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- PDB-5z3a: Glycosidase Wild Type -

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Basic information

Entry
Database: PDB / ID: 5z3a
TitleGlycosidase Wild Type
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
CITRIC ACID / Isomaltose glucohydrolase
Similarity search - Component
Biological speciesKribbella flavida DSM 17836 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.401 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 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._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 1.2May 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)44,5896
Polymers44,0281
Non-polymers5615
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-2 kcal/mol
Surface area13610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.743, 104.743, 89.486
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-602-

HOH

21A-706-

HOH

31A-732-

HOH

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Components

#1: Protein Glycoside hydrolase 15-related protein


Mass: 44028.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kribbella flavida DSM 17836 (bacteria) / Strain: DSM 17836 / JCM 10339 / NBRC 14399 / Gene: Kfla_1896 / Production host: Escherichia coli (E. coli) / References: UniProt: D2PPM8
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


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


Mass: 18.015 Da / Num. of mol.: 340 / 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: 55.87 %
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% PEG monomethyl ether 2000, 2mM glucose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→89.49 Å / Num. obs: 97738 / % possible obs: 99.9 % / Redundancy: 14.4 % / Net I/σ(I): 26.69
Reflection shellResolution: 1.4→1.48 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.401→46.842 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 11.67
RfactorNum. reflection% reflectionSelection details
Rfree0.1397 4886 5 %RANDOM
Rwork0.1158 ---
obs0.1171 97723 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.401→46.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2862 0 37 340 3239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013077
X-RAY DIFFRACTIONf_angle_d1.2884210
X-RAY DIFFRACTIONf_dihedral_angle_d12.8721057
X-RAY DIFFRACTIONf_chiral_restr0.073437
X-RAY DIFFRACTIONf_plane_restr0.008552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4007-1.41670.20091560.18773013X-RAY DIFFRACTION99
1.4167-1.43330.19971650.15913043X-RAY DIFFRACTION100
1.4333-1.45080.18771550.14073070X-RAY DIFFRACTION100
1.4508-1.46920.17091610.13293037X-RAY DIFFRACTION100
1.4692-1.48850.15821630.12463055X-RAY DIFFRACTION100
1.4885-1.50890.15511620.11483071X-RAY DIFFRACTION100
1.5089-1.53050.13881620.1093059X-RAY DIFFRACTION100
1.5305-1.55330.15961600.1053043X-RAY DIFFRACTION100
1.5533-1.57760.1281610.09893076X-RAY DIFFRACTION100
1.5776-1.60340.14621620.09723073X-RAY DIFFRACTION100
1.6034-1.63110.1391620.09523051X-RAY DIFFRACTION100
1.6311-1.66080.13991610.09253079X-RAY DIFFRACTION100
1.6608-1.69270.11911620.09083062X-RAY DIFFRACTION100
1.6927-1.72730.10351600.0863070X-RAY DIFFRACTION100
1.7273-1.76480.12441630.08763093X-RAY DIFFRACTION100
1.7648-1.80590.11071620.08893065X-RAY DIFFRACTION100
1.8059-1.8510.13151590.09493066X-RAY DIFFRACTION100
1.851-1.90110.11561650.09213107X-RAY DIFFRACTION100
1.9011-1.9570.11581610.09773058X-RAY DIFFRACTION100
1.957-2.02020.12471640.09633115X-RAY DIFFRACTION100
2.0202-2.09240.12361630.09983089X-RAY DIFFRACTION100
2.0924-2.17620.11591610.09883096X-RAY DIFFRACTION100
2.1762-2.27520.12691650.10063102X-RAY DIFFRACTION100
2.2752-2.39520.11251640.1023116X-RAY DIFFRACTION100
2.3952-2.54520.15041640.11173120X-RAY DIFFRACTION100
2.5452-2.74170.13561640.11243134X-RAY DIFFRACTION100
2.7417-3.01760.15491670.12673144X-RAY DIFFRACTION100
3.0176-3.45410.13611660.13613179X-RAY DIFFRACTION100
3.4541-4.35130.14891680.1243196X-RAY DIFFRACTION100
4.3513-46.86870.16321780.14463355X-RAY DIFFRACTION99

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