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- PDB-2wyn: Structure of family 37 trehalase from Escherichia coli in complex... -

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Basic information

Entry
Database: PDB / ID: 2wyn
TitleStructure of family 37 trehalase from Escherichia coli in complex with a casuarine-6-O-a-D-glucoside analogue
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
alpha-D-glucopyranose / Chem-LG9 / Periplasmic trehalase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGloster, T.M. / Roberts, S.M. / Davies, G.J. / Cardona, F. / Goti, A. / Parmeggiani, C. / Parenti, P. / Fusi, P. / Forcella, M. / Cipolla, L.
CitationJournal: Chem.Commun.(Camb.) / Year: 2010
Title: Casuarine-6-O-alpha-D-glucoside and its analogues are tight binding inhibitors of insect and bacterial trehalases.
Authors: Cardona, F. / Goti, A. / Parmeggiani, C. / Parenti, P. / Forcella, M. / Fusi, P. / Cipolla, L. / Roberts, S.M. / Davies, G.J. / Gloster, T.M.
History
DepositionNov 17, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp / citation ...chem_comp / citation / pdbx_database_status / struct_conn
Item: _chem_comp.type / _citation.journal_id_ISSN ..._chem_comp.type / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Oct 16, 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)246,81845
Polymers242,1064
Non-polymers4,71241
Water27,1671508
1
B: PERIPLASMIC TREHALASE
D: PERIPLASMIC TREHALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,38922
Polymers121,0532
Non-polymers2,33620
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9860 Å2
ΔGint-252.8 kcal/mol
Surface area34300 Å2
MethodPISA
2
A: PERIPLASMIC TREHALASE
C: PERIPLASMIC TREHALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,42923
Polymers121,0532
Non-polymers2,37621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-223.6 kcal/mol
Surface area34420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.349, 117.017, 203.565
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 / 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, 1545 molecules

#2: Chemical
ChemComp-LG9 / (1R,2R,3R,6R,7R,7AR)-3,7-BIS(HYDROXYMETHYL)HEXAHYDRO-1H-PYRROLIZINE-1,2,6-TRIOL / CASUARINE ANALOGUE


Mass: 219.235 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H17NO5
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1508 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsGLUCOSE (GLC): COVALENTLY LINKED TO CASUARINE ANALOGUE HENCE MISSING H ATOM
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: 11MG/ML PROTEIN, 2.0M AMMONIUM SULPHATE, 0.1M CITRATE BUFFER, PH 3.5, 10MM SARCOSINE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 131010 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.9
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JJB

2jjb


Resolution: 2.1→101.53 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.053 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20918 6578 5 %RANDOM
Rwork0.15924 ---
obs0.16173 124186 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.087 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å20 Å2
2---0.13 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.1→101.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16032 0 265 1508 17805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02217041
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.95623341
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.25252093
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94524.713855
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.917152658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3161594
X-RAY DIFFRACTIONr_chiral_restr0.0990.22467
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02113298
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_it0.7221.510214
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.302216503
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.16536827
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2774.56793
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: 2.103→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 495 -
Rwork0.184 8923 -
obs--98.3 %

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