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YRZ

1yrz


Resolution: 2.494→33.313 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.68
RfactorNum. reflection% reflection
Rfree0.2419 2741 10.06 %
Rwork0.1967 --
obs0.2013 15356 87.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.74 Å2 / Biso mean: 38.8627 Å2 / Biso min: 11.95 Å2
Refinement stepCycle: final / Resolution: 2.494→33.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4073 0 1 58 4132
Biso mean--73.57 29.59 -
Num. residues----511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034200
X-RAY DIFFRACTIONf_angle_d0.7565714
X-RAY DIFFRACTIONf_chiral_restr0.046583
X-RAY DIFFRACTIONf_plane_restr0.004748
X-RAY DIFFRACTIONf_dihedral_angle_d17.8962428
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4935-2.53650.40721030.336982292560
2.5365-2.58260.36311150.3071982109770
2.5826-2.63230.3251300.30971127125780
2.6323-2.6860.34261230.26561196131987
2.686-2.74440.31351340.27221249138388
2.7444-2.80820.28611440.26211203134787
2.8082-2.87840.31181330.25541257139090
2.8784-2.95610.35981360.24791270140690
2.9561-3.04310.26431370.2241277141492
3.0431-3.14120.27421340.21161311144593
3.1412-3.25340.28231480.21321309145792
3.2534-3.38350.28991420.20651202134488
3.3835-3.53740.21941340.19171234136888
3.5374-3.72360.24181320.18121322145494
3.7236-3.95660.19771520.17821270142291
3.9566-4.26150.21591340.15051280141491
4.2615-4.68930.17171590.14031299145894
4.6893-5.36540.17711460.14571280142692
5.3654-6.75060.22621480.18541257140590
6.7506-33.31610.19781570.18021357151497
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)
14.2376-0.71070.97014.6175-2.59513.69530.09770.0282-0.2978-0.04390.05850.39750.1037-0.1347-0.14810.21210.00320.04180.1602-0.02430.165555.515213.45914.2654
22.2094-0.20620.85123.4509-1.17013.05080.1441-0.145-0.04470.17550.0140.60840.0032-0.4591-0.1320.1872-0.03140.03690.2894-0.05850.287241.925313.333721.1811
34.4271.78111.14894.65281.94524.26540.4678-0.80360.81290.3148-0.44440.7048-0.0433-0.4575-0.02370.37880.01990.10130.4513-0.11950.387143.078817.569132.6195
43.30660.4628-1.10031.31840.58152.04940.3268-0.77760.20.5137-0.30370.1767-0.1488-0.0699-0.05150.3409-0.05220.00270.4273-0.04460.208559.281117.814933.2783
51.38810.3075-0.47410.8127-0.31321.79250.06570.11630.0118-0.0478-0.07780.00150.0606-0.0517-0.00090.17850.04130.0120.1734-0.05410.280560.446621.82431.994
61.9254-0.0044-0.76570.93190.29891.96840.1090.25970.0731-0.0232-0.17610.157-0.148-0.19160.03640.22390.06760.01390.19830.02670.27163.197127.1024-3.2728
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 77 )A5 - 77
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 146 )A78 - 146
3X-RAY DIFFRACTION3chain 'A' and (resid 147 through 186 )A147 - 186
4X-RAY DIFFRACTION4chain 'A' and (resid 187 through 263 )A187 - 263
5X-RAY DIFFRACTION5chain 'A' and (resid 264 through 447 )A264 - 447
6X-RAY DIFFRACTION6chain 'A' and (resid 448 through 515 )A448 - 515

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