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- PDB-8oz1: CjCel5D endo-xyloglucanase bounc to CB665 covalent inhibitor -

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Basic information

Entry
Database: PDB / ID: 8oz1
TitleCjCel5D endo-xyloglucanase bounc to CB665 covalent inhibitor
ComponentsCellulase, putative, cel5D
KeywordsHYDROLASE / Carbohydrate / inhibitor / covalent / xyloglucanase
Function / homology
Function and homology information


glucan catabolic process / cellulase / cellulase activity / beta-glucosidase activity / cell surface / extracellular region
Similarity search - Function
Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily
Similarity search - Domain/homology
BORIC ACID / Chem-RBH / alpha-D-xylopyranose / Chem-YLL / Cellulase, putative, cel5D
Similarity search - Component
Biological speciesCellvibrio japonicus Ueda107 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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
DepositionMay 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellulase, putative, cel5D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1985
Polymers44,3961
Non-polymers8024
Water7,620423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint3 kcal/mol
Surface area14140 Å2
Unit cell
Length a, b, c (Å)52.360, 57.132, 65.951
Angle α, β, γ (deg.)90.000, 98.528, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Cellulase, putative, cel5D


Mass: 44396.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellvibrio japonicus Ueda107 (bacteria)
Gene: cel5D, CJA_3010 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B3PD52, cellulase
#5: 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

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Non-polymers , 4 types, 426 molecules

#2: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20 mg/mL enzyme in 50 mM NaPi pH 7.0 mixed 1:1 with 0.1 M MIB buffer, pH 4, 25% PEG1500

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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: Dec 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.3→51.78 Å / Num. obs: 91883 / % possible obs: 97.2 % / Redundancy: 11.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.044 / Net I/σ(I): 8.3
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 5 % / Rmerge(I) obs: 1.113 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3497 / CC1/2: 0.577 / Rpim(I) all: 0.542 / % possible all: 75.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→51.78 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.204 / SU ML: 0.039 / Cross valid method: FREE R-VALUE / ESU R: 0.045 / ESU R Free: 0.045
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1691 4537 4.939 %Random selection
Rwork0.1344 87325 --
all0.136 ---
obs-91862 97.103 %-
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: 16.393 Å2
Baniso -1Baniso -2Baniso -3
1-0.888 Å20 Å20.919 Å2
2---1.644 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.3→51.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 0 38 424 3416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0113115
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162824
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.6444248
X-RAY DIFFRACTIONr_angle_other_deg0.7331.5696487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9165386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.304515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46410490
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.51510161
X-RAY DIFFRACTIONr_chiral_restr0.0930.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023713
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02763
X-RAY DIFFRACTIONr_nbd_refined0.2710.2618
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2180.22663
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21555
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21564
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2304
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1180.25
X-RAY DIFFRACTIONr_nbd_other0.1650.225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2820.227
X-RAY DIFFRACTIONr_mcbond_it2.0841.6631505
X-RAY DIFFRACTIONr_mcbond_other2.0841.6631505
X-RAY DIFFRACTIONr_mcangle_it2.613.0021883
X-RAY DIFFRACTIONr_mcangle_other2.6223.0061884
X-RAY DIFFRACTIONr_scbond_it2.5031.8841610
X-RAY DIFFRACTIONr_scbond_other2.5031.8841611
X-RAY DIFFRACTIONr_scangle_it3.1823.3662358
X-RAY DIFFRACTIONr_scangle_other3.1823.3662359
X-RAY DIFFRACTIONr_lrange_it3.93118.6313767
X-RAY DIFFRACTIONr_lrange_other3.68916.743621
X-RAY DIFFRACTIONr_rigid_bond_restr4.32935939
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.3340.2782730.2615089X-RAY DIFFRACTION77.0181
1.334-1.370.2462940.2295677X-RAY DIFFRACTION87.8993
1.37-1.410.222950.2036070X-RAY DIFFRACTION96.2498
1.41-1.4530.2033150.1686022X-RAY DIFFRACTION99.124
1.453-1.5010.1823170.1345922X-RAY DIFFRACTION99.8719
1.501-1.5540.1672720.125737X-RAY DIFFRACTION100
1.554-1.6120.1553110.1045495X-RAY DIFFRACTION99.9828
1.612-1.6780.1472640.1065313X-RAY DIFFRACTION100
1.678-1.7520.1722560.1065114X-RAY DIFFRACTION100
1.752-1.8380.162470.14889X-RAY DIFFRACTION100
1.838-1.9370.1552490.1174652X-RAY DIFFRACTION100
1.937-2.0550.1682540.1254353X-RAY DIFFRACTION100
2.055-2.1960.1712250.1244121X-RAY DIFFRACTION100
2.196-2.3720.1522070.1193847X-RAY DIFFRACTION100
2.372-2.5980.1541990.1073540X-RAY DIFFRACTION100
2.598-2.9030.1391600.1173235X-RAY DIFFRACTION100
2.903-3.3510.1571420.1362847X-RAY DIFFRACTION100
3.351-4.0990.1521230.1392427X-RAY DIFFRACTION100
4.099-5.7790.187790.161897X-RAY DIFFRACTION100
5.779-51.780.24550.1881078X-RAY DIFFRACTION99.5606

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