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- PDB-7p6i: Crystal structure of the endoglucanase RBcel1 Y201F -

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Basic information

Entry
Database: PDB / ID: 7p6i
TitleCrystal structure of the endoglucanase RBcel1 Y201F
ComponentsEndoglucanase
KeywordsHYDROLASE / Transglycosylase / GH5_5 family
Function / homologyglucan catabolic process / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / cellulase / cellulase activity / Glycoside hydrolase superfamily / Endoglucanase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 Å
AuthorsCollet, L. / Dutoit, R.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Highlighting the factors governing transglycosylation in the GH5_5 endo-1,4-beta-glucanase RBcel1.
Authors: Collet, L. / Vander Wauven, C. / Oudjama, Y. / Galleni, M. / Dutoit, R.
History
DepositionJul 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)36,7324
Polymers36,3661
Non-polymers3663
Water8,701483
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, RBcel1 Y201F variant is a monomer based on size exclusion chromatography using a superdex75 column.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint8 kcal/mol
Surface area13800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.040, 63.060, 98.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endoglucanase


Mass: 36366.051 Da / Num. of mol.: 1 / Mutation: Y201F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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.: 483 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Reservoir: 0.1M Tris, 17.5% PEG600, pH7. Protein:14.1 mg/ml in 20 mM sodium phosphate buffer pH6.5. Drop: 2 ul reservoir + 2 ul protein. Cryoprotectant: 50% PEG600 added to the drop for 40 s.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2014
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.47→38.898 Å / Num. obs: 55784 / % possible obs: 99.2 % / Redundancy: 13.935 % / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.113 / Χ2: 1.043 / Net I/σ(I): 16.27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.47-1.5113.2781.5211.7237240.5861.58190.7
1.51-1.5514.261.1872.7639760.7211.23199.5
1.55-1.5914.2510.9883.5938810.8231.02599.6
1.59-1.6414.2490.7994.8337670.9040.82999.7
1.64-1.714.2490.6566.1536720.9420.68199.9
1.7-1.7614.3140.4928.2435610.9750.5199.9
1.76-1.8214.4130.37610.3234170.9820.3999.9
1.82-1.914.3430.32812.2333300.9880.3499.9
1.9-1.9813.8650.23515.9231880.990.244100
1.98-2.0814.3070.15219.4330480.9950.158100
2.08-2.1914.1810.11922.6728910.9960.124100
2.19-2.3213.2790.11624.827530.9960.12100
2.32-2.4813.8220.08927.7426150.9970.093100
2.48-2.6813.6950.08129.6923980.9980.084100
2.68-2.9413.6190.07432.0122440.9980.077100
2.94-3.2813.8350.06636.1120510.9980.068100
3.28-3.7913.360.06337.2618020.9980.066100
3.79-4.6413.4210.05638.2515530.9990.058100
4.64-6.5713.1460.05538.0512300.9980.057100
6.57-38.89811.0640.0634.376830.9970.06394.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.64 Å46.05 Å

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Processing

Software
NameVersionClassification
XDS20190315data reduction
XSCALE20190315data scaling
PHASER2.8.3phasing
PHENIX1.11_2563refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EE9

4ee9


Resolution: 1.47→38.898 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1934 4764 8.54 %
Rwork0.178 51012 -
obs0.1794 55776 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.8 Å2 / Biso mean: 21.0184 Å2 / Biso min: 8.13 Å2
Refinement stepCycle: final / Resolution: 1.47→38.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 24 483 3077
Biso mean--22.66 34.09 -
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032871
X-RAY DIFFRACTIONf_angle_d0.653927
X-RAY DIFFRACTIONf_chiral_restr0.077394
X-RAY DIFFRACTIONf_plane_restr0.004512
X-RAY DIFFRACTIONf_dihedral_angle_d2.3442243
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.47-1.48520.4633920.4038138880
1.4852-1.50270.49131170.33811735100
1.5027-1.5210.36641210.31861715100
1.521-1.54020.31731160.2994172899
1.5402-1.56050.3171130.28691712100
1.5605-1.58190.25941480.2772170699
1.5819-1.60450.29751300.26771711100
1.6045-1.62840.26711220.245171699
1.6284-1.65390.23711500.23271687100
1.6539-1.6810.28091430.19991705100
1.681-1.710.20331300.1971736100
1.71-1.74110.19951430.17211729100
1.7411-1.77460.22361540.17381705100
1.7746-1.81080.21341750.17121662100
1.8108-1.85010.18581650.17861696100
1.8501-1.89320.22381750.18841701100
1.8932-1.94050.21441530.1821697100
1.9405-1.9930.221720.17931701100
1.993-2.05160.20631690.1731696100
2.0516-2.11790.20141850.17661669100
2.1179-2.19350.17981880.17181701100
2.1935-2.28140.19781930.16951688100
2.2814-2.38520.16581580.16111722100
2.3852-2.51090.18411750.17251697100
2.5109-2.66820.2041800.17351723100
2.6682-2.87410.19491810.17521708100
2.8741-3.16330.17551900.15841716100
3.1633-3.62070.16591990.1531721100
3.6207-4.56060.16291980.14571761100
4.5606-38.8980.16632290.1598178098
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.82280.0289-0.10760.7643-0.08780.77580.0485-0.102-0.00570.0898-0.05910.1080.0555-0.0604-0.00080.1106-0.02080.00590.114-0.01670.104735.647933.400132.2799
20.43660.1075-0.01530.13480.07670.35960.00640.03810.1278-0.0014-0.0529-0.059-0.10360.09210.01110.11510.00470.00190.10930.00570.137147.639542.496818.2023
30.4810.4344-0.06480.57610.18960.58520.03310.08410.0172-0.1154-0.01790.09290.0163-0.0422-0.00150.12590.0186-0.01770.11420.00170.110337.902735.715812.6937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 184 )A1 - 184
2X-RAY DIFFRACTION2chain 'A' and (resid 185 through 237 )A185 - 237
3X-RAY DIFFRACTION3chain 'A' and (resid 238 through 321 )A238 - 321

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