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- PDB-7c25: Glycosidase Wild Type at pH8.0 -

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Basic information

Entry
Database: PDB / ID: 7c25
TitleGlycosidase Wild Type at pH8.0
ComponentsIsomaltose glucohydrolase
KeywordsHYDROLASE / Glycoside hydrolase
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 / AMMONIUM ION / Isomaltose glucohydrolase
Similarity search - Component
Biological speciesKribbella flavida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.505 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)44,6237
Polymers44,0441
Non-polymers5796
Water7,476415
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-1 kcal/mol
Surface area13750 Å2
Unit cell
Length a, b, c (Å)105.462, 105.462, 89.952
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-568-

HOH

21A-688-

HOH

31A-760-

HOH

41A-777-

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.: 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: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H4N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Ammonium citrate (pH8.0), 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: 1.5→47.21 Å / Num. obs: 74640 / % possible obs: 92.6 % / Redundancy: 26.1 % / CC1/2: 1 / Rrim(I) all: 0.077 / Rsym value: 0.076 / Net I/σ(I): 0.265
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 24.2 % / Mean I/σ(I) obs: 0.028 / Num. unique obs: 12800 / CC1/2: 0.855 / Rrim(I) all: 1.357 / Rsym value: 1.329 / % 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: 5Z3A

5z3a


Resolution: 1.505→47.209 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.158 / WRfactor Rwork: 0.127 / SU B: 2.069 / SU ML: 0.038 / Average fsc free: 0.9498 / Average fsc work: 0.9594 / Cross valid method: FREE R-VALUE / ESU R: 0.06 / ESU R Free: 0.059
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1726 3721 4.985 %
Rwork0.1362 70919 -
all0.138 --
obs-74640 92.577 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.889 Å2
Baniso -1Baniso -2Baniso -3
1--0.171 Å2-0 Å2-0 Å2
2---0.171 Å2-0 Å2
3---0.341 Å2
Refinement stepCycle: LAST / Resolution: 1.505→47.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2864 0 38 415 3317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0133061
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172722
X-RAY DIFFRACTIONr_angle_refined_deg1.9471.6214190
X-RAY DIFFRACTIONr_angle_other_deg1.7441.5786247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6955387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.03520.118170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.56415414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7781528
X-RAY DIFFRACTIONr_chiral_restr0.1250.2362
X-RAY DIFFRACTIONr_chiral_restr_other0.5560.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023574
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02742
X-RAY DIFFRACTIONr_nbd_refined0.2280.2760
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.22666
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21538
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21327
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2289
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3680.29
X-RAY DIFFRACTIONr_nbd_other0.240.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.180.217
X-RAY DIFFRACTIONr_mcbond_it2.7172.1821527
X-RAY DIFFRACTIONr_mcbond_other2.7042.1791526
X-RAY DIFFRACTIONr_mcangle_it2.8973.2791921
X-RAY DIFFRACTIONr_mcangle_other2.8973.2831922
X-RAY DIFFRACTIONr_scbond_it3.682.4621533
X-RAY DIFFRACTIONr_scbond_other3.682.4581530
X-RAY DIFFRACTIONr_scangle_it4.0863.6132268
X-RAY DIFFRACTIONr_scangle_other4.0853.6152269
X-RAY DIFFRACTIONr_lrange_it4.0444617.1513859
X-RAY DIFFRACTIONr_lrange_other3.7534760.9343741
X-RAY DIFFRACTIONr_rigid_bond_restr4.21235782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.505-1.5440.2482930.2165534X-RAY DIFFRACTION99.3182
1.544-1.5860.2222860.1755439X-RAY DIFFRACTION99.9825
1.586-1.6320.2082810.1555298X-RAY DIFFRACTION99.8747
1.632-1.6830.1842680.145154X-RAY DIFFRACTION99.8343
1.683-1.7380.1842640.1334982X-RAY DIFFRACTION99.8667
1.738-1.7990.1942540.1264838X-RAY DIFFRACTION99.6673
1.799-1.8670.2072380.1484630X-RAY DIFFRACTION99.1648
1.867-1.9430.307850.2031681X-RAY DIFFRACTION37.3757
1.943-2.0290.1971910.1493633X-RAY DIFFRACTION83.3479
2.029-2.1280.172160.1274125X-RAY DIFFRACTION99.7014
2.128-2.2430.2081780.1463386X-RAY DIFFRACTION85.6937
2.243-2.3790.1551230.1272368X-RAY DIFFRACTION63.1112
2.379-2.5430.1561820.1133505X-RAY DIFFRACTION99.3801
2.543-2.7470.1471740.1093287X-RAY DIFFRACTION99.6832
2.747-3.0090.1641610.1223063X-RAY DIFFRACTION99.8452
3.009-3.3630.1721440.1342758X-RAY DIFFRACTION99.5882
3.363-3.8830.1681300.1522459X-RAY DIFFRACTION99.7304
3.883-4.7530.1351120.1142113X-RAY DIFFRACTION99.7758
4.753-6.7130.157880.141673X-RAY DIFFRACTION99.9432
6.713-47.2090.185530.159993X-RAY DIFFRACTION98.9593

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