PDB-9jeo: Chito oligosaccharide deacetylase from vibrio campbellii (VhCOD) ...

ID or keywords:

Entry

Database: PDB / ID: 9jeo

Title

Chito oligosaccharide deacetylase from vibrio campbellii (VhCOD) in complex with N-acetyl-beta-D-glucosaminyl-1,4-D-glucosaminium(GlcNAcGlcN)

Components

NodB homology domain-containing protein

Keywords

HYDROLASE / Vibrio campbellii / Chito oligosaccharide deacetylase / Deacetylase Enzyme / CE4 family member

Function / homology

Function and homology information

hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / extracellular region / metal ion binding
Similarity search - Function

Biological species

Vibrio campbellii ATCC BAA-1116 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.87 Å

Authors

Sirikan, P. / Tamo, F. / Robinson, R.C. / Wipa, S.

Funding support

Thailand, 1items

Citation

Journal: J.Biol.Chem. / Year: 2025
Title: Structure and loop dynamics of a chitooligosaccharide deacetylase from the marine bacterium Vibrio campbellii (harveyi).
Authors: Pongnan, S. / Robinson, R.C. / Lampela, O. / Juffer, A. / Fukamizo, T. / Suginta, W.

History

Deposition	Sep 3, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 10, 2025	Provider: repository / Type: Initial release
Revision 1.1	Oct 22, 2025	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9jeo.cif.gz	687.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9jeo.ent.gz	564.1 KB	Display	PDB format
PDBx/mmJSON format	9jeo.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	9jeo_validation.pdf.gz	4.7 MB	Display	wwPDB validaton report
Full document	9jeo_full_validation.pdf.gz	4.7 MB	Display
Data in XML	9jeo_validation.xml.gz	83.3 KB	Display
Data in CIF	9jeo_validation.cif.gz	118.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/je/9jeo ftp://data.pdbj.org/pub/pdb/validation_reports/je/9jeo	HTTPS FTP

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Related structure data

Related structure data	8yfpC 8yh4C 9jenC 9jt0C 9jt8C 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
Related items in Molecule of the Month	#203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (1)

Deposited unit

A: NodB homology domain-containing protein

B: NodB homology domain-containing protein

C: NodB homology domain-containing protein

D: NodB homology domain-containing protein

hetero molecules

184 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: NodB homology domain-containing protein

hetero molecules

defined by author&software
Evidence: SAXS
46.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: NodB homology domain-containing protein

hetero molecules

defined by author&software
46.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: NodB homology domain-containing protein

hetero molecules

defined by author&software
46 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: NodB homology domain-containing protein

hetero molecules

defined by author&software
46.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	61.128, 118.714, 254.613
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein

NodB homology domain-containing protein

Mass: 45596.020 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Vibrio campbellii ATCC BAA-1116 (bacteria)
Gene: VIBHAR_03626 / Production host:

Escherichia coli M15 (bacteria) / References: UniProt: A7MSF4

#2: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 382.364 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2N][a2122h-1b_1-5_2NCC/3=O]/1-2/a4-b1	WURCS	PDB2Glycan 1.1.0
[][b-D-GlcpN]{[(4+1)][b-D-GlcpNAc]{}}	LINUCS	PDB-CARE

#3: Chemical

ChemComp-ZN / ZINC ION

Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

#4: Chemical

ChemComp-NA / SODIUM ION

Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1718 / Source method: isolated from a natural source / Formula: H₂O

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: 2.53 Å³/Da / Density % sol: 51.43 %
Crystal grow	Temperature: 292.15 K / Method: vapor diffusion, sitting drop Details: 0.2M Sodium formate, 0.1M Bis-Tris propane pH 8.5, 20% W/V PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

NSRRC

/ Beamline: TPS 05A / Wavelength: 0.97622 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 18, 2021

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97622 Å / Relative weight: 1

