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- PDB-5z5h: Crystal structure of a thermostable glycoside hydrolase family 43... -

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Basic information

Entry
Database: PDB / ID: 5z5h
TitleCrystal structure of a thermostable glycoside hydrolase family 43 {beta}-1,4-xylosidase from Geobacillus thermoleovorans IT-08 in complex with D-xylose
ComponentsBeta-xylosidase
KeywordsHYDROLASE / Xylanolytic / GH43 / oligosaccharide / saccharification
Function / homology
Function and homology information


xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / 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 / Jelly Rolls - #200 ...: / 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 / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-D-xylopyranose / Beta-xylosidase
Similarity search - Component
Biological speciesGeobacillus thermoleovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRohman, A. / van Oosterwijk, N. / Puspaningsih, N.N.T. / Dijkstra, B.W.
Citation
Journal: PLoS ONE / Year: 2018
Title: Structural basis of product inhibition by arabinose and xylose of the thermostable GH43 beta-1,4-xylosidase from Geobacillus thermoleovorans IT-08.
Authors: Rohman, A. / van Oosterwijk, N. / Puspaningsih, N.N.T. / Dijkstra, B.W.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2007
Title: Purification, crystallization and preliminary X-ray analysis of a thermostable glycoside hydrolase family 43 beta-xylosidase from Geobacillus thermoleovorans IT-08.
Authors: Rohman, A. / van Oosterwijk, N. / Kralj, S. / Dijkhuizen, L. / Dijkstra, B.W. / Puspaningsih, N.N.
History
DepositionJan 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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.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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7943
Polymers61,6031
Non-polymers1902
Water9,566531
1
A: Beta-xylosidase
hetero molecules

A: Beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,5876
Polymers123,2072
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3720 Å2
ΔGint-36 kcal/mol
Surface area36570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.453, 62.453, 276.672
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Beta-xylosidase / {beta}-1 / 4-xylosidase


Mass: 61603.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermoleovorans (bacteria) / Gene: xyl / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2I2N4, xylan 1,4-beta-xylosidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-XYS / alpha-D-xylopyranose / alpha-D-xylose / D-xylose / xylose / XYLOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-xylopyranoseCOMMON NAMEGMML 1.0
a-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / 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: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES (N-(2-hydroxyethyl)piperazine-N-(2-ethanesulfonic acid)) buffer, pH 7.0, 5% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.93 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.825→46.354 Å / Num. obs: 44217 / % possible obs: 99.1 % / Redundancy: 3.4 % / Rpim(I) all: 0.054 / Rrim(I) all: 0.102 / Rsym value: 0.086 / Net I/av σ(I): 5.7 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.9-23.10.2971.761520.1990.3610.29796.7
2-2.123.30.2312.260410.1520.280.23199.9
2.12-2.273.40.2621.856850.1740.3180.26299.9
2.27-2.453.40.1256.153380.0780.1480.125100
2.45-2.693.50.0917.649340.0560.1070.091100
2.69-33.50.05912.844900.0350.0690.05999.9
3-3.473.50.05112.239960.030.060.05199.7
3.47-4.253.50.0648.733850.0380.0750.06499.3
4.25-6.013.50.03418.426450.020.040.03498
6.01-46.3543.20.0339.615510.0210.0390.03395.3

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
COMBATdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yif

1yif


Resolution: 1.9→46.35 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.884 / SU B: 4.648 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.17
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 2186 5.1 %RANDOM
Rwork0.2161 ---
obs0.2183 40994 96.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 63.23 Å2 / Biso mean: 19.91 Å2 / Biso min: 6.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å2-0 Å2-
2--0.19 Å20 Å2
3----0.39 Å2
Refinement stepCycle: final / Resolution: 1.9→46.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4053 0 11 531 4595
Biso mean--24.73 29.97 -
Num. residues----504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194199
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9365714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.165506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49324.05200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90915659
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9691517
X-RAY DIFFRACTIONr_chiral_restr0.0990.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213241
LS refinement shellResolution: 1.899→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.476 131 -
Rwork0.521 2704 -
all-2835 -
obs--88.1 %

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