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- PDB-2bhu: Crystal structure of Deinococcus radiodurans maltooligosyltrehalo... -

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Basic information

Entry
Database: PDB / ID: 2bhu
TitleCrystal structure of Deinococcus radiodurans maltooligosyltrehalose trehalohydrolase
ComponentsMALTOOLIGOSYLTREHALOSE TREHALOHYDROLASE
KeywordsHYDROLASE / TREHALOSE / ALPHA-AMYLASE / PROTEIN-CARBOHYDRATE COMPLEX / DESICCATION RESISTANCE
Function / homology
Function and homology information


4-alpha-D-{(1->4)-alpha-D-glucano}trehalose trehalohydrolase / 4-alpha-D-(1->4)-alpha-D-glucanotrehalose trehalohydrolase activity / trehalose biosynthetic process / cytoplasm
Similarity search - Function
Malto-oligosyltrehalose trehalohydrolase, E-set domain superfamily / Malto-oligosyltrehalose trehalohydrolase / Glycosyl hydrolase, C-terminal (DUF3459) / Domain of unknown function (DUF3459) / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II ...Malto-oligosyltrehalose trehalohydrolase, E-set domain superfamily / Malto-oligosyltrehalose trehalohydrolase / Glycosyl hydrolase, C-terminal (DUF3459) / Domain of unknown function (DUF3459) / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Malto-oligosyltrehalose trehalohydrolase
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.1 Å
AuthorsTimmins, J. / Leiros, H.-K.S. / Leonard, G. / Leiros, I. / McSweeney, S.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structure of Maltooligosyltrehalose Trehalohydrolase from Deinococcus Radiodurans in Complex with Disaccharides
Authors: Timmins, J. / Leiros, H.-K.S. / Leonard, G. / Leiros, I. / Mcsweeney, S.
History
DepositionJan 18, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MALTOOLIGOSYLTREHALOSE TREHALOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4984
Polymers67,2021
Non-polymers2973
Water20,3571130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.580, 66.620, 152.510
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 MALTOOLIGOSYLTREHALOSE TREHALOHYDROLASE


Mass: 67201.711 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Strain: R1 / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RX51, alpha-amylase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1130 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A INSERTION MUTATION BETWEEN RESIDUES 430 AND 431 IN THE UNIPROT ENTRY. RESIDUES THR431 AND ...CHAIN A INSERTION MUTATION BETWEEN RESIDUES 430 AND 431 IN THE UNIPROT ENTRY. RESIDUES THR431 AND LEU432 INSERTED AT THIS POSITION.

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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: 1.75 Å3/Da / Density % sol: 29.22 %
Crystal growpH: 8.5
Details: 20% PEG 2000 MME, 0.1 M TRIS-HCL PH8.5, 0.1 M MGCL2, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.005
DetectorDate: Jul 30, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 1.1→46.93 Å / Num. obs: 216600 / % possible obs: 88.3 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.1
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.3 / % possible all: 82.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
XDSdata reduction
XDSdata scaling
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.1→44.41 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.99 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. WARNING: THIS ENTRY CONTAINS ATOMS THAT HAVE BEEN REFINED WITH AN OCCUPANCY OF 0.00.
RfactorNum. reflection% reflectionSelection details
Rfree0.159 10891 5 %RANDOM
Rwork0.128 ---
obs0.129 205610 88.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2---0.39 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.1→44.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4601 0 19 1130 5750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0215187
X-RAY DIFFRACTIONr_bond_other_d0.0020.024551
X-RAY DIFFRACTIONr_angle_refined_deg1.7971.9297122
X-RAY DIFFRACTIONr_angle_other_deg0.951310547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9745672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7922.984258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.58815770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.391547
X-RAY DIFFRACTIONr_chiral_restr0.1260.2735
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026135
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021171
X-RAY DIFFRACTIONr_nbd_refined0.2650.21126
X-RAY DIFFRACTIONr_nbd_other0.2060.25146
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22582
X-RAY DIFFRACTIONr_nbtor_other0.0870.23006
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2842
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined1.0750.241
X-RAY DIFFRACTIONr_symmetry_vdw_other0.5670.2175
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.2104
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9411.54039
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.35325127
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.11632357
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9334.51995
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: 1.1→1.13 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.279 707
Rwork0.258 13628

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