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

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Basic information

Entry
Database: PDB / ID: 5gll
TitleCrystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinofuranosidase from a compostmicrobial metagenome, calcium-bound 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 / 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 1.2Nov 8, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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

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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)77,75714
Polymers77,0592
Non-polymers69812
Water9,494527
1
A: Glycoside hydrolase family 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9548
Polymers38,5301
Non-polymers4247
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase family 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8036
Polymers38,5301
Non-polymers2735
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.490, 60.935, 78.901
Angle α, β, γ (deg.)90.00, 95.05, 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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Non-polymers , 5 types, 539 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 64759 / % possible obs: 99.2 % / Observed criterion σ(I): -0.3 / Redundancy: 6.8 % / Biso Wilson estimate: 12.349 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 13.5
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.838 / Mean I/σ(I) obs: 2.6 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MLG

4mlg


Resolution: 1.8→78.59 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.457 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.105 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1852 3324 5.2 %RANDOM
Rwork0.15762 ---
obs0.15906 60994 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.359 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0.16 Å2
2--0.09 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→78.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5198 0 42 527 5767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195418
X-RAY DIFFRACTIONr_bond_other_d0.0020.024800
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.9377365
X-RAY DIFFRACTIONr_angle_other_deg0.915311117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.775654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76624.129264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03915805
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7081519
X-RAY DIFFRACTIONr_chiral_restr0.0780.2749
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216156
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021265
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_it1.1152.1312627
X-RAY DIFFRACTIONr_mcbond_other1.1092.1272624
X-RAY DIFFRACTIONr_mcangle_it1.923.1793274
X-RAY DIFFRACTIONr_mcangle_other1.923.183275
X-RAY DIFFRACTIONr_scbond_it1.2792.2462791
X-RAY DIFFRACTIONr_scbond_other1.2792.2472792
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1563.314092
X-RAY DIFFRACTIONr_long_range_B_refined4.7917.7536560
X-RAY DIFFRACTIONr_long_range_B_other4.66317.5916467
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
Rfree0.288 222 -
Rwork0.236 4056 -
obs--87.74 %

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