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- PDB-7p6j: Crystal structure of glycosyl-enzyme intermediate of RBcel1 Y201F -

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Basic information

Entry
Database: PDB / ID: 7p6j
TitleCrystal structure of glycosyl-enzyme intermediate of RBcel1 Y201F
ComponentsEndoglucanase
KeywordsHYDROLASE / Transglycosylase / GH5_5 family / complex / glycosyl-enzyme intermediate
Function / homology
Function and homology information


glucan catabolic process / cellulase / cellulase activity
Similarity search - Function
Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-cellobiose / beta-cellotetraose / alpha-cellotriose / beta-D-glucopyranose / Endoglucanase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase
B: Endoglucanase
C: Endoglucanase
D: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,00413
Polymers145,4644
Non-polymers4,5409
Water20,8791159
1
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3753
Polymers36,3661
Non-polymers1,0092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6993
Polymers36,3661
Non-polymers1,3332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5373
Polymers36,3661
Non-polymers1,1712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3934
Polymers36,3661
Non-polymers1,0273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.560, 90.540, 89.680
Angle α, β, γ (deg.)90.000, 118.770, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Non-polymers , 2 types, 1163 molecules ABCD

#1: Protein
Endoglucanase


Mass: 36366.051 Da / Num. of mol.: 4 / Mutation: Y201F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pBAD-TOPO / Production host: Escherichia coli MC1061 (bacteria) / Strain (production host): MC1061 / References: UniProt: C1JI15, cellulase
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1159 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 6 types, 9 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 3 / Source method: obtained synthetically / 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
#4: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2-2-2-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: oligosaccharide / References: alpha-cellotriose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotetraose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#7: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY
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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Reservoir: 0.1M Tris, 21% PEG600, pH7 Protein-ligand mix: 100 ul protein (14.1 mg/ml in 20 mM sodium phosphate buffer pH6.5) + 36 ul 212 mM cellotriose. Drop: 2 ul reservoir + 2 ul protein- ...Details: Reservoir: 0.1M Tris, 21% PEG600, pH7 Protein-ligand mix: 100 ul protein (14.1 mg/ml in 20 mM sodium phosphate buffer pH6.5) + 36 ul 212 mM cellotriose. Drop: 2 ul reservoir + 2 ul protein-ligand mix + 0.2 ul microseeds.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 13, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→44.82 Å / Num. obs: 124776 / % possible obs: 98.8 % / Redundancy: 6.78 % / Biso Wilson estimate: 28.45 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.073 / Χ2: 1.088 / Net I/σ(I): 13.54 / Num. measured all: 845927
Reflection shellResolution: 1.75→44.82 Å / Redundancy: 6.23 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 1.57 / Num. measured obs: 9542 / Num. possible: 1498 / Num. unique obs: 1467 / CC1/2: 0.998 / Rrim(I) all: 0.037 / % possible all: 93.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.77 Å44.82 Å
Translation2.77 Å44.82 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
XDS20190315data reduction
XSCALE20190315data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EE9

