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- PDB-1ur4: The structure of endo-beta-1,4-galactanase from Bacillus lichenif... -

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Basic information

Entry
Database: PDB / ID: 1ur4
TitleThe structure of endo-beta-1,4-galactanase from Bacillus licheniformis in complex with two oligosaccharide products.
ComponentsGALACTANASEArabinogalactan endo-1,4-beta-galactosidase
KeywordsHYDROLASE / BETA-1 / 4-GALACTANASE / GLYCOSIDE HYDROLASE / SUBSTRATE SPECIFICITY / PECTIN / GH-A / FAMILY 53 / PLANT CELL WALL DEGRADATION
Function / homology
Function and homology information


arabinogalactan endo-beta-1,4-galactanase / arabinogalactan endo-1,4-beta-galactosidase activity / glucosidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / metabolic process / 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
4beta-beta-galactobiose / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / : / Endo-beta-1,4-galactanase
Similarity search - Component
Biological speciesBACILLUS LICHENIFORMIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRyttersgaard, C. / Le Nours, J. / Lo Leggio, L. / Jorgensen, C.T. / Christensen, L.L.H. / 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.H. / Bjornvad, M. / Larsen, S.
History
DepositionOct 24, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_asym_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_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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: GALACTANASE
B: GALACTANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6849
Polymers87,5572
Non-polymers1,1277
Water3,711206
1
A: GALACTANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2674
Polymers43,7781
Non-polymers4883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: GALACTANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4175
Polymers43,7781
Non-polymers6394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.330, 79.520, 104.890
Angle α, β, γ (deg.)90.00, 100.52, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.18421, 0.68455, 0.70531), (-0.89888, -0.4076, 0.16084), (0.39759, -0.60437, 0.69041)
Vector: 174.44279, -1.514, 0.7045)

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein GALACTANASE / Arabinogalactan endo-1,4-beta-galactosidase


Mass: 43778.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FRAGMENTS OF PEG AND GALACTOBIOSE BOUND. / Source: (gene. exp.) BACILLUS LICHENIFORMIS (bacteria) / Production host: BACILLUS SUBTILIS (bacteria) / Strain (production host): PL2306
References: GenBank: 28075822, UniProt: Q65CX5*PLUS, arabinogalactan endo-beta-1,4-galactanase
#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-galactopyranose / 4beta-beta-galactobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-galactobiose
DescriptorTypeProgram
DGalpb1-4DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2112h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 211 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 5 / Details: 26% PEG 1500, pH 5.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.813
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2003 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.813 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 40969 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.098
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.374 / % possible all: 96.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 121417.09 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3702 10 %RANDOM
Rwork0.205 ---
obs0.205 36894 89.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.4957 Å2 / ksol: 0.370551 e/Å3
Displacement parametersBiso mean: 29.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å24.21 Å2
2--6.84 Å20 Å2
3----6.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6007 0 72 206 6285
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 512 10.2 %
Rwork0.262 4493 -
obs--73.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4GAL2.PARGAL2.TOP

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