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- PDB-5z5d: Crystal structure of a thermostable glycoside hydrolase family 43... -

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Basic information

Entry
Database: PDB / ID: 5z5d
TitleCrystal structure of a thermostable glycoside hydrolase family 43 {beta}-1,4-xylosidase from Geobacillus thermoleovorans IT-08
ComponentsBeta-xylosidaseXylan 1,4-b-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
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 / Concanavalin A-like lectin/glucanase domain superfamily ...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
Biological speciesGeobacillus thermoleovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 17, 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 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)62,1047
Polymers61,6031
Non-polymers5016
Water10,269570
1
A: Beta-xylosidase
hetero molecules

A: Beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,20814
Polymers123,2072
Non-polymers1,00112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area5550 Å2
ΔGint-52 kcal/mol
Surface area35800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.076, 62.076, 275.789
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 / Xylan 1,4-b-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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 570 / 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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES (N-(2-hydroxyethyl)piperazine-N-(2-ethanesulfonic acid)), 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: 0.912 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: 0.912 Å / Relative weight: 1
ReflectionResolution: 1.643→46.133 Å / Num. obs: 60040 / % possible obs: 99 % / Redundancy: 4.2 % / Rpim(I) all: 0.042 / Rrim(I) all: 0.091 / Rsym value: 0.08 / Net I/av σ(I): 6.6 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.7-1.7930.386285050.2620.470.38697.6
1.79-1.94.30.2523.181870.1350.2870.25299.2
1.9-2.034.40.1574.977020.0820.1780.15799.2
2.03-2.194.40.1136.572320.0590.1280.11399.4
2.19-2.44.40.0937.666820.0480.1050.09399.8
2.4-2.694.40.0788.661120.0410.0890.07899.8
2.69-3.14.40.06210.154100.0320.070.06299.6
3.1-3.84.40.05410.145690.0280.0610.05499.1
3.8-5.384.30.0510.435790.0250.0570.0597.9
5.38-46.1334.10.04810.120620.0250.0550.04895.6

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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: 1.7→46.13 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.8 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.088
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1759 3060 5.1 %RANDOM
Rwork0.1482 ---
obs0.1496 56950 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 66.63 Å2 / Biso mean: 16.322 Å2 / Biso min: 5.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å2-0 Å2-0 Å2
2--0.47 Å20 Å2
3----0.94 Å2
Refinement stepCycle: final / Resolution: 1.7→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4053 0 37 570 4660
Biso mean--29.27 29.11 -
Num. residues----504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194244
X-RAY DIFFRACTIONr_bond_other_d0.0020.023777
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9395772
X-RAY DIFFRACTIONr_angle_other_deg0.96738797
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0595516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55424.08201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84215666
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3851517
X-RAY DIFFRACTIONr_chiral_restr0.1010.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214702
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02911
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 222 -
Rwork0.249 4045 -
all-4267 -
obs--96.89 %

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