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- PDB-8bn7: CjCel5C endo-glucanase -

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Basic information

Entry
Database: PDB / ID: 8bn7
TitleCjCel5C endo-glucanase
ComponentsCellulase, putative, cel5C
KeywordsHYDROLASE / Carbohydrate / inhibitor / covalent / cellulase
Function / homologycellulase / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / cellulase activity / polysaccharide catabolic process / Glycoside hydrolase superfamily / Cellulase, putative, cel5C
Function and homology information
Biological speciesCellvibrio japonicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.182 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 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 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
CCC: Cellulase, putative, cel5C
AAA: Cellulase, putative, cel5C
BBB: Cellulase, putative, cel5C


Theoretical massNumber of molelcules
Total (without water)120,6063
Polymers120,6063
Non-polymers00
Water3,243180
1
CCC: Cellulase, putative, cel5C


Theoretical massNumber of molelcules
Total (without water)40,2021
Polymers40,2021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
AAA: Cellulase, putative, cel5C


Theoretical massNumber of molelcules
Total (without water)40,2021
Polymers40,2021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
BBB: Cellulase, putative, cel5C


Theoretical massNumber of molelcules
Total (without water)40,2021
Polymers40,2021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.332, 175.709, 115.283
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
11CCC
21AAA
32CCC
42BBB
53AAA
63BBB

NCS domain segments:

End auth comp-ID: ASN / End label comp-ID: ASN

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRCCCA8 - 3378 - 337
211THRTHRAAAB8 - 3378 - 337
322GLNGLNCCCA6 - 3376 - 337
422GLNGLNBBBC6 - 3376 - 337
533THRTHRAAAB8 - 3378 - 337
633THRTHRBBBC8 - 3378 - 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 (bacteria) / Strain: Ueda107 / Gene: cel5C, CJA_3369 / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B3PF55, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.65 Å3/Da / Density % sol: 53.62 % / 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.
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: Mar 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.18→102.57 Å / Num. obs: 60843 / % possible obs: 91 % / Observed criterion σ(I): 1 / Redundancy: 13.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.264 / Rpim(I) all: 0.074 / Rrim(I) all: 0.274 / Net I/σ(I): 8.3
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 13.9 % / Rmerge(I) obs: 3.784 / Num. unique obs: 3330 / CC1/2: 0.351 / Rpim(I) all: 1.044 / Rrim(I) all: 3.926 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
BUCCANEERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HTY

4hty


Resolution: 2.182→102.57 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.002 / SU ML: 0.165 / Cross valid method: FREE R-VALUE / ESU R: 0.252 / ESU R Free: 0.197
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 2991 4.938 %0.05
Rwork0.1874 57576 --
all0.189 ---
obs-60567 90.555 %-
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: 39.267 Å2
Baniso -1Baniso -2Baniso -3
1--0.783 Å2-0 Å2-0 Å2
2--1.5 Å2-0 Å2
3----0.717 Å2
Refinement stepCycle: LAST / Resolution: 2.182→102.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8122 0 0 180 8302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138410
X-RAY DIFFRACTIONr_bond_other_d0.0010.0187574
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.63611442
X-RAY DIFFRACTIONr_angle_other_deg1.3111.58217364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.41751001
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95222.209498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39151310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4231555
X-RAY DIFFRACTIONr_chiral_restr0.0830.21033
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029728
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022194
X-RAY DIFFRACTIONr_nbd_refined0.2030.21629
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.27108
X-RAY DIFFRACTIONr_nbtor_refined0.1740.24068
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.23841
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2233
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1480.222
X-RAY DIFFRACTIONr_nbd_other0.1910.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2140.210
X-RAY DIFFRACTIONr_mcbond_it3.764.0383995
X-RAY DIFFRACTIONr_mcbond_other3.7394.0373994
X-RAY DIFFRACTIONr_mcangle_it5.2956.044990
X-RAY DIFFRACTIONr_mcangle_other5.2966.0424991
X-RAY DIFFRACTIONr_scbond_it4.0574.264415
X-RAY DIFFRACTIONr_scbond_other4.0574.2624416
X-RAY DIFFRACTIONr_scangle_it5.7986.2576449
X-RAY DIFFRACTIONr_scangle_other5.7996.2576449
X-RAY DIFFRACTIONr_lrange_it7.25244.69614
X-RAY DIFFRACTIONr_lrange_other7.23944.5539593
X-RAY DIFFRACTIONr_ncsr_local_group_10.060.0511777
X-RAY DIFFRACTIONr_ncsr_local_group_20.0640.0511769
X-RAY DIFFRACTIONr_ncsr_local_group_30.0560.0511799
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11CCCX-RAY DIFFRACTIONLocal ncs0.059990.05009
12AAAX-RAY DIFFRACTIONLocal ncs0.059990.05009
23CCCX-RAY DIFFRACTIONLocal ncs0.063510.05009
24BBBX-RAY DIFFRACTIONLocal ncs0.063510.05009
35AAAX-RAY DIFFRACTIONLocal ncs0.055520.05009
36BBBX-RAY DIFFRACTIONLocal ncs0.055520.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.182-2.2380.3232100.3243999X-RAY DIFFRACTION85.8279
2.238-2.30.3131180.2922392X-RAY DIFFRACTION52.368
2.3-2.3660.2882380.2774367X-RAY DIFFRACTION99.8482
2.366-2.4390.2782310.2614296X-RAY DIFFRACTION99.8897
2.439-2.5190.3011960.2474193X-RAY DIFFRACTION99.9772
2.519-2.6080.2791980.2194006X-RAY DIFFRACTION99.9762
2.608-2.7060.2711600.2172585X-RAY DIFFRACTION66.8046
2.706-2.8160.2331870.1933740X-RAY DIFFRACTION100
2.816-2.9420.2811980.23594X-RAY DIFFRACTION100
2.942-3.0850.2481690.1883456X-RAY DIFFRACTION100
3.085-3.2520.2231720.183251X-RAY DIFFRACTION100
3.252-3.4490.2361250.1972578X-RAY DIFFRACTION82.0832
3.449-3.6870.2661180.1982007X-RAY DIFFRACTION69.0159
3.687-3.9820.2111330.1732337X-RAY DIFFRACTION85.6449
3.982-4.3610.1671500.1382492X-RAY DIFFRACTION100
4.361-4.8750.1441160.1222306X-RAY DIFFRACTION100
4.875-5.6280.154960.1342033X-RAY DIFFRACTION100
5.628-6.8880.207740.1671760X-RAY DIFFRACTION100
6.888-9.7240.184610.1461384X-RAY DIFFRACTION100
9.724-102.570.252410.233800X-RAY DIFFRACTION99.6445

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