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- PDB-8bqa: CjCel5B endo-glucanase bound to CB665 covalent inhibitor -

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Basic information

Entry
Database: PDB / ID: 8bqa
TitleCjCel5B endo-glucanase bound to CB665 covalent inhibitor
ComponentsEndoglucanase
KeywordsHYDROLASE / Carbohydrate / inhibitor / covalent / 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
Chem-RBH / alpha-D-xylopyranose / Chem-YLL / Endoglucanase
Similarity search - Component
Biological speciesCellvibrio japonicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsMcGregor, N.G.S. / de Boer, C. / Overkleeft, H.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 2.0Jan 24, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id
Revision 2.1Jun 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
AAA: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2594
Polymers33,5191
Non-polymers7403
Water3,549197
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)45.490, 51.830, 64.560
Angle α, β, γ (deg.)90.000, 110.427, 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) / References: UniProt: B3PCS3, cellulase
#2: Chemical ChemComp-RBH / ~{N}-[(2~{S},3~{S},4~{S},5~{R})-2-(hydroxymethyl)-4,5,6-tris(oxidanyl)oxan-3-yl]-2-oxidanyl-ethanamide


Mass: 395.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H27N4O9 / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-XYS / alpha-D-xylopyranose / alpha-D-xylose / D-xylose / xylose / XYLOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DXylpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-xylopyranoseCOMMON NAMEGMML 1.0
a-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-YLL / (1R,2S,3S,4S,5R,6R)-6-(HYDROXYMETHYL)CYCLOHEXANE-1,2,3,4,5-PENTOL


Mass: 194.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.19 % / 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 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.67→32.92 Å / Num. obs: 32027 / % possible obs: 97.5 % / Observed criterion σ(I): 1 / Redundancy: 6.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.08 / Rrim(I) all: 0.198 / Net I/σ(I): 6.6
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 6.3 % / Rmerge(I) obs: 2.556 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1580 / CC1/2: 0.341 / Rpim(I) all: 1.095 / Rrim(I) all: 2.784 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1tvn

1tvn


Resolution: 1.67→32.92 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.219 / SU ML: 0.099 / Cross valid method: FREE R-VALUE / ESU R: 0.112 / ESU R Free: 0.112
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 1561 4.876 %0.05
Rwork0.1857 30450 --
all0.188 ---
obs-32011 97.467 %-
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: 23.653 Å2
Baniso -1Baniso -2Baniso -3
1-0.774 Å20 Å21.597 Å2
2---1.93 Å20 Å2
3----0.027 Å2
Refinement stepCycle: LAST / Resolution: 1.67→32.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2293 0 36 197 2526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132393
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182147
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.6273268
X-RAY DIFFRACTIONr_angle_other_deg1.4351.5814918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2335297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09824.454119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33115341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.526156
X-RAY DIFFRACTIONr_chiral_restr0.0720.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022795
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02577
X-RAY DIFFRACTIONr_nbd_refined0.2070.2527
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.22086
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21195
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21086
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2187
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1790.28
X-RAY DIFFRACTIONr_nbd_other0.1430.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1470.216
X-RAY DIFFRACTIONr_mcbond_it1.5942.4161191
X-RAY DIFFRACTIONr_mcbond_other1.5932.4131190
X-RAY DIFFRACTIONr_mcangle_it2.0883.6181487
X-RAY DIFFRACTIONr_mcangle_other2.0873.6211488
X-RAY DIFFRACTIONr_scbond_it2.1382.5751202
X-RAY DIFFRACTIONr_scbond_other2.1372.5751203
X-RAY DIFFRACTIONr_scangle_it3.0353.81781
X-RAY DIFFRACTIONr_scangle_other3.0343.81782
X-RAY DIFFRACTIONr_lrange_it3.8329.2422883
X-RAY DIFFRACTIONr_lrange_other3.77228.9852845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.7130.361940.3422216X-RAY DIFFRACTION96.4107
1.713-1.760.3221160.3072175X-RAY DIFFRACTION96.3415
1.76-1.8110.3311290.3022059X-RAY DIFFRACTION96.3877
1.811-1.8670.338950.2742047X-RAY DIFFRACTION96.9231
1.867-1.9280.2981280.2771968X-RAY DIFFRACTION96.8577
1.928-1.9960.255760.2241941X-RAY DIFFRACTION97.0645
1.996-2.0710.2441120.2011872X-RAY DIFFRACTION96.875
2.071-2.1550.216900.1871793X-RAY DIFFRACTION97.5142
2.155-2.2510.226970.1861691X-RAY DIFFRACTION97.0684
2.251-2.3610.23870.1721659X-RAY DIFFRACTION97.5964
2.361-2.4880.226790.1641570X-RAY DIFFRACTION97.574
2.488-2.6390.24640.1631499X-RAY DIFFRACTION98.2401
2.639-2.8210.204690.1661435X-RAY DIFFRACTION98.3649
2.821-3.0460.241800.1651319X-RAY DIFFRACTION98.6601
3.046-3.3360.239420.1871231X-RAY DIFFRACTION98.8354
3.336-3.7290.23610.1681118X-RAY DIFFRACTION99.0756
3.729-4.3030.155370.1461002X-RAY DIFFRACTION99.2359
4.303-5.2630.151540.143818X-RAY DIFFRACTION98.8662
5.263-7.4150.139260.145660X-RAY DIFFRACTION99.2764
7.415-32.920.199250.148377X-RAY DIFFRACTION97.8102

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