4ee9


Resolution: 1.75→44.82 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.202 6235 5 %
Rwork0.172 118499 -
obs0.174 124734 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.4 Å2 / Biso mean: 37.47 Å2 / Biso min: 16.31 Å2
Refinement stepCycle: final / Resolution: 1.75→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10202 0 302 1159 11663
Biso mean--37.02 41.4 -
Num. residues----1274
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.760.48021790.42213399357886
1.76-1.790.35782050.3543922412799
1.79-1.810.37742090.33183974418399
1.81-1.830.32442060.3083912411899
1.83-1.850.28772090.27043953416299
1.85-1.880.28152050.23713908411399
1.88-1.910.2522060.223911411799
1.91-1.940.25652090.21143954416399
1.94-1.970.25092080.20873956416499
1.97-20.25512070.20673939414699
2-2.030.26172080.20023940414899
2.03-2.070.25282100.1933991420199
2.07-2.110.23462090.19373965417499
2.11-2.150.25032080.20043949415799
2.15-2.20.22712080.20239544162100
2.2-2.250.21452080.186239684176100
2.25-2.310.19852080.169939494157100
2.31-2.370.19272090.171639654174100
2.37-2.440.20922090.171839984207100
2.44-2.520.20962100.179239714181100
2.52-2.610.19252090.174539804189100
2.61-2.710.20892090.178839674176100
2.71-2.830.20882100.186640044214100
2.83-2.980.22072100.180239714181100
2.98-3.170.22012090.173139864195100
3.17-3.420.19462110.161340034214100
3.42-3.760.20252110.155739994210100
3.76-4.30.15872100.13440084218100
4.3-5.420.13732110.128240124223100
5.42-44.820.16762150.15114091430699
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)
11.20350.2381.11220.50010.24622.7369-0.12780.14510.1174-0.06270.13-0.0219-0.54120.19530.02430.3306-0.02520.03960.18140.03170.2343-24.074620.5837-27.0973
21.46290.15320.73341.0690.36542.97380.02270.0194-0.1390.01230.0948-0.02840.0470.0537-0.14790.20520.01090.02770.16450.01120.2522-21.52058.2362-18.6741
31.78060.39490.4741.18130.74463.7121-0.1255-0.2308-0.24720.10940.15280.08150.1399-0.0021-0.07340.2090.01650.01970.17270.03740.2231-18.404313.3582-7.2975
42.2490.18540.44831.88460.69643.6967-0.025-0.42030.19720.10670.06140.1137-0.5924-0.3065-0.07070.36150.0550.06440.3189-0.00710.2164-22.562423.5094-2.2449
52.3402-0.0055-0.20051.96160.20871.8176-0.1344-0.16940.3718-0.28630.12430.1291-1.064-0.00920.08050.63380.02740.00490.237-0.03470.2847-19.977831.8943-8.6492
61.55090.00810.41.21270.28432.3537-0.2248-0.03120.3034-0.27250.0888-0.0171-0.88680.07770.0940.54830.00550.02190.21810.00560.2679-19.77929.9262-17.479
71.9167-0.2802-0.62671.73890.29931.4481-0.04470.20360.202-0.05020.06910.36580.1177-0.57190.01450.1874-0.05060.00320.38760.0770.3227-52.696518.3894-44.4039
81.50590.0439-0.25321.2718-0.27722.83440.01860.12950.2147-0.01230.11310.3358-0.3239-0.6719-0.13530.17530.0532-0.0180.33180.05950.2769-49.653328.595-48.3265
91.698-0.4837-0.70862.0952-0.11423.01120.09780.06630.2694-0.13130.0410.0742-0.3569-0.247-0.12810.22540.01010.00930.20810.04630.2804-40.151731.3699-52.203
102.8398-0.5154-0.36632.45-0.01953.20910.12210.3979-0.1047-0.4628-0.0608-0.16420.2968-0.1906-0.07250.2731-0.01670.01770.25950.02240.1809-34.209615.7765-61.3364
112.489-0.173-0.43831.666-0.12362.4037-0.12130.0795-0.3717-0.2710.07650.08650.5681-0.27480.02640.2944-0.0854-0.01140.20130.02220.2568-40.17457.8915-53.0919
121.5634-0.7297-0.34251.68340.13722.668-0.17760.0309-0.23510.03630.09820.12780.5264-0.29570.04290.3611-0.05280.02920.21430.03140.277-39.54737.511-46.8872
131.59960.215-0.63652.36640.22932.9362-0.05940.2045-0.0951-0.3414-0.0311-0.08030.08220.03380.07640.20390.030.03660.2086-0.00240.20231.92720.5388-64.3819
142.14730.6256-1.04811.8171-0.04723.1966-0.12330.1836-0.3069-0.1875-0.0305-0.09010.26760.04540.1450.24430.04640.03850.2252-0.01840.26151.086613.8195-61.3885
151.60790.2187-0.47871.77370.10832.4586-0.06240.1284-0.2886-0.1632-0.0692-0.18560.42460.21590.1620.30560.06840.06940.2172-0.00830.31594.04679.5147-56.7635
