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- PDB-5ljf: Crystal structure of the endo-1,4-glucanase RBcel1 E135A with cel... -

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Basic information

Entry
Database: PDB / ID: 5ljf
TitleCrystal structure of the endo-1,4-glucanase RBcel1 E135A with cellotriose
ComponentsEndoglucanase
KeywordsHYDROLASE / GLYCOSYL HYDROLASE FAMILY 5 / CELLULASE / TIM BARREL / BETA-1 / 4-ENDOGLUCANASE
Function / homology
Function and homology information


glucan catabolic process / cellulase / cellulase activity
Similarity search - Function
Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-cellotriose / Endoglucanase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73439601224 Å
AuthorsDutoit, R. / Collet, L. / Galleni, M. / Bauvois, C.
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Glycoside hydrolase family 5: structural snapshots highlighting the involvement of two conserved residues in catalysis.
Authors: Collet, L. / Vander Wauven, C. / Oudjama, Y. / Galleni, M. / Dutoit, R.
#1: Journal: ISME J / Year: 2009
Title: Insights into bacterial cellulose biosynthesis by functional metagenomics on Antarctic soil samples.
Authors: Berlemont, R. / Delsaute, M. / Pipers, D. / D'Amico, S. / Feller, G. / Galleni, M. / Power, P.
#2: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2013
Title: Three-dimensional structure of RBcel1, a metagenome-derived psychrotolerant family GH5 endoglucanase.
Authors: Delsaute, M. / Berlemont, R. / Dehareng, D. / Van Elder, D. / Galleni, M. / Bauvois, C.
History
DepositionJul 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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_validate_close_contact / 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_atom_id / _atom_site.label_comp_id / _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.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Jul 21, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / citation_author / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn
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_seq_id / _atom_site.label_asym_id / _chem_comp.pdbx_synonyms / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_value_order
Revision 3.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6574
Polymers72,6482
Non-polymers1,0092
Water14,790821
1
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8282
Polymers36,3241
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8282
Polymers36,3241
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.690, 99.310, 148.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Endoglucanase


Mass: 36324.016 Da / Num. of mol.: 2 / Mutation: E135A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pET-22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C1JI15, cellulase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellotriose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotriose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 821 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Crystals were grown at 19 C using the hanging drop method by mixing 2 uL of protein solution (385 uM of protein in 20 mM NaPi pH 6.5 and cellotriose 5 mM) , with 2 uL of resevoir buffer (100 ...Details: Crystals were grown at 19 C using the hanging drop method by mixing 2 uL of protein solution (385 uM of protein in 20 mM NaPi pH 6.5 and cellotriose 5 mM) , with 2 uL of resevoir buffer (100 mM Tris HCl pH 7.4 with 17.5 pc w/v polyethylene glycol 600) containing seeds. Crystals were cryoprotected by equilibrating 2 hours the drop against 500 uL reservoir containing 0.1M Tris PEG 600 30pc pH 7.4.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.73→47.09 Å / Num. obs: 70572 / % possible obs: 99 % / Redundancy: 8.6 % / Biso Wilson estimate: 20.2870816768 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 15.81
Reflection shellResolution: 1.73→1.8 Å / Redundancy: 8 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.54 / % possible all: 94

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphenix.automr_1.10.1_2155phasing
PHENIXphenix.autobuild_1.10.1_2155model building
Coot0.7.1model building
PHENIX1.10.1_2155refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EE9 polyalanine

4ee9


Resolution: 1.73439601224→38.918562621 Å / SU ML: 0.198744573079 / Cross valid method: FREE R-VALUE / σ(F): 1.35787498699 / Phase error: 21.8447173464
RfactorNum. reflection% reflection
Rfree0.212305648019 3529 5.00120459731 %
Rwork0.175578724123 --
obs0.177417744335 70563 99.3397342043 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.3568679699 Å2
Refinement stepCycle: LAST / Resolution: 1.73439601224→38.918562621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5065 0 68 821 5954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006430963695375308
X-RAY DIFFRACTIONf_angle_d0.9203292852187213
X-RAY DIFFRACTIONf_chiral_restr0.0564654844079746
X-RAY DIFFRACTIONf_plane_restr0.00658217571003926
X-RAY DIFFRACTIONf_dihedral_angle_d10.79410975063110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7344-1.75820.3297946494181220.3245329240972314X-RAY DIFFRACTION85.7142857143
1.7582-1.78330.3176051874151380.264620610762614X-RAY DIFFRACTION99.9636759898
1.7833-1.80990.2902793384631400.2464396884182678X-RAY DIFFRACTION100
1.8099-1.83820.2933856133921410.2263893741852666X-RAY DIFFRACTION100
1.8382-1.86830.2444499913141380.2140329233512630X-RAY DIFFRACTION99.9277978339
1.8683-1.90050.2664939444361430.2037149133752714X-RAY DIFFRACTION100
1.9005-1.93510.2525614361751380.2068550224242628X-RAY DIFFRACTION100
1.9351-1.97230.2801765955531410.2194537941482670X-RAY DIFFRACTION100
1.9723-2.01260.2727549818491400.2172518310442668X-RAY DIFFRACTION100
2.0126-2.05630.2949539228541410.2113006582232670X-RAY DIFFRACTION100
2.0563-2.10410.2704401860131420.2047872278572702X-RAY DIFFRACTION100
2.1041-2.15680.2459951361081400.1987025189292657X-RAY DIFFRACTION99.9642601858
2.1568-2.21510.2344871909771410.1928789409472676X-RAY DIFFRACTION100
2.2151-2.28020.2553902233721420.1874030024642707X-RAY DIFFRACTION100
2.2802-2.35380.2307902521611400.1903667832462659X-RAY DIFFRACTION100
2.3538-2.43790.2743038278211420.1810672723792687X-RAY DIFFRACTION100
2.4379-2.53550.25464743921430.1918093016982724X-RAY DIFFRACTION100
2.5355-2.65090.200164715551410.1811187419392670X-RAY DIFFRACTION99.9644381223
2.6509-2.79060.2184360826541420.1800962456962699X-RAY DIFFRACTION100
2.7906-2.96540.2170826884531430.177147165872717X-RAY DIFFRACTION100
2.9654-3.19430.2075452308431430.1709260572392718X-RAY DIFFRACTION100
3.1943-3.51560.1796047913771440.1573350417082752X-RAY DIFFRACTION100
3.5156-4.02380.1753094809381440.1461633856912735X-RAY DIFFRACTION99.8959056211
4.0238-5.06780.1285910963761480.1255886535622796X-RAY DIFFRACTION99.8982015609
5.0678-38.92830.1722907851261520.1479186146172883X-RAY DIFFRACTION98.3792544571

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