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- PDB-6nzs: Dextranase AoDex KQ11 -

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Basic information

Entry
Database: PDB / ID: 6nzs
TitleDextranase AoDex KQ11
ComponentsDextranase
KeywordsHYDROLASE / Dextranase from marine Arthrobacter oxydans / Double-displacement mechanism of retaining enzyme / Thermostability
Function / homology
Function and homology information


dextranase / dextranase activity
Similarity search - Function
Dex49a from penicillium minioluteum complex, domain 1 / Dextranase, N-terminal / Glycoside hydrolase, family 49, C-terminal / Glycoside hydrolase, family 49, N-terminal domain / Dextranase, N-terminal / Isopullulanase beta-solenoid repeat / Dextranase, beta solenoid repeat / Glycosyl hydrolase family 49 / Glycosyl hydrolase family 49 N-terminal Ig-like domain / Isopullulanase beta-solenoid repeat ...Dex49a from penicillium minioluteum complex, domain 1 / Dextranase, N-terminal / Glycoside hydrolase, family 49, C-terminal / Glycoside hydrolase, family 49, N-terminal domain / Dextranase, N-terminal / Isopullulanase beta-solenoid repeat / Dextranase, beta solenoid repeat / Glycosyl hydrolase family 49 / Glycosyl hydrolase family 49 N-terminal Ig-like domain / Isopullulanase beta-solenoid repeat / Beta solenoid repeat from Dextranase / Pectin lyase fold / Pectin lyase fold/virulence factor / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPseudarthrobacter oxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsRen, W. / Yan, W. / Gu, L. / Feng, Y. / Dong, D. / Wang, S. / Wang, C. / Lyu, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31471719 China
CitationJournal: To Be Published
Title: Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus
Authors: Ren, W. / Yan, W. / Gu, L. / Feng, Y. / Dong, D. / Wang, S. / Wang, C. / Lyu, M.
History
DepositionFeb 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Dextranase


Theoretical massNumber of molelcules
Total (without water)66,3731
Polymers66,3731
Non-polymers00
Water12,124673
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)214.071, 55.099, 62.188
Angle α, β, γ (deg.)90.000, 92.450, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Dextranase


Mass: 66372.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudarthrobacter oxydans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4V8H044*PLUS, dextranase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 673 / Source method: isolated from a natural source / Formula: H2O

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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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: magnesium chloride, HEPES, PEG

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.39→50 Å / Num. obs: 143197 / % possible obs: 98.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.4
Reflection shellResolution: 1.39→1.41 Å / Rmerge(I) obs: 0.42

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WWG

3wwg


Resolution: 1.4→43.596 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18
RfactorNum. reflection% reflection
Rfree0.1825 6938 4.94 %
Rwork0.1676 --
obs0.1683 140387 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 57.88 Å2 / Biso mean: 16.7457 Å2 / Biso min: 6.83 Å2
Refinement stepCycle: final / Resolution: 1.4→43.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4679 0 0 673 5352
Biso mean---27.86 -
Num. residues----587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054804
X-RAY DIFFRACTIONf_angle_d0.8246545
X-RAY DIFFRACTIONf_chiral_restr0.087690
X-RAY DIFFRACTIONf_plane_restr0.005858
X-RAY DIFFRACTIONf_dihedral_angle_d4.1581704
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.41590.24212310.23464512474399
1.4159-1.43260.24342280.22754430465899
1.4326-1.450.26562200.22184469468999
1.45-1.46840.2362000.21864432463299
1.4684-1.48770.25182170.2134474469199
1.4877-1.50810.25082270.21294406463399
1.5081-1.52960.21672290.20314466469599
1.5296-1.55250.23212080.19394441464999
1.5525-1.57670.21272460.19094323456996
1.5767-1.60260.20562360.18914431466799
1.6026-1.63020.20582420.18124467470999
1.6302-1.65990.22482200.17824457467799
1.6599-1.69180.18972480.17284425467399
1.6918-1.72630.18412440.17454490473499
1.7263-1.76390.2052380.17224396463499
1.7639-1.80490.18572470.17114383463098
1.8049-1.850.18752390.16184388462798
1.85-1.90010.18122440.16054389463397
1.9001-1.9560.17871880.158645304718100
1.956-2.01910.16862260.15094457468399
2.0191-2.09130.17832230.15584469469299
2.0913-2.1750.16562190.15394467468699
2.175-2.2740.16732470.15944405465298
2.274-2.39390.18382560.15974372462896
2.3939-2.54380.19532080.15984472468099
2.5438-2.74020.19222500.16294497474799
2.7402-3.01590.17052570.1594464472199
3.0159-3.45220.13682220.15034429465196
3.4522-4.34870.15162240.14844538476299
4.3487-43.61720.18772540.18294570482498

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