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- PDB-5glo: Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinof... -

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Basic information

Entry
Database: PDB / ID: 5glo
TitleCrystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinofuranosidase from a compostmicrobial metagenome in complex with l-arabinose, calcium-free form
ComponentsGlycoside hydrolase family 43
KeywordsHYDROLASE / Glycoside hydrolase family 43
Function / homology
Function and homology information


xylan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding
Similarity search - Function
: / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / alpha-L-arabinopyranose / beta-L-arabinofuranose / Glycoside hydrolase family 43
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMatsuzawa, T. / Kishine, N. / Fujimoto, Z. / Yaoi, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
New Energy and Industrial Technology Development Organization (NEDO) Japan
Citation
Journal: J. Biochem. / Year: 2017
Title: Crystal structure of metagenomic beta-xylosidase/ alpha-l-arabinofuranosidase activated by calcium.
Authors: Matsuzawa, T. / Kaneko, S. / Kishine, N. / Fujimoto, Z. / Yaoi, K.
#1: Journal: Appl. Microbiol. Biotechnol. / Year: 2015
Title: Screening, identification, and characterization of a GH43 family beta-xylosidase/alpha-arabinofuranosidase from a compost microbial metagenome.
Authors: Matsuzawa, T. / Kaneko, S. / Yaoi, K.
History
DepositionJul 12, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 43
B: Glycoside hydrolase family 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,81111
Polymers77,0592
Non-polymers7529
Water12,250680
1
A: Glycoside hydrolase family 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9356
Polymers38,5301
Non-polymers4055
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase family 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8765
Polymers38,5301
Non-polymers3464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.764, 61.385, 79.239
Angle α, β, γ (deg.)90.00, 95.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glycoside hydrolase family 43 / beta-xylosidase / alpha-arabinofuranosidase


Mass: 38529.520 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 47-369
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: coxyl43 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H5BL38

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Sugars , 2 types, 4 molecules

#3: Sugar ChemComp-FUB / beta-L-arabinofuranose / beta-L-arabinose / L-arabinose / arabinose


Type: L-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O5
IdentifierTypeProgram
LArafbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-arabinofuranoseCOMMON NAMEGMML 1.0
b-L-ArafIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-ARA / alpha-L-arabinopyranose / alpha-L-arabinose / L-arabinose / arabinose


Type: L-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O5
IdentifierTypeProgram
LArapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-arabinopyranoseCOMMON NAMEGMML 1.0
a-L-ArapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 685 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / 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: 2.49 Å3/Da / Density % sol: 50.7 % / Description: Plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 25% PEG3350, 8% Tacsimate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 25, 2015
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. obs: 66570 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 16.149 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 16.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GLK

5glk


Resolution: 1.8→78.89 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.281 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.099 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17476 3334 5 %RANDOM
Rwork0.15487 ---
obs0.15592 63040 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.468 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.13 Å2
2---0.15 Å20 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.8→78.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5190 0 48 680 5918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195468
X-RAY DIFFRACTIONr_bond_other_d0.0020.024845
X-RAY DIFFRACTIONr_angle_refined_deg1.3031.9417446
X-RAY DIFFRACTIONr_angle_other_deg1.075311241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5885654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.93224.164269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35315823
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9961520
X-RAY DIFFRACTIONr_chiral_restr0.0820.2771
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216165
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021273
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9822.0332622
X-RAY DIFFRACTIONr_mcbond_other0.9822.0322621
X-RAY DIFFRACTIONr_mcangle_it1.6843.043273
X-RAY DIFFRACTIONr_mcangle_other1.6843.0413274
X-RAY DIFFRACTIONr_scbond_it1.1532.1372846
X-RAY DIFFRACTIONr_scbond_other1.1532.1372846
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9423.1524173
X-RAY DIFFRACTIONr_long_range_B_refined4.78917.5156848
X-RAY DIFFRACTIONr_long_range_B_other4.67417.2326698
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 246 -
Rwork0.236 4606 -
obs--99.24 %

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