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- PDB-4ee9: Crystal structure of the RBcel1 endo-1,4-glucanase -

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Basic information

Entry
Database: PDB / ID: 4ee9
TitleCrystal structure of the RBcel1 endo-1,4-glucanase
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
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.381 Å
AuthorsDelsaute, M. / Berlemont, R. / Van Elder, D. / Galleni, M. / Bauvois, C.
Citation
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.
#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.
History
DepositionMar 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7484
Polymers36,3821
Non-polymers3663
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.200, 63.090, 98.920
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


Mass: 36382.051 Da / Num. of mol.: 1 / Fragment: UNP residues 31-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: C1JI15, cellulase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 17% PEG 600, 0.1M Tris-HCl pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.38→30.05 Å / Num. all: 67174 / Num. obs: 67782 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.5
Reflection shellResolution: 1.38→1.46 Å / Redundancy: 8 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.3 / Num. unique all: 9218 / % possible all: 94.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASER(phenix.automr_1.6.4-486)phasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.381→30.05 Å / SU ML: 0.13 / σ(F): 1.99 / Phase error: 18.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1765 5362 8 %INHERITED
Rwork0.154 ---
obs0.156 67049 99.01 %-
all-67062 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.101 Å2 / ksol: 0.376 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.112 Å20 Å2-0 Å2
2---7.666 Å2-0 Å2
3---8.778 Å2
Refinement stepCycle: LAST / Resolution: 1.381→30.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2547 0 24 557 3128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012774
X-RAY DIFFRACTIONf_angle_d1.353791
X-RAY DIFFRACTIONf_dihedral_angle_d15.1051063
X-RAY DIFFRACTIONf_chiral_restr0.108384
X-RAY DIFFRACTIONf_plane_restr0.009495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.381-1.39680.3034850.2251730X-RAY DIFFRACTION82
1.3968-1.41320.24821080.19472091X-RAY DIFFRACTION98
1.4132-1.43040.23591030.18612080X-RAY DIFFRACTION99
1.4304-1.44850.23511230.17752079X-RAY DIFFRACTION99
1.4485-1.46760.20211410.16662087X-RAY DIFFRACTION99
1.4676-1.48770.22891350.16252073X-RAY DIFFRACTION99
1.4877-1.50890.20611350.14282051X-RAY DIFFRACTION99
1.5089-1.53150.19731430.13222089X-RAY DIFFRACTION99
1.5315-1.55540.21961510.13632047X-RAY DIFFRACTION100
1.5554-1.58090.17231560.14122107X-RAY DIFFRACTION99
1.5809-1.60810.18621630.14372042X-RAY DIFFRACTION100
1.6081-1.63740.17551530.13662087X-RAY DIFFRACTION100
1.6374-1.66890.18531840.132056X-RAY DIFFRACTION100
1.6689-1.70290.18711590.13872068X-RAY DIFFRACTION100
1.7029-1.740.16441680.13572080X-RAY DIFFRACTION100
1.74-1.78040.16781890.14372044X-RAY DIFFRACTION100
1.7804-1.8250.1592100.14412016X-RAY DIFFRACTION100
1.825-1.87430.15991980.14322065X-RAY DIFFRACTION100
1.8743-1.92940.17661960.14652062X-RAY DIFFRACTION100
1.9294-1.99170.17752020.14682042X-RAY DIFFRACTION100
1.9917-2.06290.1852110.14582034X-RAY DIFFRACTION100
2.0629-2.14540.14812210.14122037X-RAY DIFFRACTION100
2.1454-2.24310.16072440.14192017X-RAY DIFFRACTION100
2.2431-2.36130.17051820.14062089X-RAY DIFFRACTION100
2.3613-2.50910.16782230.14632055X-RAY DIFFRACTION100
2.5091-2.70280.18752160.15732050X-RAY DIFFRACTION100
2.7028-2.97450.18092290.15942074X-RAY DIFFRACTION100
2.9745-3.40440.16922200.15512095X-RAY DIFFRACTION100
3.4044-4.28730.15282470.15212090X-RAY DIFFRACTION100
4.2873-30.0610.19772670.18632150X-RAY DIFFRACTION98

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