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- PDB-2jf4: Family 37 trehalase from Escherichia coli in complex with validox... -

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Basic information

Entry
Database: PDB / ID: 2jf4
TitleFamily 37 trehalase from Escherichia coli in complex with validoxylamine
ComponentsPERIPLASMIC TREHALASE
KeywordsHYDROLASE / FAMILY 37 / INHIBITOR / TREHALASE / GLYCOSIDE HYDROLASE / PERIPLASMIC / GLYCOSIDASE / VALIDOXYLAMINE
Function / homology
Function and homology information


alpha,alpha-trehalase / trehalose catabolic process / alpha,alpha-trehalase activity / 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. / 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 speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsGibson, R.P. / Gloster, T.M. / Roberts, S. / Warren, R.A.J. / Storch De Gracia, I. / Garcia, A. / Chiara, J.L. / Davies, G.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2007
Title: Molecular Basis for Trehalase Inhibition Revealed by the Structure of Trehalase in Complex with Potent Inhibitors.
Authors: Gibson, R.P. / Gloster, T.M. / Roberts, S. / Warren, R.A.J. / Storch De Gracia, I. / Garcia, A. / Chiara, J.L. / Davies, G.J.
History
DepositionJan 25, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PERIPLASMIC TREHALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5182
Polymers61,1831
Non-polymers3351
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.399, 102.696, 103.174
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 61183.055 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-565
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P13482, alpha,alpha-trehalase
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 30 RESIDUES CORRESPOND TO A SIGNAL PEPTIDE THAT IS PREDICTED TO HAVE CLEAVED DURING ...THE FIRST 30 RESIDUES CORRESPOND TO A SIGNAL PEPTIDE THAT IS PREDICTED TO HAVE 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: 2.2 Å3/Da / Density % sol: 43.2 %
Crystal growpH: 6.5
Details: 15 MG/ML PROTEIN. 25% PEG3350 AND 0.1 M BIS-TRIS HCL, PH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97931
DetectorType: ADSC CCD / Detector: CCD / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) OR SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 27378 / % possible obs: 99.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→28.57 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.672 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NO ELECTRON DENSITY CAN BE OBSERVED FOR THE CHAIN BETWEEN 101 AND 113.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1384 5.1 %RANDOM
Rwork0.163 ---
obs0.166 25985 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20 Å2
2--1.29 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3979 0 23 296 4298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224161
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9465682
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.085512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10224.623212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72415657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5171525
X-RAY DIFFRACTIONr_chiral_restr0.0880.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023273
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.21892
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22841
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2258
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.219
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1441.52590
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.29724050
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.13431846
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.134.51625
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: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.254 98
Rwork0.173 1891

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