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- PDB-7c24: Glycosidase F290Y at pH8.0 -

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Basic information

Entry
Database: PDB / ID: 7c24
TitleGlycosidase F290Y at pH8.0
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
AMMONIUM ION / Isomaltose glucohydrolase
Similarity search - Component
Biological speciesKribbella flavida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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)44,5397
Polymers44,0601
Non-polymers4796
Water6,287349
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-0 kcal/mol
Surface area13590 Å2
Unit cell
Length a, b, c (Å)104.806, 104.806, 89.819
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-665-

HOH

21A-675-

HOH

31A-729-

HOH

41A-749-

HOH

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Components

#1: Protein Isomaltose glucohydrolase


Mass: 44060.059 Da / Num. of mol.: 1 / Mutation: F290Y
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 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


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


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Ammonium citrate (pH 8.0), 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: 1.71→41.59 Å / Num. obs: 54864 / % possible obs: 99.9 % / Redundancy: 26.1 % / CC1/2: 0.999 / Rrim(I) all: 0.226 / Rsym value: 0.222 / Net I/σ(I): 0.134
Reflection shellResolution: 1.71→1.81 Å / Redundancy: 25.5 % / Mean I/σ(I) obs: 0.0084 / Num. unique obs: 8723 / CC1/2: 0.529 / Rrim(I) all: 4.667 / Rsym value: 4.575 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z3D

5z3d


Resolution: 1.71→41.59 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.562 / SU ML: 0.075 / Cross valid method: FREE R-VALUE / ESU R: 0.082 / ESU R Free: 0.083
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1894 2740 4.994 %
Rwork0.1633 --
all0.165 --
obs-54862 99.893 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.482 Å2
Baniso -1Baniso -2Baniso -3
1-0.489 Å20 Å20 Å2
2--0.489 Å20 Å2
3----0.978 Å2
Refinement stepCycle: LAST / Resolution: 1.71→41.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2865 0 31 349 3245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133026
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172696
X-RAY DIFFRACTIONr_angle_refined_deg1.651.624138
X-RAY DIFFRACTIONr_angle_other_deg1.5481.5786185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9985381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.32620.238168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41215408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0091527
X-RAY DIFFRACTIONr_chiral_restr0.0880.2359
X-RAY DIFFRACTIONr_chiral_restr_other0.1860.21
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023515
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02730
X-RAY DIFFRACTIONr_nbd_refined0.220.2708
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.22602
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21489
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21216
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2271
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3090.29
X-RAY DIFFRACTIONr_nbd_other0.2440.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.224
X-RAY DIFFRACTIONr_mcbond_it2.2642.7071512
X-RAY DIFFRACTIONr_mcbond_other2.2322.7041511
X-RAY DIFFRACTIONr_mcangle_it2.9554.0431897
X-RAY DIFFRACTIONr_mcangle_other2.9624.0471898
X-RAY DIFFRACTIONr_scbond_it3.0462.9941514
X-RAY DIFFRACTIONr_scbond_other3.0472.9951515
X-RAY DIFFRACTIONr_scangle_it4.3034.3882241
X-RAY DIFFRACTIONr_scangle_other4.3024.392242
X-RAY DIFFRACTIONr_lrange_it5.75333.2993729
X-RAY DIFFRACTIONr_lrange_other5.532.5973635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.7510.3491990.3423798X-RAY DIFFRACTION99.5021
1.751-1.7990.321910.33684X-RAY DIFFRACTION99.9226
1.799-1.8510.3011910.2883583X-RAY DIFFRACTION99.9206
1.851-1.9080.2821830.2693525X-RAY DIFFRACTION99.9461
1.908-1.970.2581800.2373394X-RAY DIFFRACTION99.9161
1.97-2.0390.2491750.2173291X-RAY DIFFRACTION99.9712
2.039-2.1160.2281670.1913158X-RAY DIFFRACTION100
2.116-2.2030.2091600.1683073X-RAY DIFFRACTION100
2.203-2.30.1711510.1522958X-RAY DIFFRACTION99.9678
2.3-2.4130.1751530.1452811X-RAY DIFFRACTION99.9663
2.413-2.5430.2051390.1572694X-RAY DIFFRACTION99.8238
2.543-2.6970.1811350.1452553X-RAY DIFFRACTION99.9257
2.697-2.8830.1751250.1422411X-RAY DIFFRACTION100
2.883-3.1140.191190.1442237X-RAY DIFFRACTION100
3.114-3.4110.1921110.1462083X-RAY DIFFRACTION99.9544
3.411-3.8130.159990.1451899X-RAY DIFFRACTION99.9
3.813-4.4010.139880.1221681X-RAY DIFFRACTION99.7744
4.401-5.3870.141770.1181441X-RAY DIFFRACTION99.8684
5.387-7.6050.145610.1421163X-RAY DIFFRACTION100
7.605-41.5880.163360.152687X-RAY DIFFRACTION98.7705

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