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- PDB-1we5: Crystal Structure of Alpha-Xylosidase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1we5
TitleCrystal Structure of Alpha-Xylosidase from Escherichia coli
ComponentsPutative family 31 glucosidase yicI
KeywordsHYDROLASE / TIM BARREL / Glycoside Hydrolase / GH family 31
Function / homology
Function and homology information


xyloglucan 1,6-alpha-xylosidase activity / alpha-D-xyloside xylohydrolase / alpha-D-xyloside xylohydrolase / carbohydrate binding / carbohydrate metabolic process / identical protein binding
Similarity search - Function
glycosyl hydrolase (family 31) / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...glycosyl hydrolase (family 31) / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Crystal 1 SINGLE WAVELENGTH PROTOCOL, Crysatl 2 MAD PROTOCOL / Resolution: 2.4 Å
AuthorsOse, T. / Kitamura, M. / Okuyama, M. / Mori, H. / Kimura, A. / Watanabe, N. / Yao, M. / Tanaka, I.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Alpha-Xylosidase from Escherichia coli
Authors: Ose, T. / Kitamura, M. / Okuyama, M. / Mori, H. / Kimura, A. / Watanabe, N. / Yao, M. / Tanaka, I.
History
DepositionMay 24, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative family 31 glucosidase yicI
B: Putative family 31 glucosidase yicI
C: Putative family 31 glucosidase yicI
D: Putative family 31 glucosidase yicI
E: Putative family 31 glucosidase yicI
F: Putative family 31 glucosidase yicI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)535,55612
Polymers534,3856
Non-polymers1,1716
Water9,332518
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25860 Å2
ΔGint-72 kcal/mol
Surface area144300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.337, 174.791, 209.629
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a hexamer that is composed of six chains in the asymmetric unit.

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Components

#1: Protein
Putative family 31 glucosidase yicI / alpha-xylosidase


Mass: 89064.172 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YicI / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P31434, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 20000, MES, glycerol, isopropanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44XU10.9
20.9792, 0.9795, 0.9685
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Dec 8, 2003
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97921
30.97951
40.96851
ReflectionResolution: 2.4→50 Å / Num. all: 228852 / Num. obs: 228852 / % possible obs: 99.2 % / Redundancy: 5.2 % / Biso Wilson estimate: 55.5 Å2 / Rsym value: 0.066 / Net I/σ(I): 10
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4.4 % / Num. unique all: 10957 / Rsym value: 0.406 / % possible all: 95.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
SnBphasing
DMphasing
RefinementMethod to determine structure: Crystal 1 SINGLE WAVELENGTH PROTOCOL, Crysatl 2 MAD PROTOCOL
Resolution: 2.4→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 20469 -RANDOM
Rwork0.2055 ---
all-227868 --
obs-227868 99.3 %-
Displacement parametersBiso mean: 49.6565 Å2
Baniso -1Baniso -2Baniso -3
1--1.698 Å20 Å20 Å2
2--15.046 Å20 Å2
3----13.348 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36712 0 72 518 37302
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006653
X-RAY DIFFRACTIONc_angle_deg1.40118
X-RAY DIFFRACTIONc_dihedral_angle_d25.00712
X-RAY DIFFRACTIONc_improper_angle_d0.88446
X-RAY DIFFRACTIONc_mcbond_it1.296
X-RAY DIFFRACTIONc_mcangle_it2.133
X-RAY DIFFRACTIONc_scbond_it2.114
X-RAY DIFFRACTIONc_scangle_it3.029
LS refinement shellResolution: 2.4→2.49 Å
RfactorNum. reflection
Rfree0.3208 2005
Rwork0.2803 -
obs-19897
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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