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- PDB-8bqc: CjCel5B endo-glucanase -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8bqc
TitleCjCel5B endo-glucanase
ComponentsEndoglucanase
KeywordsHYDROLASE / Carbohydrate / cellulase
Function / homology
Function and homology information


cellulose binding / cellulase / cellulase activity / cellulose catabolic process
Similarity search - Function
Carbohydrate binding module family 10 / CBM10 superfamily / Cellulose or protein binding domain / Cellulose or protein binding domain / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II ...Carbohydrate binding module family 10 / CBM10 superfamily / Cellulose or protein binding domain / Cellulose or protein binding domain / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesCellvibrio japonicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsMcGregor, N.G.S. / Davies, G.J.
Funding support United Kingdom, European Union, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001162/1 United Kingdom
European Research Council (ERC)2020-SyG-951231European Union
CitationJournal: Acs Cent.Sci. / Year: 2023
Title: A Multiplexing Activity-Based Protein-Profiling Platform for Dissection of a Native Bacterial Xyloglucan-Degrading System.
Authors: McGregor, N.G.S. / de Boer, C. / Foucart, Q.P.O. / Beenakker, T. / Offen, W.A. / Codee, J.D.C. / Willems, L.I. / Overkleeft, H.S. / Davies, G.J.
History
DepositionNov 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase


Theoretical massNumber of molelcules
Total (without water)33,5191
Polymers33,5191
Non-polymers00
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.339, 53.481, 63.224
Angle α, β, γ (deg.)90.000, 109.746, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endoglucanase


Mass: 33519.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellvibrio japonicus (bacteria) / Gene: cel5B, CJA_2983 / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B3PCS3, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.15 Å3/Da / Density % sol: 42.85 % / Description: Plate clusters
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PS: 10 mg/mL in 5 mM Na-MOPS pH 7.5, 25 mM NaCl 1:1 with WS containing 0.2 M LiCl, 20% PEG3350
PH range: 5.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.57→42.05 Å / Num. obs: 35379 / % possible obs: 88.5 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.062 / Rrim(I) all: 0.16 / Net I/σ(I): 7.7
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 6.9 % / Rmerge(I) obs: 2.693 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1983 / CC1/2: 0.32 / Rpim(I) all: 1.093 / Rrim(I) all: 2.91 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1tvn

1tvn


Resolution: 1.57→42.05 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.909 / SU ML: 0.093 / Cross valid method: FREE R-VALUE / ESU R: 0.102 / ESU R Free: 0.104
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 1760 4.981 %0.05
Rwork0.1839 33573 --
all0.186 ---
obs-35333 88.374 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.864 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å2-0 Å20.257 Å2
2--0.404 Å2-0 Å2
3---0.629 Å2
Refinement stepCycle: LAST / Resolution: 1.57→42.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 0 0 247 2537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0112395
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162076
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.6283286
X-RAY DIFFRACTIONr_angle_other_deg0.4791.5574831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2975311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.04758
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40610352
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.73110114
X-RAY DIFFRACTIONr_chiral_restr0.0610.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022797
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02495
X-RAY DIFFRACTIONr_nbd_refined0.2180.2475
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.21874
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21176
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21209
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2180
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1150.210
X-RAY DIFFRACTIONr_nbd_other0.1170.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0790.215
X-RAY DIFFRACTIONr_mcbond_it1.1791.9241205
X-RAY DIFFRACTIONr_mcbond_other1.1791.9241205
X-RAY DIFFRACTIONr_mcangle_it1.6512.881508
X-RAY DIFFRACTIONr_mcangle_other1.6522.8831509
X-RAY DIFFRACTIONr_scbond_it1.7432.0621190
X-RAY DIFFRACTIONr_scbond_other1.7272.0621190
X-RAY DIFFRACTIONr_scangle_it2.5843.041771
X-RAY DIFFRACTIONr_scangle_other2.5833.0421772
X-RAY DIFFRACTIONr_lrange_it3.50626.3462873
X-RAY DIFFRACTIONr_lrange_other3.40125.5452818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.610.3421600.3252731X-RAY DIFFRACTION98.7363
1.61-1.6540.3031590.3082678X-RAY DIFFRACTION99.789
1.654-1.7010.281530.292654X-RAY DIFFRACTION99.9644
1.701-1.7540.2731070.272591X-RAY DIFFRACTION99.963
1.754-1.8110.2761310.2432495X-RAY DIFFRACTION99.9239
1.811-1.8750.2751110.2332407X-RAY DIFFRACTION99.9206
1.875-1.9450.353370.355504X-RAY DIFFRACTION21.8498
1.945-2.0240.2661130.2111893X-RAY DIFFRACTION85.5437
2.024-2.1140.313680.2051374X-RAY DIFFRACTION63.4404
2.114-2.2170.205720.1812088X-RAY DIFFRACTION99.9537
2.217-2.3370.253660.1711384X-RAY DIFFRACTION69.9469
2.337-2.4780.2191120.1681830X-RAY DIFFRACTION99.8971
2.478-2.6480.28760.1611765X-RAY DIFFRACTION99.8915
2.648-2.860.184830.1511325X-RAY DIFFRACTION81.4344
2.86-3.1310.214760.1671492X-RAY DIFFRACTION100
3.131-3.4980.169690.1761133X-RAY DIFFRACTION82.7254
3.498-4.0350.215640.15899X-RAY DIFFRACTION76.7331
4.035-4.930.199440.1241046X-RAY DIFFRACTION100
4.93-6.9250.152400.137812X-RAY DIFFRACTION100
6.925-42.050.123190.134473X-RAY DIFFRACTION100

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