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- PDB-5z66: Structure of periplasmic trehalase from Diamondback moth gut bact... -

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Basic information

Entry
Database: PDB / ID: 5z66
TitleStructure of periplasmic trehalase from Diamondback moth gut bacteria complexed with validoxylamine
ComponentsPeriplasmic trehalase
KeywordsHYDROLASE / Trehalase from insect gut bacterium / inhibitor validoxylamine-bound structure
Function / homology
Function and homology information


alpha,alpha-trehalase / trehalose catabolic process / alpha,alpha-trehalase activity / cellular hyperosmotic response / periplasmic space
Similarity search - Function
Trehalase, periplasmic / Trehalase signature 1. / Glycoside hydrolase, family 37, conserved site / Trehalase signature 2. / Glycoside hydrolase, family 37 / Trehalase / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase ...Trehalase, periplasmic / Trehalase signature 1. / Glycoside hydrolase, family 37, conserved site / Trehalase signature 2. / Glycoside hydrolase, family 37 / Trehalase / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Chem-VDM / Periplasmic trehalase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHarne, S.R. / Adhav, A.S. / Joshi, R.S. / Gayathri, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science and Technology, SERB, Government of IndiaECR/2015/000502 India
CitationJournal: Febs J. / Year: 2019
Title: Mechanistic insights into enzymatic catalysis by trehalase from the insect gut endosymbiont Enterobacter cloacae.
Authors: Adhav, A. / Harne, S. / Bhide, A. / Giri, A. / Gayathri, P. / Joshi, R.
History
DepositionJan 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 22, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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: Periplasmic trehalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,36311
Polymers63,1681
Non-polymers1,19610
Water11,205622
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-76 kcal/mol
Surface area19390 Å2
Unit cell
Length a, b, c (Å)122.030, 51.450, 96.400
Angle α, β, γ (deg.)90.00, 106.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1293-

HOH

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Components

#1: Protein Periplasmic trehalase / Alpha / alpha-trehalase / alpha-trehalose glucohydrolase


Mass: 63167.527 Da / Num. of mol.: 1 / Mutation: A553V
Source method: isolated from a genetically manipulated source
Details: cDNA prepared from Larval extract of Diamond black moth gut bacterium, Plutella xylostella
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: treA, SAMEA2273171_02252 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: A0A156C5X3, alpha,alpha-trehalase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-VDM / (1S,2S,3R,6S)-4-(HYDROXYMETHYL)-6-{[(1S,2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-(HYDROXYMETHYL)CYCLOHEXYL]AMINO}CYCLOHEX-4-ENE-1,2,3-TRIOL / VALIDOXYLAMINE


Mass: 335.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H25NO8 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 622 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe authors state that the difference with the sequence database might arise from the natural ...The authors state that the difference with the sequence database might arise from the natural variation in the population or errors in genome sequences.

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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: 2.5 Å3/Da / Density % sol: 50.78 % / Description: Plate-like
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M Ammonium sulphate, 28% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97937 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 1.8→30.5 Å / Num. obs: 53185 / % possible obs: 97.9 % / Redundancy: 3 % / Biso Wilson estimate: 12.3 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.082 / Rrim(I) all: 0.12 / Net I/σ(I): 9.4
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3172 / CC1/2: 0.634 / Rpim(I) all: 0.521 / Rrim(I) all: 0.758 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JG0

2jg0


Resolution: 1.8→30.497 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1936 2698 5.07 %
Rwork0.1628 --
obs0.1643 53176 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→30.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4031 0 69 622 4722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044235
X-RAY DIFFRACTIONf_angle_d0.7295783
X-RAY DIFFRACTIONf_dihedral_angle_d14.172497
X-RAY DIFFRACTIONf_chiral_restr0.043611
X-RAY DIFFRACTIONf_plane_restr0.005746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83270.27231460.25532663X-RAY DIFFRACTION100
1.8327-1.8680.26531360.23452595X-RAY DIFFRACTION100
1.868-1.90610.28731410.22642669X-RAY DIFFRACTION99
1.9061-1.94750.27221710.22042609X-RAY DIFFRACTION99
1.9475-1.99280.2491210.20562656X-RAY DIFFRACTION100
1.9928-2.04270.25171650.19432602X-RAY DIFFRACTION99
2.0427-2.09790.24261240.19392656X-RAY DIFFRACTION100
2.0979-2.15960.23841280.19122645X-RAY DIFFRACTION100
2.1596-2.22930.21091450.17482670X-RAY DIFFRACTION100
2.2293-2.30890.21361460.16592616X-RAY DIFFRACTION99
2.3089-2.40130.1911390.15992639X-RAY DIFFRACTION100
2.4013-2.51060.21331390.16142640X-RAY DIFFRACTION100
2.5106-2.64290.18491380.15612674X-RAY DIFFRACTION100
2.6429-2.80840.17651410.15542662X-RAY DIFFRACTION100
2.8084-3.0250.17191450.1512675X-RAY DIFFRACTION100
3.025-3.32910.17661410.1462659X-RAY DIFFRACTION100
3.3291-3.810.14491270.12942692X-RAY DIFFRACTION100
3.81-4.79720.13641500.11972705X-RAY DIFFRACTION100
4.7972-30.50150.17221550.15912751X-RAY DIFFRACTION99

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