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- PDB-8bqb: CjCel5C endo-glucanase bound to CB396 covalent inhibitor -

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Basic information

Entry
Database: PDB / ID: 8bqb
TitleCjCel5C endo-glucanase bound to CB396 covalent inhibitor
ComponentsCellulase, putative, cel5C
KeywordsHYDROLASE / Carbohydrate / inhibitor / covalent / cellulase
Function / homology: / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / cellulase / cellulase activity / Glycoside hydrolase superfamily / beta-D-glucopyranose / Chem-YLL / Cellulase, putative, cel5C
Function and homology information
Biological speciesCellvibrio japonicus Ueda107 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 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 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

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Assembly

Deposited unit
A: Cellulase, putative, cel5C
B: Cellulase, putative, cel5C
C: Cellulase, putative, cel5C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,7299
Polymers120,6063
Non-polymers1,1236
Water39622
1
A: Cellulase, putative, cel5C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5763
Polymers40,2021
Non-polymers3742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellulase, putative, cel5C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5763
Polymers40,2021
Non-polymers3742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cellulase, putative, cel5C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5763
Polymers40,2021
Non-polymers3742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.441, 176.159, 115.701
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A

NCS domain segments:

Beg auth comp-ID: SER / Beg label comp-ID: SER / Auth asym-ID: A / Label asym-ID: A

Dom-IDComponent-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth seq-IDLabel seq-ID
111GLUGLU9 - 3369 - 336
211GLUGLU9 - 3369 - 336
322GLUGLU9 - 3369 - 336
422GLUGLU9 - 3369 - 336
533ASNASN9 - 3379 - 337
633ASNASN9 - 3379 - 337

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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Components

#1: Protein Cellulase, putative, cel5C


Mass: 40201.941 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellvibrio japonicus Ueda107 (bacteria)
Gene: cel5C / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B3PF55
#2: 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.: 3 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.67 Å3/Da / Density % sol: 53.95 % / Description: Plate clusters
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PS: 12 mg/mL in 20 mM MOPS 7.5, 50 mM NaCl 1.5:1 with WS containing 30% MPD, 6% PEG4000, with seeding from higher [PEG] crystals. Soaked with ligand overnight.
PH range: 7.5-8

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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: 2.7→102.72 Å / Num. obs: 33580 / % possible obs: 93.8 % / Observed criterion σ(I): 1 / Redundancy: 11.6 % / CC1/2: 0.989 / Rmerge(I) obs: 0.352 / Rpim(I) all: 0.108 / Rrim(I) all: 0.369 / Net I/σ(I): 6.8
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 10.6 % / Rmerge(I) obs: 2.98 / Num. unique obs: 1744 / CC1/2: 0.377 / Rpim(I) all: 0.948 / Rrim(I) all: 3.131 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
autoPROCdata reduction
autoPROCdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HTY

4hty


Resolution: 2.701→102.72 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.933 / SU B: 14.439 / SU ML: 0.268 / Cross valid method: FREE R-VALUE / ESU R Free: 0.319
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 1688 5.043 %0.05
Rwork0.1851 31785 --
all0.187 ---
obs-33473 93.492 %-
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: 47.418 Å2
Baniso -1Baniso -2Baniso -3
1--3.298 Å20 Å2-0 Å2
2--1.679 Å20 Å2
3---1.618 Å2
Refinement stepCycle: LAST / Resolution: 2.701→102.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8043 0 69 22 8134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0128378
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167193
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.64211396
X-RAY DIFFRACTIONr_angle_other_deg0.4471.56316750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9145986
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.177551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.27101279
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.09510435
X-RAY DIFFRACTIONr_chiral_restr0.0590.21158
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029602
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021850
X-RAY DIFFRACTIONr_nbd_refined0.2190.21707
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.26811
X-RAY DIFFRACTIONr_nbtor_refined0.1840.24127
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.24176
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2142
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1760.226
X-RAY DIFFRACTIONr_nbd_other0.220.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.260.27
X-RAY DIFFRACTIONr_mcbond_it3.8554.8563953
X-RAY DIFFRACTIONr_mcbond_other3.8544.8573953
X-RAY DIFFRACTIONr_mcangle_it5.7087.2624936
X-RAY DIFFRACTIONr_mcangle_other5.7087.2624937
X-RAY DIFFRACTIONr_scbond_it3.6544.9794425
X-RAY DIFFRACTIONr_scbond_other3.6544.9794426
X-RAY DIFFRACTIONr_scangle_it5.3957.3746460
X-RAY DIFFRACTIONr_scangle_other5.3957.3746461
X-RAY DIFFRACTIONr_lrange_it7.08458.2669646
X-RAY DIFFRACTIONr_lrange_other7.08358.2669647
X-RAY DIFFRACTIONr_ncsr_local_group_10.060.0511605
X-RAY DIFFRACTIONr_ncsr_local_group_20.0550.0511678
X-RAY DIFFRACTIONr_ncsr_local_group_30.0610.0511637
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.059670.0501
12AX-RAY DIFFRACTIONLocal ncs0.059670.0501
23AX-RAY DIFFRACTIONLocal ncs0.055230.0501
24AX-RAY DIFFRACTIONLocal ncs0.055230.0501
35AX-RAY DIFFRACTIONLocal ncs0.061170.0501
36AX-RAY DIFFRACTIONLocal ncs0.061170.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.701-2.7710.3791190.3232383X-RAY DIFFRACTION95.8988
2.771-2.8470.3291170.2922424X-RAY DIFFRACTION99.9213
2.847-2.9290.321460.2782349X-RAY DIFFRACTION99.9599
2.929-3.0190.2961150.2642277X-RAY DIFFRACTION99.8747
3.019-3.1180.3011030.232238X-RAY DIFFRACTION100
3.118-3.2280.2581090.2292151X-RAY DIFFRACTION99.9558
3.228-3.3490.2781210.2232052X-RAY DIFFRACTION100
3.349-3.4860.273510.216984X-RAY DIFFRACTION49.0289
3.486-3.6410.256950.1911925X-RAY DIFFRACTION99.8517
3.641-3.8180.216810.1731290X-RAY DIFFRACTION70.4522
3.818-4.0240.203580.1541236X-RAY DIFFRACTION70.1735
4.024-4.2680.191030.1371659X-RAY DIFFRACTION100
4.268-4.5620.171860.1271557X-RAY DIFFRACTION100
4.562-4.9270.189770.1341472X-RAY DIFFRACTION100
4.927-5.3960.153800.1291330X-RAY DIFFRACTION100
5.396-6.0310.193640.141242X-RAY DIFFRACTION100
6.031-6.960.208610.1521085X-RAY DIFFRACTION100
6.96-8.5140.169410.13945X-RAY DIFFRACTION100
8.514-120.141380.114741X-RAY DIFFRACTION100
12-102.720.166230.3445X-RAY DIFFRACTION99.5745

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