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- PDB-4m24: Crystal structure of the endo-1,4-glucanase, RBcel1, in complex w... -

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Basic information

Entry
Database: PDB / ID: 4m24
TitleCrystal structure of the endo-1,4-glucanase, RBcel1, in complex with cellobiose
ComponentsEndoglucanaseCellulase
KeywordsHYDROLASE / GLYCOSYL HYDROLASE FAMILY 5 / CELLULASE / TIM BARREL / BETA-1 / 4-ENDOGLUCANASE
Function / homology
Function and homology information


: / 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-cellobiose / Endoglucanase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.386 Å
AuthorsDelsaute, M. / Berlemont, R. / Van elder, D. / Galleni, M. / Bauvois, C.
Citation
Journal: To be Published
Title: Characterisation of two GH family 5 cellulases required for bacterial cellulose production
Authors: Delsaute, M. / Bauvois, C. / Wei, Q. / Dehareng, D. / Byttebier, V. / Van elder, D. / Paquot, M. / Cornelis, P. / Galleni, M. / Berlemont, 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 / 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
DepositionAug 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9694
Polymers36,3821
Non-polymers5873
Water10,683593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.700, 63.250, 98.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endoglucanase / Cellulase / RBcel1 ENDO-1 / 4-GLUCANASE


Mass: 36382.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pET-22b:RBcel1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C1JI15, cellulase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: RBCel1 in 20 mM NaPi pH 6.5 and cellobiose 1% , was mixed 2:2 with well buffer (100mM Tris HCl pH 6.0 with 20 % w/v polyethylene glycol 600) using the hanging drop method with 500mL well ...Details: RBCel1 in 20 mM NaPi pH 6.5 and cellobiose 1% , was mixed 2:2 with well buffer (100mM Tris HCl pH 6.0 with 20 % w/v polyethylene glycol 600) using the hanging drop method with 500mL well buffer in the well of the crystallization tray, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979718 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979718 Å / Relative weight: 1
ReflectionResolution: 1.386→49.26 Å / Num. all: 66287 / Num. obs: 64593 / % possible obs: 97.6 % / Observed criterion σ(F): -3 / Redundancy: 13.8 % / Biso Wilson estimate: 9.82 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 30.3
Reflection shellResolution: 1.39→1.44 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 4.3 / Num. unique all: 6112 / % possible all: 93.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASER(phenix.automr: 1.8.2_1309)phasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GZJ

1gzj


Resolution: 1.386→30.112 Å / SU ML: 0.1 / σ(F): 2 / Phase error: 14.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1489 5154 7.99 %INHERITED
Rwork0.124 ---
obs0.1263 64527 97.35 %-
all-64531 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.386→30.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2549 0 39 593 3181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082817
X-RAY DIFFRACTIONf_angle_d1.1773860
X-RAY DIFFRACTIONf_dihedral_angle_d12.0641079
X-RAY DIFFRACTIONf_chiral_restr0.09399
X-RAY DIFFRACTIONf_plane_restr0.007503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3861-1.40180.1981790.1691834X-RAY DIFFRACTION88
1.4018-1.41830.2197960.13721979X-RAY DIFFRACTION96
1.4183-1.43560.19351080.13092016X-RAY DIFFRACTION95
1.4356-1.45380.1781150.12521978X-RAY DIFFRACTION97
1.4538-1.47290.1911180.11651977X-RAY DIFFRACTION95
1.4729-1.49310.15581340.1111975X-RAY DIFFRACTION97
1.4931-1.51440.16721280.10831970X-RAY DIFFRACTION96
1.5144-1.5370.1641390.10531982X-RAY DIFFRACTION97
1.537-1.56110.17571340.10431978X-RAY DIFFRACTION97
1.5611-1.58670.14521550.10811947X-RAY DIFFRACTION97
1.5867-1.6140.1521400.11352002X-RAY DIFFRACTION97
1.614-1.64340.13591710.10661951X-RAY DIFFRACTION97
1.6434-1.6750.16441700.11351968X-RAY DIFFRACTION97
1.675-1.70920.14921430.11651987X-RAY DIFFRACTION97
1.7092-1.74630.16081680.11111943X-RAY DIFFRACTION98
1.7463-1.78690.14261910.1171978X-RAY DIFFRACTION98
1.7869-1.83160.14451950.11411961X-RAY DIFFRACTION98
1.8316-1.88110.15841950.11721946X-RAY DIFFRACTION98
1.8811-1.93650.13691870.11531969X-RAY DIFFRACTION98
1.9365-1.9990.14862010.11941971X-RAY DIFFRACTION98
1.999-2.07040.16512060.11691965X-RAY DIFFRACTION98
2.0704-2.15330.13482110.12121960X-RAY DIFFRACTION98
2.1533-2.25120.1262360.11951957X-RAY DIFFRACTION98
2.2512-2.36990.14361730.12082006X-RAY DIFFRACTION99
2.3699-2.51830.15012150.12911983X-RAY DIFFRACTION99
2.5183-2.71260.14742070.13462007X-RAY DIFFRACTION99
2.7126-2.98540.16342270.14021995X-RAY DIFFRACTION99
2.9854-3.41680.14792120.13012039X-RAY DIFFRACTION99
3.4168-4.30290.12352360.12322042X-RAY DIFFRACTION99
4.3029-30.1190.1612640.14122107X-RAY DIFFRACTION99

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