164.976-0.8769-1.352.96150.0863.8629-0.5456-0.0397-0.58530.32360.1042-0.12450.83050.13480.38740.37430.01820.04780.19060.01770.3236-1.18285.7954-48.215
171.62950.1182-0.851.3660.42842.8821-0.2197-0.3492-0.41170.24970.0019-0.04440.57570.31720.18460.26150.05940.01870.25310.05920.24641.213412.787-42.8709
181.5723-0.78590.11122.8478-0.95332.29640.016-0.1910.14310.1472-0.02220.0392-0.22020.04280.01430.2022-0.01940.00960.2312-0.03790.2176-2.756531.6091-43.3151
192.65490.4809-0.36491.9311.52123.64260.08590.3290.216-0.3589-0.10690.0745-0.4986-0.11850.01960.22770.01630.01420.21970.0150.2397-0.291633.2034-58.5941
201.1812-0.0361-0.59493.1714-0.90241.5988-0.0174-0.33790.07730.1382-0.1294-0.6795-0.10880.43590.16760.27-0.05440.01820.35140.00210.372711.3432.8327-47.1117
214.2702-1.1732-0.04263.28830.59662.5815-0.2012-0.4196-0.34510.52980.18640.27330.4587-0.4641-0.04830.3643-0.03210.09660.33690.01440.27678.839621.1699-10.5599
224.3368-1.0207-0.25353.33940.95983.8764-0.2644-0.39920.76550.50040.4761-0.0658-0.3086-0.2696-0.06590.37020.02110.02150.3342-0.07740.472313.618931.8804-11.8279
234.628-1.18560.80273.63220.88964.1448-0.0387-0.31080.65860.32320.2768-0.0933-0.6965-0.2541-0.1920.41950.00960.02710.2829-0.10610.454114.783932.1876-12.8345
242.9605-0.22930.94753.13210.71981.7497-0.0692-0.32970.91360.25810.3698-0.6587-0.63820.3361-0.11790.4295-0.0598-0.03240.3613-0.16660.61824.629533.8815-12.2091
251.22461.17861.46392.98421.22121.80540.07620.23210.56060.00710.3286-1.0396-0.23790.8935-0.39540.33-0.0681-0.06620.6236-0.22430.856635.354530.154-16.1286
262.8881-1.2522-0.3094.23920.98363.80170.07910.2737-0.43950.25160.0798-0.18580.63940.2084-0.14280.34270.0294-0.03860.2591-0.07270.413223.841411.2454-20.0534
277.06013.0985-1.36295.03640.55361.4765-0.0232-1.4325-0.08011.4396-0.0762-0.39670.78490.62320.12650.82530.1101-0.15290.52860.00310.54827.00529.2432-6.8381
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 40 )A0
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 41 THROUGH 157 )A0
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 158 THROUGH 180 )A0
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 181 THROUGH 237 )A0
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 238 THROUGH 268 )A0
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 269 THROUGH 318 )A0
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 1 THROUGH 40 )B0
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 41 THROUGH 106 )B0
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 107 THROUGH 176 )B0
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 177 THROUGH 237 )B0
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 238 THROUGH 285 )B0
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 286 THROUGH 321 )B0
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 1 THROUGH 64 )C0
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 65 THROUGH 106 )C0
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 107 THROUGH 137 )C0
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 138 THROUGH 158 )C0
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 159 THROUGH 193 )C0
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 194 THROUGH 268 )C0
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 269 THROUGH 297 )C0
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 298 THROUGH 318 )C0
21X-RAY DIFFRACTION21CHAIN 'D' AND (RESID 2 THROUGH 40 )D0
22X-RAY DIFFRACTION22CHAIN 'D' AND (RESID 41 THROUGH 64 )D0
23X-RAY DIFFRACTION23CHAIN 'D' AND (RESID 65 THROUGH 106 )D0
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESID 107 THROUGH 176 )D0
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESID 177 THROUGH 199 )D0
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESID 200 THROUGH 297 )D0
27X-RAY DIFFRACTION27CHAIN 'D' AND (RESID 298 THROUGH 318 )D0

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