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- PDB-5zn6: Crystal structure of GH31 alpha-xylosidase from a soil metagenome -

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Basic information

Entry
Database: PDB / ID: 5zn6
TitleCrystal structure of GH31 alpha-xylosidase from a soil metagenome
ComponentsAlpha-xylosidase MeXyl31
KeywordsHYDROLASE / Hydolase
Biological speciessoil metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: 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)631,77660
Polymers626,9878
Non-polymers4,78952
Water67,1783729
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)316,34835
Polymers313,4944
Non-polymers2,85531
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22430 Å2
ΔGint-30 kcal/mol
Surface area80920 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)315,42725
Polymers313,4944
Non-polymers1,93421
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19430 Å2
ΔGint-29 kcal/mol
Surface area80790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.146, 124.174, 177.453
Angle α, β, γ (deg.)90.00, 116.81, 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: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 52 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3729 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.7 %
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: Dec 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 561527 / % possible obs: 91.2 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 23616 / % possible all: 77.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.894 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.11
RfactorNum. reflection% reflectionSelection details
Rfree0.19497 27623 4.9 %RANDOM
Rwork0.17423 ---
obs0.17525 533902 91.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20 Å2-0.09 Å2
2---0.38 Å20 Å2
3----0.77 Å2
Refinement stepCycle: 1 / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43498 0 312 3729 47539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01945068
X-RAY DIFFRACTIONr_bond_other_d0.0020.0240176
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.93961168
X-RAY DIFFRACTIONr_angle_other_deg0.919393132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37355429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.623.9592271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.457157153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.87515313
X-RAY DIFFRACTIONr_chiral_restr0.0790.26290
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02150636
X-RAY DIFFRACTIONr_gen_planes_other0.0010.029885
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_it0.7211.66421716
X-RAY DIFFRACTIONr_mcbond_other0.7211.66321715
X-RAY DIFFRACTIONr_mcangle_it1.2282.49127145
X-RAY DIFFRACTIONr_mcangle_other1.2282.49227146
X-RAY DIFFRACTIONr_scbond_it0.9511.75823352
X-RAY DIFFRACTIONr_scbond_other0.9511.75823352
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5652.59134024
X-RAY DIFFRACTIONr_long_range_B_refined3.16719.40352245
X-RAY DIFFRACTIONr_long_range_B_other2.93619.08651404
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.802→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 1869 -
Rwork0.296 32993 -
obs--76.74 %

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