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- PDB-5z3k: Crystal structure of glucosidase from Croceicoccus marinus at 1.8... -

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Basic information

Entry
Database: PDB / ID: 5z3k
TitleCrystal structure of glucosidase from Croceicoccus marinus at 1.8 Angstrom resolution
Componentsglucosidase
KeywordsHYDROLASE / glycoside hydrolase / glucosidase / GH39 / Croceicoccus marinus
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
: / Glycosyl hydrolases family 39 / : / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Glycosyl hydrolases family 39 N-terminal catalytic domain-containing protein
Similarity search - Component
Biological speciesCroceicoccus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.802 Å
AuthorsShen, Y.F. / Hu, X.J. / Li, J.X.
CitationJournal: Front Microbiol / Year: 2019
Title: Structural and Functional Insights Into CmGH1, a Novel GH39 Family beta-Glucosidase From Deep-Sea Bacterium.
Authors: Shen, Y. / Li, Z. / Huo, Y.Y. / Bao, L. / Gao, B. / Xiao, P. / Hu, X. / Xu, X.W. / Li, J.
History
DepositionJan 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation / citation_author
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
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glucosidase
B: glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,2815
Polymers108,0042
Non-polymers2763
Water18,5011027
1
A: glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0942
Polymers54,0021
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1863
Polymers54,0021
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.911, 95.911, 100.908
Angle α, β, γ (deg.)90.00, 98.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein glucosidase


Mass: 54002.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Croceicoccus marinus (bacteria) / Gene: A9D14_15590 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1Z1FG87
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 1027 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M Ammonium acetate, 0.1M Bis-Tris pH 5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→48.35 Å / Num. obs: 82629 / % possible obs: 97.3 % / Redundancy: 1.9 % / Net I/σ(I): 15.03
Reflection shellResolution: 1.8→1.86 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data collection
PHENIXphasing
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.802→48.347 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 4123 4.99 %RANDOM
Rwork0.1549 ---
obs0.1568 82629 97.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.802→48.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7461 0 18 1027 8506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067691
X-RAY DIFFRACTIONf_angle_d0.82810475
X-RAY DIFFRACTIONf_dihedral_angle_d3.645347
X-RAY DIFFRACTIONf_chiral_restr0.0571117
X-RAY DIFFRACTIONf_plane_restr0.0061397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8016-1.82280.30481200.24072584X-RAY DIFFRACTION92
1.8228-1.8450.31621410.22622596X-RAY DIFFRACTION96
1.845-1.86840.26251240.21832728X-RAY DIFFRACTION96
1.8684-1.8930.24211270.21452693X-RAY DIFFRACTION97
1.893-1.91890.22981470.20762683X-RAY DIFFRACTION97
1.9189-1.94630.24911420.19852693X-RAY DIFFRACTION97
1.9463-1.97540.23851420.18752647X-RAY DIFFRACTION97
1.9754-2.00620.2421250.17652692X-RAY DIFFRACTION97
2.0062-2.03910.18841530.16522740X-RAY DIFFRACTION97
2.0391-2.07430.21461510.16362648X-RAY DIFFRACTION97
2.0743-2.1120.23021440.16162699X-RAY DIFFRACTION97
2.112-2.15260.20961430.15962711X-RAY DIFFRACTION97
2.1526-2.19660.19931470.15282694X-RAY DIFFRACTION97
2.1966-2.24430.20651640.15052709X-RAY DIFFRACTION97
2.2443-2.29650.22051470.15852674X-RAY DIFFRACTION98
2.2965-2.3540.19781450.15572716X-RAY DIFFRACTION98
2.354-2.41760.1771330.15442717X-RAY DIFFRACTION98
2.4176-2.48880.22831370.15242729X-RAY DIFFRACTION98
2.4888-2.56910.19951460.15132745X-RAY DIFFRACTION98
2.5691-2.66090.19171360.15422717X-RAY DIFFRACTION98
2.6609-2.76740.21281480.15292727X-RAY DIFFRACTION98
2.7674-2.89340.19631390.15962764X-RAY DIFFRACTION98
2.8934-3.04590.19941320.15772768X-RAY DIFFRACTION99
3.0459-3.23670.17861460.1522733X-RAY DIFFRACTION98
3.2367-3.48650.16271340.13772761X-RAY DIFFRACTION98
3.4865-3.83730.17951600.13032715X-RAY DIFFRACTION98
3.8373-4.39220.13631560.11852723X-RAY DIFFRACTION98
4.3922-5.53240.14231450.12812728X-RAY DIFFRACTION97
5.5324-48.36410.19091490.16452772X-RAY DIFFRACTION97

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