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- PDB-1fhl: CRYSTAL STRUCTURE OF BETA-1,4-GALACTANASE FROM ASPERGILLUS ACULEA... -

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Basic information

Entry
Database: PDB / ID: 1fhl
TitleCRYSTAL STRUCTURE OF BETA-1,4-GALACTANASE FROM ASPERGILLUS ACULEATUS AT 293K
ComponentsBETA-1,4-GALACTANASE
KeywordsHYDROLASE / B/A barrel / glycosyl hydrolase / family 53 / clan GH-A
Function / homology
Function and homology information


arabinogalactan endo-beta-1,4-galactanase / arabinogalactan endo-1,4-beta-galactosidase activity / glucosidase activity / pectin catabolic process
Similarity search - Function
Glycosyl hydrolase family 53 / Glycosyl hydrolase family 53 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Arabinogalactan endo-beta-1,4-galactanase
Similarity search - Component
Biological speciesAspergillus aculeatus (mold)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsRyttersgaard, C. / Larsen, S.
Citation
Journal: Biochemistry / Year: 2002
Title: Aspergillus aculeatus beta-1,4-Galactanase: Substrate Recognition and Relations to Other Glycoside Hydrolases in Clan GH-A
Authors: Ryttersgaard, C. / Leggio, L.L. / Coutinho, P.M. / Henrissat, B. / Larsen, S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary X-ray Studies of beta-1,4-galactanase from Aspergillus aculeatus
Authors: Ryttersgaard, C. / Poulsen, J. / Christgau, S. / Sandal, T. / Dalboge, H. / Larsen, S.
History
DepositionAug 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-1,4-GALACTANASE


Theoretical massNumber of molelcules
Total (without water)36,7751
Polymers36,7751
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.420, 88.940, 129.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

DetailsThe biological assembly is a monomer

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Components

#1: Protein BETA-1,4-GALACTANASE


Mass: 36775.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aspergillus aculeatus (mold)
References: UniProt: P48842, arabinogalactan endo-beta-1,4-galactanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, calcium chloride, sodium hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Ryttersgaard, C., (1999) Acta Crystallogr.,Sect.D, 55, 929.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130 %(v/v)PEG4001reservoir
20.2 M1reservoirCaCl2
30.1 Msodium HEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 14, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→28.8 Å / Num. all: 15582 / Num. obs: 15582 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 30.82 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 7.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.392 / Num. unique all: 2154 / % possible all: 95.6
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 28.9 Å
Reflection shell
*PLUS
% possible obs: 95.6 % / Mean I/σ(I) obs: 61.4

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Processing

Software
NameVersionClassification
TRUNCATEdata reduction
SHARPphasing
X-PLOR3.851refinement
CCP4(TRUNCATE)data scaling
RefinementResolution: 2.3→28.8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1578 -RANDOM
Rwork0.166 ---
all0.174 15582 --
obs0.174 15582 100 %-
Refinement stepCycle: LAST / Resolution: 2.3→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2598 0 0 59 2657
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.384
X-RAY DIFFRACTIONx_dihedral_angle_d25.252
X-RAY DIFFRACTIONx_improper_angle_d0.734
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 28.9 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.252
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.734

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