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- PDB-6zz3: RBcel1 cellulase variant Y201F with cellotriose covalently bound -

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Basic information

Entry
Database: PDB / ID: 6zz3
TitleRBcel1 cellulase variant Y201F with cellotriose covalently bound
ComponentsEndoglucanase
KeywordsHYDROLASE / Cellulase / Complex / cellotriose / Y201F variant
Function / homologyglucan catabolic process / cellulase / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / cellulase activity / Glycoside hydrolase superfamily / alpha-cellotriose / Endoglucanase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.095 Å
AuthorsCollet, L. / Dutoit, R.
CitationJournal: 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.
History
DepositionAug 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 20, 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)147,0889
Polymers144,9484
Non-polymers2,1405
Water8,413467
1
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8643
Polymers36,2371
Non-polymers6272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7412
Polymers36,2371
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7412
Polymers36,2371
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7412
Polymers36,2371
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.000, 61.890, 177.260
Angle α, β, γ (deg.)90.000, 97.110, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 17 or (resid 18...
21(chain B and ((resid 1 and (name CA or name...
31(chain C and ((resid 1 and (name CA or name...
41(chain D and ((resid 1 and (name CA or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLYGLY(chain A and (resid 1 through 17 or (resid 18...AA1 - 171 - 17
12LYSLYSLYSLYS(chain A and (resid 1 through 17 or (resid 18...AA1818
13SERSERLYSLYS(chain A and (resid 1 through 17 or (resid 18...AA1 - 3191 - 319
21SERSERSERSER(chain B and ((resid 1 and (name CA or name...BB11
22SERSERALAALA(chain B and ((resid 1 and (name CA or name...BB1 - 3201 - 320
23SERSERALAALA(chain B and ((resid 1 and (name CA or name...BB1 - 3201 - 320
31SERSERSERSER(chain C and ((resid 1 and (name CA or name...CC11
32SERSERLYSLYS(chain C and ((resid 1 and (name CA or name...CC1 - 3191 - 319
33SERSERLYSLYS(chain C and ((resid 1 and (name CA or name...CC1 - 3191 - 319
41SERSERSERSER(chain D and ((resid 1 and (name CA or name...DD11
42SERSERALAALA(chain D and ((resid 1 and (name CA or name...DD1 - 3201 - 320
43SERSERALAALA(chain D and ((resid 1 and (name CA or name...DD1 - 3201 - 320

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Components

#1: Protein
Endoglucanase


Mass: 36236.938 Da / Num. of mol.: 4 / Mutation: Y201F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pBad / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: C1JI15, cellulase
#2: 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.: 4
Source method: isolated from a genetically manipulated 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
[][D-1-deoxy-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20.5% PEG600, 100mM Tris, 1mM 2-Chloro-4-nitrophenyl-b-cellotrioside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 15, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.095→45.101 Å / Num. obs: 72131 / % possible obs: 99.5 % / Redundancy: 6.921 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.094 / Χ2: 1.016 / Net I/σ(I): 11.93
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.156.681.3021.2633332528749900.511.40994.4
2.15-2.217.1131.1341.5637549528452790.6371.22399.9
2.21-2.277.0060.9961.8235361504550470.6741.076100
2.27-2.346.8530.7112.5933109483348310.8180.77100
2.34-2.426.5490.5223.3731048474547410.8790.56899.9
2.42-2.56.9060.4214.2831886461946170.9180.456100
2.5-2.66.6870.325.3429926447844750.9550.34899.9
2.6-2.77.1850.2576.9430801428342870.9710.278100
2.7-2.827.2320.2048.829515408440810.9810.2299.9
2.82-2.967.1770.15411.2928193392839280.9890.166100
2.96-3.127.0330.11814.3526253373437330.9940.128100
3.12-3.316.870.09617.4424376354835480.9950.104100
3.31-3.546.5990.07521.2221955333033270.9970.08199.9
3.54-3.836.7250.06823.6221124314731410.9970.07399.8
3.83-4.197.2120.05429.5820510284328440.9980.058100
4.19-4.687.2460.04732.918840260126000.9990.05100
4.68-5.417.1140.04433.4916285229022890.9990.047100
5.41-6.636.6040.04531.1412963196319630.9980.049100
6.63-9.376.760.03734.9610478154915500.9990.04100
9.37-45.1016.6830.03238.0357478738600.9990.03498.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.66 Å45.1 Å
Translation4.66 Å45.1 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.7.15phasing
PHENIX1.11-2563refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ee9

4ee9


Resolution: 2.095→45.101 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2287 3604 5 %
Rwork0.1954 68488 -
obs0.197 72092 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.77 Å2 / Biso mean: 48.4076 Å2 / Biso min: 23.31 Å2
Refinement stepCycle: final / Resolution: 2.095→45.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10084 0 140 467 10691
Biso mean--45.93 48.78 -
Num. residues----1278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610659
X-RAY DIFFRACTIONf_angle_d0.87514513
X-RAY DIFFRACTIONf_chiral_restr0.0541495
X-RAY DIFFRACTIONf_plane_restr0.0071886
X-RAY DIFFRACTIONf_dihedral_angle_d3.928564
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5565X-RAY DIFFRACTION8.076TORSIONAL
12B5565X-RAY DIFFRACTION8.076TORSIONAL
13C5565X-RAY DIFFRACTION8.076TORSIONAL
14D5565X-RAY DIFFRACTION8.076TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0951-2.12270.35291230.309233889
2.1227-2.15180.33291380.29132624100
2.1518-2.18250.33731390.28762628100
2.1825-2.21510.32221390.27932640100
2.2151-2.24970.33061370.2712607100
2.2497-2.28660.27261400.25972666100
2.2866-2.3260.30281360.24782586100
2.326-2.36830.31841410.24892667100
2.3683-2.41390.32191360.24412598100
2.4139-2.46310.30271410.2332671100
2.4631-2.51670.29611370.23662595100
2.5167-2.57520.27841400.22442660100
2.5752-2.63960.29671380.22332621100
2.6396-2.7110.27581400.2272675100
2.711-2.79070.25671360.23462588100
2.7907-2.88080.27131400.23572657100
2.8808-2.98380.26961400.22162654100
2.9838-3.10320.24621390.21842643100
3.1032-3.24440.26261400.20942649100
3.2444-3.41540.24841380.21492624100
3.4154-3.62930.24791400.19532666100
3.6293-3.90930.18921400.17692652100
3.9093-4.30250.1581400.15282658100
4.3025-4.92440.17171410.14392686100
4.9244-6.20170.19111420.15842702100
6.2017-45.1010.1851430.1634273399

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