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- PDB-5z3f: Glycosidase E335A in complex with glucose -

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Basic information

Entry
Database: PDB / ID: 5z3f
TitleGlycosidase E335A in complex with glucose
ComponentsGlycoside hydrolase 15-related protein
KeywordsHYDROLASE / Glycosidase
Function / homology
Function and homology information


isomaltose glucohydrolase / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / cytoplasm
Similarity search - Function
GH15-like domain / Glycosyl hydrolases family 15 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
beta-D-glucopyranose / CITRIC ACID / Isomaltose glucohydrolase
Similarity search - Component
Biological speciesKribbella flavida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.1 Å
AuthorsTanaka, Y. / Chen, M. / Tagami, T. / Yao, M. / Kimura, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Platform for Drug Discovery, Informatics, and Structural Life Science(PDIS) Japan
CitationJournal: Febs J. / Year: 2022
Title: Structural insights reveal the second base catalyst of isomaltose glucohydrolase.
Authors: Tagami, T. / Chen, M. / Furunaga, Y. / Kikuchi, A. / Sadahiro, J. / Lang, W. / Okuyama, M. / Tanaka, Y. / Iwasaki, T. / Yao, M. / Kimura, A.
History
DepositionJan 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 23, 2022Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _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.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase 15-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6196
Polymers43,9701
Non-polymers6495
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-1 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.830, 104.830, 89.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-559-

HOH

21A-695-

HOH

31A-737-

HOH

41A-792-

HOH

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Components

#1: Protein Glycoside hydrolase 15-related protein


Mass: 43970.023 Da / Num. of mol.: 1 / Mutation: E335A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399) (bacteria)
Strain: DSM 17836 / JCM 10339 / NBRC 14399 / Gene: Kfla_1896 / Production host: Escherichia coli (E. coli) / References: UniProt: D2PPM8
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.79 Å3/Da / Density % sol: 55.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium citrate tribasic (pH 6.8), 0.1M Sodium citrate (pH 5.5), 12% PEGmonomethyl ether 2000, 2mM isomaltose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→46.88 Å / Num. obs: 200183 / % possible obs: 99.9 % / Redundancy: 18.8 % / Net I/σ(I): 16.39
Reflection shellResolution: 1.1→1.16 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.1→46.88 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.457 / SU ML: 0.01 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12089 10011 5 %RANDOM
Rwork0.1076 ---
obs0.10827 190172 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.669 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.2 Å2-0 Å2
3----0.39 Å2
Refinement stepCycle: 1 / Resolution: 1.1→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2858 0 43 430 3331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193077
X-RAY DIFFRACTIONr_bond_other_d0.0090.022871
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.9284217
X-RAY DIFFRACTIONr_angle_other_deg0.9283.0016467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4445390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55521.972142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.69315418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.291529
X-RAY DIFFRACTIONr_chiral_restr0.1350.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213583
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02780
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_it5.1141.1791530
X-RAY DIFFRACTIONr_mcbond_other5.0241.1751529
X-RAY DIFFRACTIONr_mcangle_it5.6391.7731927
X-RAY DIFFRACTIONr_mcangle_other5.6691.7771928
X-RAY DIFFRACTIONr_scbond_it4.6881.4321547
X-RAY DIFFRACTIONr_scbond_other4.6841.4281545
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0332.0612289
X-RAY DIFFRACTIONr_long_range_B_refined5.71511.7064169
X-RAY DIFFRACTIONr_long_range_B_other5.71511.7114170
X-RAY DIFFRACTIONr_rigid_bond_restr6.4335948
X-RAY DIFFRACTIONr_sphericity_free23.817584
X-RAY DIFFRACTIONr_sphericity_bonded13.97756200
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.172 728 -
Rwork0.157 13806 -
obs--99.05 %

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