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- PDB-5h9x: Crystal structure of GH family 64 laminaripentaose-producing beta... -

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Basic information

Entry
Database: PDB / ID: 5h9x
TitleCrystal structure of GH family 64 laminaripentaose-producing beta-1,3-glucanase from Paenibacillus barengoltzii
Componentsbeta-1,3-glucanase
KeywordsHYDROLASE / beta-1 / 3-glucan recognition / glycoside hydrolase family 64 / 3-glucanase / GH64-TLP-SF superfamily
Function / homology
Function and homology information


glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity
Similarity search - Function
Glycosyl hydrolases family 64 (GH64) domain profile. / Beta-1,3-glucanase, N-terminal / Glucan endo-1,3-beta-glucosidase / Beta-1,3-glucanase / : / CBM56 (carbohydrate binding type-56) domain profile. / Osmotin/thaumatin-like superfamily
Similarity search - Domain/homology
Biological speciesPaenibacillus barengoltzii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å
AuthorsZhen, Q. / Yan, Q. / Yang, S. / Jiang, Z. / You, X.
CitationJournal: Chem. Commun. (Camb.) / Year: 2017
Title: The recognition mechanism of triple-helical beta-1,3-glucan by a beta-1,3-glucanase
Authors: Qin, Z. / Yang, D. / You, X. / Liu, Y. / Hu, S. / Yan, Q. / Yang, S. / Jiang, Z.
History
DepositionDec 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
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 / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: beta-1,3-glucanase


Theoretical massNumber of molelcules
Total (without water)49,0761
Polymers49,0761
Non-polymers00
Water6,251347
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18280 Å2
Unit cell
Length a, b, c (Å)134.108, 65.810, 61.628
Angle α, β, γ (deg.)90.00, 105.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein beta-1,3-glucanase


Mass: 49075.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus barengoltzii / Strain: CAU904
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1S4NYE1*PLUS, glucan endo-1,3-beta-D-glucosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS KU363233 FOR THIS SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Optimized crystals suitable for diffraction were grown in drops containing 2 microliter of protein solution and 0.5 microliter of reservoir solution (1.2M di-Ammonium Tartrate pH 7.0) at 293 ...Details: Optimized crystals suitable for diffraction were grown in drops containing 2 microliter of protein solution and 0.5 microliter of reservoir solution (1.2M di-Ammonium Tartrate pH 7.0) at 293 K. The crystals were observed 10 days later.
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.91→32.32 Å / Num. obs: 36956 / % possible obs: 91.16 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.095 / Rsym value: 0.052 / Net I/σ(I): 13.72
Reflection shellResolution: 1.91→1.97 Å / % possible all: 89.91

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.91→32.317 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2166 1999 5.42 %
Rwork0.1936 --
obs0.1948 36902 91.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.91→32.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 0 347 3583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073329
X-RAY DIFFRACTIONf_angle_d1.1994544
X-RAY DIFFRACTIONf_dihedral_angle_d13.0321160
X-RAY DIFFRACTIONf_chiral_restr0.082477
X-RAY DIFFRACTIONf_plane_restr0.005601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9059-1.95350.52521370.51632380X-RAY DIFFRACTION87
1.9535-2.00630.30021510.27462652X-RAY DIFFRACTION97
2.0063-2.06540.24911530.21982683X-RAY DIFFRACTION98
2.0654-2.1320.22031530.20762670X-RAY DIFFRACTION98
2.132-2.20820.23051510.20532647X-RAY DIFFRACTION98
2.2082-2.29660.3891730.3381237X-RAY DIFFRACTION45
2.2966-2.40110.23661510.20872657X-RAY DIFFRACTION98
2.4011-2.52760.23661550.19922689X-RAY DIFFRACTION99
2.5276-2.68590.23931550.1932730X-RAY DIFFRACTION99
2.6859-2.89320.20421560.19332705X-RAY DIFFRACTION99
2.8932-3.18410.19331550.18642705X-RAY DIFFRACTION99
3.1841-3.64430.19661350.16682381X-RAY DIFFRACTION95
3.6443-4.58930.16771130.13761964X-RAY DIFFRACTION85
4.5893-32.32130.15461610.14622803X-RAY DIFFRACTION99

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