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- PDB-1r8l: The structure of endo-beta-1,4-galactanase from Bacillus licheniformis -

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Basic information

Entry
Database: PDB / ID: 1r8l
TitleThe structure of endo-beta-1,4-galactanase from Bacillus licheniformis
Componentsendo-beta-1,4-galactanase
KeywordsHYDROLASE / (beta-alpha)8-barrel / calcium ion / 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 / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / metal ion binding
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
Endo-beta-1,4-galactanase
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRyttersgaard, C. / Le Nours, J. / Lo Leggio, L. / Jorgensen, C.T. / Christensen, L.L. / Bjornvad, M. / Larsen, S.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The structure of endo-beta-1,4-galactanase from Bacillus licheniformis in complex with two oligosaccharide products
Authors: Ryttersgaard, C. / Le Nours, J. / Lo Leggio, L. / Jorgensen, C.T. / Christensen, L.L. / Bjornvad, M. / Larsen, S.
History
DepositionOct 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: endo-beta-1,4-galactanase
B: endo-beta-1,4-galactanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6374
Polymers87,5572
Non-polymers802
Water2,234124
1
A: endo-beta-1,4-galactanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8192
Polymers43,7781
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: endo-beta-1,4-galactanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8192
Polymers43,7781
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.910, 81.190, 104.880
Angle α, β, γ (deg.)90.00, 98.53, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer of either chain A or B

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Components

#1: Protein endo-beta-1,4-galactanase


Mass: 43778.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Plasmid: pMOL94 / Production host: Bacillus subtilis (bacteria) / Strain (production host): PL2306
References: UniProt: Q65CX5, arabinogalactan endo-beta-1,4-galactanase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 1500, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→19.67 Å / Num. all: 25224 / Num. obs: 25224 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 38.871 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 8.61
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2 / Num. unique all: 1239 / % possible all: 95.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDN ENTRY 1FHL

1fhl


Resolution: 2.6→19.67 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2524 -RANDOM
Rwork0.186 ---
all0.189 25190 --
obs0.189 25190 95.1 %-
Displacement parametersBiso mean: 31.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6005 0 2 124 6131
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.016
RfactorNum. reflection% reflection
Rfree0.312 396 -
Rwork0.289 --
obs-3714 95.1 %

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