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- PDB-3mi6: Crystal structure of the alpha-galactosidase from Lactobacillus b... -

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Basic information

Entry
Database: PDB / ID: 3mi6
TitleCrystal structure of the alpha-galactosidase from Lactobacillus brevis, Northeast Structural Genomics Consortium Target LbR11.
ComponentsAlpha-galactosidase
KeywordsHYDROLASE / NESG / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


raffinose alpha-galactosidase activity / alpha-galactosidase / carbohydrate catabolic process
Similarity search - Function
alpha-galactosidase from lactobacil brevis / Glycosyl hydrolase family 36, N-terminal / Glycosyl hydrolase family 36, C-terminal / Alpha-galactosidase, N-terminal domain superfamily / Glycosyl hydrolase family 36 C-terminal domain / Glycosyl hydrolase family 36 N-terminal domain / Glycoside hydrolase family 36 / Melibiase / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. ...alpha-galactosidase from lactobacil brevis / Glycosyl hydrolase family 36, N-terminal / Glycosyl hydrolase family 36, C-terminal / Alpha-galactosidase, N-terminal domain superfamily / Glycosyl hydrolase family 36 C-terminal domain / Glycosyl hydrolase family 36 N-terminal domain / Glycoside hydrolase family 36 / Melibiase / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / Beta-galactosidase; Chain A, domain 5 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Distorted Sandwich / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesLactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.704 Å
AuthorsVorobiev, S. / Chen, Y. / Seetharaman, J. / Belote, R. / Sahdev, S. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. ...Vorobiev, S. / Chen, Y. / Seetharaman, J. / Belote, R. / Sahdev, S. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the alpha-galactosidase from Lactobacillus brevis.
Authors: Vorobiev, S. / Chen, Y. / Seetharaman, J. / Belote, R. / Sahdev, S. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionApr 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-galactosidase
B: Alpha-galactosidase
C: Alpha-galactosidase
D: Alpha-galactosidase


Theoretical massNumber of molelcules
Total (without water)347,0434
Polymers347,0434
Non-polymers00
Water8,989499
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24350 Å2
ΔGint-58 kcal/mol
Surface area87940 Å2
MethodPISA
2
A: Alpha-galactosidase
D: Alpha-galactosidase


Theoretical massNumber of molelcules
Total (without water)173,5222
Polymers173,5222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-16 kcal/mol
Surface area50830 Å2
MethodPISA
3
B: Alpha-galactosidase
C: Alpha-galactosidase


Theoretical massNumber of molelcules
Total (without water)173,5222
Polymers173,5222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-15 kcal/mol
Surface area49430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.938, 158.818, 166.017
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsDimer according to aggregation screening

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Components

#1: Protein
Alpha-galactosidase /


Mass: 86760.812 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis (bacteria) / Strain: ATCC 367 / JCM 1170 / Gene: LVIS_1758 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) +Magic / References: UniProt: Q03PP7, alpha-galactosidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 291 K / Method: microbatch under paraffin oil / pH: 7
Details: 10% PEG MME 5000, 5% Tacsimate, pH 7.0, 0.01M galactose, 0.1M HEPES pH 7.0, microbatch under paraffin oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97908, 0.97939, 0.91837
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 30, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979081
20.979391
30.918371
ReflectionResolution: 2.7→50 Å / Num. all: 161934 / Num. obs: 161448 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 22.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 4.8 / Num. unique all: 16165 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXDEphasing
PHENIX(phenix.refine: 1.5_2)refinement
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.704→40.028 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2409 4195 4.99 %RANDOM
Rwork0.1728 ---
obs0.1762 84039 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.111 Å2 / ksol: 0.329 e/Å3
Refinement stepCycle: LAST / Resolution: 2.704→40.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23918 0 0 499 24417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00924581
X-RAY DIFFRACTIONf_angle_d1.24133410
X-RAY DIFFRACTIONf_dihedral_angle_d20.2028776
X-RAY DIFFRACTIONf_chiral_restr0.0813500
X-RAY DIFFRACTIONf_plane_restr0.0054427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7039-2.73460.32211340.22182582X-RAY DIFFRACTION98
2.7346-2.76680.3291610.2182625X-RAY DIFFRACTION99
2.7668-2.80050.31051530.22932554X-RAY DIFFRACTION99
2.8005-2.83590.31821450.22492632X-RAY DIFFRACTION99
2.8359-2.87320.32841300.21542616X-RAY DIFFRACTION99
2.8732-2.91260.26151280.20882630X-RAY DIFFRACTION99
2.9126-2.95420.32111140.20932646X-RAY DIFFRACTION100
2.9542-2.99830.34491240.21352648X-RAY DIFFRACTION100
2.9983-3.04510.27971460.21012631X-RAY DIFFRACTION99
3.0451-3.0950.27721300.20422645X-RAY DIFFRACTION100
3.095-3.14840.29451360.20952632X-RAY DIFFRACTION99
3.1484-3.20560.27171380.20692650X-RAY DIFFRACTION99
3.2056-3.26720.28391450.19222635X-RAY DIFFRACTION100
3.2672-3.33390.26541420.1872638X-RAY DIFFRACTION100
3.3339-3.40630.24481230.17382649X-RAY DIFFRACTION100
3.4063-3.48550.25251420.15672648X-RAY DIFFRACTION100
3.4855-3.57260.22421410.15272651X-RAY DIFFRACTION100
3.5726-3.66920.20331470.15742641X-RAY DIFFRACTION100
3.6692-3.7770.24571160.14562713X-RAY DIFFRACTION100
3.777-3.89890.211450.14862658X-RAY DIFFRACTION100
3.8989-4.03810.18931410.14092661X-RAY DIFFRACTION100
4.0381-4.19960.21271350.142660X-RAY DIFFRACTION100
4.1996-4.39050.19461620.13052672X-RAY DIFFRACTION100
4.3905-4.62170.20491420.12632675X-RAY DIFFRACTION100
4.6217-4.91070.18551250.12462708X-RAY DIFFRACTION100
4.9107-5.28910.17911600.12992692X-RAY DIFFRACTION100
5.2891-5.81990.23371230.1422725X-RAY DIFFRACTION100
5.8199-6.65880.21731440.15992721X-RAY DIFFRACTION100
6.6588-8.37670.22191490.16912759X-RAY DIFFRACTION100
8.3767-40.03240.20851740.1882847X-RAY DIFFRACTION100

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