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- PDB-7c26: Glycosidase Wild Type at pH4.5 -

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Basic information

Entry
Database: PDB / ID: 7c26
TitleGlycosidase Wild Type at pH4.5
ComponentsIsomaltose glucohydrolase
KeywordsHYDROLASE / Glycoside hydrolase
Function / homology
Function and homology information


isomaltose glucohydrolase / hydrolase activity, acting on glycosyl bonds / polysaccharide catabolic process / 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 / AMMONIUM ION / Isomaltose glucohydrolase
Similarity search - Component
Biological speciesKribbella flavida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.803 Å
AuthorsTagami, T. / Kikuchi, A. / Okuyama, M. / Kimura, A.
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
DepositionMay 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 12, 2021Provider: 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 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isomaltose glucohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6316
Polymers44,0441
Non-polymers5865
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint1 kcal/mol
Surface area13820 Å2
Unit cell
Length a, b, c (Å)105.345, 105.345, 90.328
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-677-

HOH

21A-678-

HOH

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Components

#1: Protein Isomaltose glucohydrolase


Mass: 44044.059 Da / Num. of mol.: 1
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 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: D2PPM8, isomaltose glucohydrolase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.84 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M Ammonium citrate (pH 7.0), 8% PEG monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→47.16 Å / Num. obs: 41276 / % possible obs: 87.1 % / Redundancy: 25.8 % / CC1/2: 0.999 / Rrim(I) all: 0.082 / Rsym value: 0.08 / Net I/σ(I): 0.286
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 26.4 % / Mean I/σ(I) obs: 0.023 / Num. unique obs: 6071 / CC1/2: 0.906 / Rrim(I) all: 1.617 / Rsym value: 1.586 / % possible all: 80.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z3A

5z3a


Resolution: 1.803→47.156 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.572 / SU ML: 0.076 / Cross valid method: FREE R-VALUE / ESU R: 0.116 / ESU R Free: 0.112
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2061 2053 4.974 %
Rwork0.1758 --
all0.177 --
obs-41275 87.078 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.327 Å2
Baniso -1Baniso -2Baniso -3
1--0.334 Å20 Å2-0 Å2
2---0.334 Å2-0 Å2
3---0.667 Å2
Refinement stepCycle: LAST / Resolution: 1.803→47.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2857 0 39 222 3118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133015
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172670
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.6194127
X-RAY DIFFRACTIONr_angle_other_deg1.531.5776121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0225378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.24620.18167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19615405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0311527
X-RAY DIFFRACTIONr_chiral_restr0.090.2357
X-RAY DIFFRACTIONr_chiral_restr_other0.2760.21
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023512
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02729
X-RAY DIFFRACTIONr_nbd_refined0.2270.2672
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.22546
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21485
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21235
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2181
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1610.27
X-RAY DIFFRACTIONr_nbd_other0.1880.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1170.217
X-RAY DIFFRACTIONr_mcbond_it2.643.0781503
X-RAY DIFFRACTIONr_mcbond_other2.6323.0751502
X-RAY DIFFRACTIONr_mcangle_it3.294.5981884
X-RAY DIFFRACTIONr_mcangle_other3.294.6011885
X-RAY DIFFRACTIONr_scbond_it3.3843.3891512
X-RAY DIFFRACTIONr_scbond_other3.3553.3831509
X-RAY DIFFRACTIONr_scangle_it4.6324.9832243
X-RAY DIFFRACTIONr_scangle_other4.6314.9852244
X-RAY DIFFRACTIONr_lrange_it5.63836.5723579
X-RAY DIFFRACTIONr_lrange_other5.61536.3663533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.803-1.850.311620.2423237X-RAY DIFFRACTION98.5217
1.85-1.9010.3731340.2842537X-RAY DIFFRACTION79.5888
1.901-1.9560.29110.348146X-RAY DIFFRACTION4.7998
1.956-2.0160.2541590.2332990X-RAY DIFFRACTION98.9008
2.016-2.0820.2631520.2132892X-RAY DIFFRACTION99.4446
2.082-2.1550.2521440.2022851X-RAY DIFFRACTION99.5347
2.155-2.2360.2761180.2282267X-RAY DIFFRACTION82.5259
2.236-2.3280.266620.2371136X-RAY DIFFRACTION43.1556
2.328-2.4310.2061320.1892516X-RAY DIFFRACTION98.7691
2.431-2.550.2341240.1722410X-RAY DIFFRACTION99.2947
2.55-2.6870.1811210.1582317X-RAY DIFFRACTION99.2671
2.687-2.850.2121140.162192X-RAY DIFFRACTION99.3966
2.85-3.0470.1791080.1652057X-RAY DIFFRACTION99.5402
3.047-3.2910.2311040.1731944X-RAY DIFFRACTION99.4658
3.291-3.6040.233940.1871785X-RAY DIFFRACTION99.576
3.604-4.0290.179860.1731639X-RAY DIFFRACTION99.8842
4.029-4.6510.144780.1331453X-RAY DIFFRACTION99.9347
4.651-5.6920.188650.1531254X-RAY DIFFRACTION100
5.692-8.0340.149530.1451000X-RAY DIFFRACTION100
8.034-47.1560.196320.182599X-RAY DIFFRACTION98.2866

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