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- PDB-2xn1: Structure of alpha-galactosidase from Lactobacillus acidophilus N... -

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Basic information

Entry
Database: PDB / ID: 2xn1
TitleStructure of alpha-galactosidase from Lactobacillus acidophilus NCFM with TRIS
ComponentsALPHA-GALACTOSIDASE
KeywordsHYDROLASE / GLYCOSIDASE
Function / homology
Function and homology information


response to raffinose / alpha-galactosidase / alpha-galactosidase activity / carbohydrate catabolic process / protein homotetramerization
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
Alpha-galactosidase Mel36A / Alpha-galactosidase Mel36A
Similarity search - Component
Biological speciesLACTOBACILLUS ACIDOPHILUS NCFM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFredslund, F. / Abou Hachem, M. / Larsen, R.J. / Sorensen, P.G. / Lo Leggio, L. / Svensson, B.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal Structure of Alpha-Galactosidase from Lactobacillus Acidophilus Ncfm: Insight Into Tetramer Formation and Substrate Binding.
Authors: Fredslund, F. / Abou Hachem, M. / Jonsgaard Larsen, R. / Gerd Sorensen, P. / Coutinho, P.M. / Lo Leggio, L. / Svensson, B.
History
DepositionJul 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Data collection / Database references / Structure summary
Revision 1.2Sep 14, 2011Group: Database references / Refinement description
Revision 2.0Jan 17, 2018Group: Atomic model / Data collection / Category: atom_site / diffrn_source
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _diffrn_source.pdbx_synchrotron_site
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" 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. THE SHEETS PRESENTED AS "BG" 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. THE SHEETS PRESENTED AS "CG" 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. THE SHEETS PRESENTED AS "DG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -5-STRANDED BARREL THIS IS REPRESENTED BY A -4-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)340,77429
Polymers338,3524
Non-polymers2,42325
Water31,8511768
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32500 Å2
ΔGint-62.2 kcal/mol
Surface area85430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.920, 150.680, 126.680
Angle α, β, γ (deg.)90.00, 94.29, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9997, 0.0244, -0.0043), (0.0248, 0.9836, -0.1787), (-0.0001, -0.1787, -0.9839)58.7341, 4.5064, 58.0567
2given(0.988, -0.0089, 0.1542), (-0.0089, -1, -0.0002), (0.1542, -0.0011, -0.988)-4.3206, -11.4165, 54.6626
3given(-0.9883, -0.0127, -0.152), (-0.015, -0.9836, 0.1797), (-0.1517, 0.1799, 0.9719)62.5521, -16.4909, 6.3498

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Components

#1: Protein
ALPHA-GALACTOSIDASE


Mass: 84587.977 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOBACILLUS ACIDOPHILUS NCFM (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7WWP9, UniProt: G1UB44*PLUS, alpha-galactosidase
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1768 / 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: 3.07 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 7.5 / Details: 8-12% PEG8000, 0.1M TRIS, 10% GLYCEROL, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03908
DetectorType: MARRESEARCH / Detector: CCD / Date: May 27, 2009 / Details: MIRRORS
RadiationMonochromator: BENT SI (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03908 Å / Relative weight: 1
ReflectionResolution: 2.3→22 Å / Num. obs: 181263 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.6
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 12.38 / % possible all: 92.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XN0

2xn0


Resolution: 2.3→21.983 Å / SU ML: 0.28 / σ(F): 1.99 / Phase error: 16.63 / Stereochemistry target values: ML / Details: RESIDUES 1-4 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.1871 2010 1.1 %
Rwork0.1468 --
obs0.1472 181263 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.216 Å2 / ksol: 0.434 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.5711 Å20 Å2-2.9516 Å2
2---3.1145 Å20 Å2
3----0.4566 Å2
Refinement stepCycle: LAST / Resolution: 2.3→21.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23744 0 158 1768 25670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01624469
X-RAY DIFFRACTIONf_angle_d1.44633021
X-RAY DIFFRACTIONf_dihedral_angle_d14.6439126
X-RAY DIFFRACTIONf_chiral_restr0.0933396
X-RAY DIFFRACTIONf_plane_restr0.0074308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2991-2.38120.19231910.132417232X-RAY DIFFRACTION96
2.3812-2.47640.1822120.128617942X-RAY DIFFRACTION100
2.4764-2.58890.18681770.129818000X-RAY DIFFRACTION100
2.5889-2.72520.20572210.14117911X-RAY DIFFRACTION100
2.7252-2.89560.19751980.139217981X-RAY DIFFRACTION100
2.8956-3.11860.19741970.145117975X-RAY DIFFRACTION100
3.1186-3.43130.19842110.14218007X-RAY DIFFRACTION100
3.4313-3.92540.16361980.131218005X-RAY DIFFRACTION100
3.9254-4.93640.13772000.115918050X-RAY DIFFRACTION100
4.9364-21.98370.17652050.148518150X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.12620.00070.04410.2675-0.00810.16520.0212-0.0618-0.03130.0867-0.0467-0.0030.03770.00680.01850.095-0.01490.0190.05770.01680.017842.6816-27.363148.9533
20.18790.05740.07280.25360.02840.17890.01960.0046-0.0437-0.0743-0.04620.10850.0501-0.05190.02640.0809-0.0014-0.01830.0668-0.05650.100315.2577-30.112114.7173
30.12640.09080.05850.307-0.00880.1538-0.03130.03350.0478-0.1292-0.02080.0209-0.04260.0270.04330.09910.0042-0.01130.03840.01570.020945.701515.535212.8884
40.12010.04490.05270.44010.05720.2621-0.0061-0.04950.11740.024-0.07580.228-0.0569-0.10950.09070.070.0264-0.00480.1004-0.10340.169413.33718.607442.4773
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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