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- PDB-2jjb: Family 37 trehalase from Escherichia coli in complex with casuari... -

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Basic information

Entry
Database: PDB / ID: 2jjb
TitleFamily 37 trehalase from Escherichia coli in complex with casuarine-6- O-alpha-glucopyranose
ComponentsPERIPLASMIC TREHALASE
KeywordsHYDROLASE / GLYCOSIDASE / GLYCOSIDE HYDROLASE
Function / homology
Function and homology information


alpha,alpha-trehalase / alpha,alpha-trehalase activity / trehalose catabolic process / cellular hyperosmotic response / outer membrane-bounded periplasmic space / DNA damage response
Similarity search - Function
Trehalase, periplasmic / Trehalase signature 1. / Glycoside hydrolase, family 37, conserved site / Trehalase signature 2. / Trehalase / Glycoside hydrolase, family 37 / 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. / Trehalase / Glycoside hydrolase, family 37 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
CASUARINE / alpha-D-glucopyranose / Periplasmic trehalase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGloster, T.M. / Roberts, S. / Davies, G.J. / Cardona, F. / Parmeggiani, C. / Bonaccini, C. / Gratteri, P. / Sim, L. / Rose, D.R. / Goti, A.
CitationJournal: Chemistry / Year: 2009
Title: Total Syntheses of Casuarine and its 6-O-Alpha-Glucoside: Complementary Inhibition Towards Glycoside Hydrolases of the Gh31 and Gh37 Families.
Authors: Cardona, F. / Parmeggiani, C. / Faggi, E. / Bonaccini, C. / Gratteri, P. / Sim, L. / Gloster, T.M. / Roberts, S. / Davies, G.J. / Rose, D.R. / Goti, A.
History
DepositionMar 28, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PERIPLASMIC TREHALASE
B: PERIPLASMIC TREHALASE
C: PERIPLASMIC TREHALASE
D: PERIPLASMIC TREHALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,48453
Polymers242,1064
Non-polymers5,37849
Water31,8871770
1
A: PERIPLASMIC TREHALASE
C: PERIPLASMIC TREHALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,15731
Polymers121,0532
Non-polymers3,10429
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9450 Å2
ΔGint-311.4 kcal/mol
Surface area34800 Å2
MethodPISA
2
B: PERIPLASMIC TREHALASE
D: PERIPLASMIC TREHALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,32722
Polymers121,0532
Non-polymers2,27420
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-222.2 kcal/mol
Surface area33730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.481, 117.863, 203.451
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
PERIPLASMIC TREHALASE / ALPHA\ / ALPHA-TREHALASE / ALPHA\ / ALPHA-TREHALOSE GLUCOHYDROLASE


Mass: 60526.531 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P13482, alpha,alpha-trehalase
#3: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 1815 molecules

#2: Chemical
ChemComp-3CU / CASUARINE / (1R,2R,3R,6S,7S,7aR)-3-(hydroxymethyl)hexahydro-1H-pyrrolizine-1,2,6,7-tetrol


Mass: 205.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO5
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1770 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE FIRST 30 RESIDUES CORRESPOND TO A SIGNAL PEPTIDE THAT IS PREDICTED TO HAVE BEEN CLEAVED DURING ...THE FIRST 30 RESIDUES CORRESPOND TO A SIGNAL PEPTIDE THAT IS PREDICTED TO HAVE BEEN CLEAVED DURING EXPRESSION OF THE PROTEIN.

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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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 3.5
Details: 10-12 MG/ML PROTEIN. CRYSTALLISED FROM 1.7M AMMONIUM SULPHATE, 0.1M CITRIC ACID BUFFER, PH 3.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 174266 / % possible obs: 99.6 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.8 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.4.0065refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JF4

2jf4


Resolution: 1.9→19.92 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.327 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 8658 5 %RANDOM
Rwork0.177 ---
obs0.179 165333 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.14 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å20 Å20 Å2
2--0.06 Å20 Å2
3----1.8 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15895 0 302 1770 17967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02217121
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.95923502
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2952145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52324.855865
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94152692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5791593
X-RAY DIFFRACTIONr_chiral_restr0.0950.22498
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113367
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6791.510231
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.197216562
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.85236890
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8234.56861
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.278 611
Rwork0.225 11455

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