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- PDB-5zn7: Crystal structure of GH31 alpha-xylosidase from a soil metagenome... -

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Basic information

Entry
Database: PDB / ID: 5zn7
TitleCrystal structure of GH31 alpha-xylosidase from a soil metagenome complexed with xylose
Componentsalpha-xylosidase MeXyl31
KeywordsHYDROLASE
Function / homologyalpha-D-xylopyranose
Function and homology information
Biological speciessoil metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsMatsuzawa, T. / Nakamichi, Y. / Watanabe, M. / Yaoi, K.
CitationJournal: To Be Published
Title: Structural insight into substrate specificity of alpha-xylosidase from a soil metagenome
Authors: Matsuzawa, T. / Nakamichi, Y. / Watanabe, M. / Yaoi, K.
History
DepositionApr 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: alpha-xylosidase MeXyl31
B: alpha-xylosidase MeXyl31
C: alpha-xylosidase MeXyl31
D: alpha-xylosidase MeXyl31
E: alpha-xylosidase MeXyl31
F: alpha-xylosidase MeXyl31
H: alpha-xylosidase MeXyl31
G: alpha-xylosidase MeXyl31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)627,73813
Polymers626,9878
Non-polymers7515
Water70,9253937
1
A: alpha-xylosidase MeXyl31
B: alpha-xylosidase MeXyl31
C: alpha-xylosidase MeXyl31
G: alpha-xylosidase MeXyl31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,7946
Polymers313,4944
Non-polymers3002
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14330 Å2
ΔGint-18 kcal/mol
Surface area83720 Å2
MethodPISA
2
D: alpha-xylosidase MeXyl31
E: alpha-xylosidase MeXyl31
F: alpha-xylosidase MeXyl31
H: alpha-xylosidase MeXyl31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,9447
Polymers313,4944
Non-polymers4503
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14770 Å2
ΔGint-17 kcal/mol
Surface area82300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.915, 124.865, 177.716
Angle α, β, γ (deg.)90.00, 116.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
alpha-xylosidase MeXyl31


Mass: 78373.375 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) soil metagenome (others) / Production host: Escherichia coli (E. coli)
#2: 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.: 5
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3937 / 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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 1.6 M lithium sulfate, 100 mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 371318 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.244 / Num. unique obs: 15857 / % possible all: 80.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.731 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.153 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19065 18670 5.1 %RANDOM
Rwork0.16546 ---
obs0.16672 350891 93.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.666 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å20 Å2-0.36 Å2
2--0.01 Å20 Å2
3----1.04 Å2
Refinement stepCycle: 1 / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43498 0 50 3937 47485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01944869
X-RAY DIFFRACTIONr_bond_other_d0.0020.0239913
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.93560991
X-RAY DIFFRACTIONr_angle_other_deg0.897392528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24655433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71523.9642273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.188157156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.46715313
X-RAY DIFFRACTIONr_chiral_restr0.0740.26260
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02150672
X-RAY DIFFRACTIONr_gen_planes_other0.0010.029889
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_it0.5621.64321726
X-RAY DIFFRACTIONr_mcbond_other0.5621.64321725
X-RAY DIFFRACTIONr_mcangle_it1.0012.46127161
X-RAY DIFFRACTIONr_mcangle_other1.0012.46227162
X-RAY DIFFRACTIONr_scbond_it0.6141.68723143
X-RAY DIFFRACTIONr_scbond_other0.6141.68723143
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0412.50433831
X-RAY DIFFRACTIONr_long_range_B_refined2.68918.84452365
X-RAY DIFFRACTIONr_long_range_B_other2.44318.56751389
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 1214 -
Rwork0.206 22179 -
obs--80.52 %

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