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

ID or keywords:

Entry

Database: PDB / ID: 8oz1

Title

CjCel5D endo-xyloglucanase bounc to CB665 covalent inhibitor

Components

Cellulase, putative, cel5D

Keywords

HYDROLASE / Carbohydrate / inhibitor / covalent / xyloglucanase

Function / homology

Function and homology information

cellulase / cellulase activity / beta-glucosidase activity / cellulose catabolic process / cell surface / extracellular region
Similarity search - Function

Biological species

Cellvibrio japonicus Ueda107 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.3 Å

Authors

McGregor, N.G.S. / de Boer, C. / Overkleeft, H.S. / Davies, G.J.

Funding support

United Kingdom, European Union, 2items

Citation

Journal: 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

Deposition	May 6, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 28, 2024	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	Group: 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
Revision 1.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8oz1.cif.gz	411.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8oz1.ent.gz	255.6 KB	Display	PDB format
PDBx/mmJSON format	8oz1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8oz1_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	8oz1_full_validation.pdf.gz	1.7 MB	Display
Data in XML	8oz1_validation.xml.gz	19.2 KB	Display
Data in CIF	8oz1_validation.cif.gz	30.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oz/8oz1 ftp://data.pdbj.org/pub/pdb/validation_reports/oz/8oz1	HTTPS FTP

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Related structure data

Related structure data	8bn7C 8bqaC 8bqbC 8bqcC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Cellulase, putative, cel5D

hetero molecules

45.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

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 number	4
Space group name H-M	P12₁1

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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

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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 interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44.02 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 2, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.3→51.78 Å / Num. obs: 91883 / % possible obs: 97.2 % / Redundancy: 11.3 % / CC_1/2: 0.997 / R_merge(I) obs: 0.149 / R_pim(I) all: 0.044 / Net I/σ(I): 8.3
Reflection shell	Resolution: 1.3→1.32 Å / Redundancy: 5 % / R_merge(I) obs: 1.113 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3497 / CC_1/2: 0.577 / R_pim(I) all: 0.542 / % possible all: 75.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0411	refinement
autoPROC		data reduction
autoPROC		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.3→51.78 Å / Cor.coef. F_o:F_c: 0.979 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1691	4537	4.939 %	Random selection
R_work	0.1344	87325	-	-
all	0.136	-	-	-
obs	-	91862	97.103 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 16.393 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.888 Å²	0 Å²	0.919 Å²
2-	-	-1.644 Å²	0 Å²
3-	-	-	0.46 Å²

Refinement step

Cycle: LAST / Resolution: 1.3→51.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2954	0	38	424	3416

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.011	3115
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2824
X-RAY DIFFRACTION	r_angle_refined_deg	1.741	1.644	4248
X-RAY DIFFRACTION	r_angle_other_deg	0.733	1.569	6487
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.916	5	386
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.304	5	15
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.464	10	490
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.515	10	161
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	461
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	3713
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	763
X-RAY DIFFRACTION	r_nbd_refined	0.271	0.2	618
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.218	0.2	2663
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.2	1555
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	1564
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.147	0.2	304
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.118	0.2	5
X-RAY DIFFRACTION	r_nbd_other	0.165	0.2	25
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.282	0.2	27
X-RAY DIFFRACTION	r_mcbond_it	2.084	1.663	1505
X-RAY DIFFRACTION	r_mcbond_other	2.084	1.663	1505
X-RAY DIFFRACTION	r_mcangle_it	2.61	3.002	1883
X-RAY DIFFRACTION	r_mcangle_other	2.622	3.006	1884
X-RAY DIFFRACTION	r_scbond_it	2.503	1.884	1610
X-RAY DIFFRACTION	r_scbond_other	2.503	1.884	1611
X-RAY DIFFRACTION	r_scangle_it	3.182	3.366	2358
X-RAY DIFFRACTION	r_scangle_other	3.182	3.366	2359
X-RAY DIFFRACTION	r_lrange_it	3.931	18.631	3767
X-RAY DIFFRACTION	r_lrange_other	3.689	16.74	3621
X-RAY DIFFRACTION	r_rigid_bond_restr	4.329	3	5939

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.3-1.334	0.278	273	0.261	5089	X-RAY DIFFRACTION	77.0181
1.334-1.37	0.246	294	0.229	5677	X-RAY DIFFRACTION	87.8993
1.37-1.41	0.22	295	0.203	6070	X-RAY DIFFRACTION	96.2498
1.41-1.453	0.203	315	0.168	6022	X-RAY DIFFRACTION	99.124
1.453-1.501	0.182	317	0.134	5922	X-RAY DIFFRACTION	99.8719
1.501-1.554	0.167	272	0.12	5737	X-RAY DIFFRACTION	100
1.554-1.612	0.155	311	0.104	5495	X-RAY DIFFRACTION	99.9828
1.612-1.678	0.147	264	0.106	5313	X-RAY DIFFRACTION	100
1.678-1.752	0.172	256	0.106	5114	X-RAY DIFFRACTION	100
1.752-1.838	0.16	247	0.1	4889	X-RAY DIFFRACTION	100
1.838-1.937	0.155	249	0.117	4652	X-RAY DIFFRACTION	100
1.937-2.055	0.168	254	0.125	4353	X-RAY DIFFRACTION	100
2.055-2.196	0.171	225	0.124	4121	X-RAY DIFFRACTION	100
2.196-2.372	0.152	207	0.119	3847	X-RAY DIFFRACTION	100
2.372-2.598	0.154	199	0.107	3540	X-RAY DIFFRACTION	100
2.598-2.903	0.139	160	0.117	3235	X-RAY DIFFRACTION	100
2.903-3.351	0.157	142	0.136	2847	X-RAY DIFFRACTION	100
3.351-4.099	0.152	123	0.139	2427	X-RAY DIFFRACTION	100
4.099-5.779	0.187	79	0.16	1897	X-RAY DIFFRACTION	100
5.779-51.78	0.24	55	0.188	1078	X-RAY DIFFRACTION	99.5606

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Protein / Sugars , 2 types, 2 molecules A

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Non-polymers , 4 types, 426 molecules

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