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- PDB-5z3c: Glycosidase E178A -

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Basic information

Entry
Database: PDB / ID: 5z3c
TitleGlycosidase E178A
ComponentsGlycoside hydrolase 15-related protein
KeywordsHYDROLASE / Glycosidase
Function / homologyisomaltose glucohydrolase / GH15-like domain / Glycosyl hydrolases family 15 / hydrolase activity, acting on glycosyl bonds / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / polysaccharide catabolic process / cytoplasm / Isomaltose glucohydrolase
Function and homology information
Biological speciesKribbella flavida DSM 17836 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,4306
Polymers43,9701
Non-polymers4605
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-1 kcal/mol
Surface area13640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.917, 104.917, 89.499
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-576-

HOH

21A-595-

HOH

31A-704-

HOH

41A-766-

HOH

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Components

#1: Protein Glycoside hydrolase 15-related protein


Mass: 43970.023 Da / Num. of mol.: 1 / Mutation: E178A
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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.8 Å3/Da / Density % sol: 56.08 %
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: 1.6→45.26 Å / Num. obs: 66196 / % possible obs: 99.9 % / Redundancy: 21.7 % / Net I/σ(I): 38.12
Reflection shellResolution: 1.6→1.69 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.6→45.257 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.91
RfactorNum. reflection% reflection
Rfree0.1571 3310 5 %
Rwork0.1338 --
obs0.135 66192 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→45.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2858 0 30 339 3227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133025
X-RAY DIFFRACTIONf_angle_d1.4254134
X-RAY DIFFRACTIONf_dihedral_angle_d12.561032
X-RAY DIFFRACTIONf_chiral_restr0.058432
X-RAY DIFFRACTIONf_plane_restr0.009537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6003-1.62310.22321340.16042540X-RAY DIFFRACTION98
1.6231-1.64740.18511370.14562581X-RAY DIFFRACTION100
1.6474-1.67310.16881350.14412576X-RAY DIFFRACTION100
1.6731-1.70050.16221380.1412592X-RAY DIFFRACTION100
1.7005-1.72990.15021330.13432575X-RAY DIFFRACTION100
1.7299-1.76130.15661360.1362589X-RAY DIFFRACTION100
1.7613-1.79520.17021370.13272588X-RAY DIFFRACTION100
1.7952-1.83180.16741380.13932602X-RAY DIFFRACTION100
1.8318-1.87170.17361360.13892586X-RAY DIFFRACTION100
1.8717-1.91520.19681360.14032601X-RAY DIFFRACTION100
1.9152-1.96310.14881360.14022577X-RAY DIFFRACTION100
1.9631-2.01620.17231380.12892609X-RAY DIFFRACTION100
2.0162-2.07550.16071360.13012593X-RAY DIFFRACTION100
2.0755-2.14250.131360.12762602X-RAY DIFFRACTION100
2.1425-2.21910.13861380.12182620X-RAY DIFFRACTION100
2.2191-2.30790.12651380.12092616X-RAY DIFFRACTION100
2.3079-2.4130.14631380.12032610X-RAY DIFFRACTION100
2.413-2.54020.17251380.12612623X-RAY DIFFRACTION100
2.5402-2.69930.13971400.12662664X-RAY DIFFRACTION100
2.6993-2.90770.17131380.1312627X-RAY DIFFRACTION100
2.9077-3.20020.15341390.13982653X-RAY DIFFRACTION100
3.2002-3.66310.17161420.14652675X-RAY DIFFRACTION100
3.6631-4.61440.13791420.12642716X-RAY DIFFRACTION100
4.6144-45.27530.16471510.14352867X-RAY DIFFRACTION100

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