Reflection

Resolution: 1.87→50 Å / Num. obs: 153525 / % possible obs: 99 % / Redundancy: 13.7 % / CC_1/2: 0.877 / CC star: 0.966 / R_merge(I) obs: 0.122 / R_pim(I) all: 0.047 / R_sym value: 0.128 / Net I/σ(I): 6.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.87-1.9	10.4	0.492	6634	0.913	0.977	0.156	0.517	0.454	86.7
1.9-1.94	11.7	0.442	7541	0.963	0.99	0.132	0.461	0.476	98.6
1.94-1.97	12	0.409	7630	0.968	0.992	0.12	0.427	0.502	99
1.97-2.01	12.4	0.372	7587	0.976	0.994	0.108	0.387	0.533	99.6
2.01-2.06	12.7	0.334	7622	0.977	0.994	0.096	0.348	0.56	99
2.06-2.11	13	0.314	7643	0.983	0.996	0.089	0.326	0.592	99.8
2.11-2.16	13.5	0.299	7626	0.987	0.997	0.083	0.31	0.62	99.4
2.16-2.22	13.8	0.269	7642	0.99	0.998	0.074	0.28	0.66	99.4
2.22-2.28	14.1	0.246	7694	0.992	0.998	0.067	0.256	0.683	99.6
2.28-2.36	14.2	0.225	7674	0.992	0.998	0.061	0.233	0.747	99.7
2.36-2.44	14.3	0.198	7711	0.993	0.998	0.054	0.205	0.805	100
2.44-2.54	14.4	0.181	7684	0.994	0.999	0.049	0.188	0.876	99.7
2.54-2.65	14.5	0.158	7706	0.995	0.999	0.043	0.163	0.978	99.8
2.65-2.79	14.7	0.139	7756	0.996	0.999	0.037	0.144	1.057	99.8
2.79-2.97	14.8	0.117	7730	0.996	0.999	0.031	0.121	1.216	100
2.97-3.2	14.9	0.104	7789	0.997	0.999	0.028	0.108	1.452	100
3.2-3.52	14.9	0.092	7795	0.997	0.999	0.025	0.095	1.834	100
3.52-4.03	14.8	0.077	7870	0.998	0.999	0.021	0.08	2.065	100
4.03-5.07	14.6	0.068	7934	0.998	1	0.018	0.07	2.094	100
5.07-50	14	0.064	8257	0.998	1	0.018	0.067	1.907	99.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.18.2_3874: 000)	refinement
HKL-2000		data scaling
iMOSFLM		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.87→29.68 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.91 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.185	7582	4.94 %
R_work	0.1539	-	-
obs	0.1555	153358	99.3 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.87→29.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12581	0	111	1718	14410

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	13073
X-RAY DIFFRACTION	f_angle_d	0.903	17938
X-RAY DIFFRACTION	f_dihedral_angle_d	15.529	4513
X-RAY DIFFRACTION	f_chiral_restr	0.061	1976
X-RAY DIFFRACTION	f_plane_restr	0.006	2348

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 (%)
1.87-1.89	0.257	203	0.1992	4350	X-RAY DIFFRACTION	89
1.89-1.91	0.2219	252	0.1712	4792	X-RAY DIFFRACTION	98
1.91-1.93	0.2076	240	0.1607	4764	X-RAY DIFFRACTION	100
1.93-1.96	0.2128	237	0.1561	4863	X-RAY DIFFRACTION	100
1.96-1.98	0.1805	250	0.1471	4761	X-RAY DIFFRACTION	98
1.98-2.01	0.1985	258	0.1484	4812	X-RAY DIFFRACTION	100
2.01-2.04	0.1891	237	0.1448	4809	X-RAY DIFFRACTION	99
2.04-2.07	0.1824	248	0.1452	4780	X-RAY DIFFRACTION	100
2.07-2.1	0.1791	268	0.145	4852	X-RAY DIFFRACTION	99
2.1-2.14	0.1967	237	0.145	4795	X-RAY DIFFRACTION	99
2.14-2.17	0.1955	244	0.1482	4884	X-RAY DIFFRACTION	100
2.17-2.21	0.1725	261	0.1482	4782	X-RAY DIFFRACTION	99
2.21-2.26	0.2105	242	0.1483	4886	X-RAY DIFFRACTION	100
2.26-2.3	0.1751	285	0.1475	4786	X-RAY DIFFRACTION	99
2.3-2.35	0.1797	243	0.1474	4869	X-RAY DIFFRACTION	100
2.35-2.41	0.1985	231	0.1529	4828	X-RAY DIFFRACTION	100
2.41-2.47	0.2111	250	0.1564	4908	X-RAY DIFFRACTION	100
2.47-2.53	0.2011	246	0.1612	4866	X-RAY DIFFRACTION	100
2.53-2.61	0.1941	275	0.1586	4815	X-RAY DIFFRACTION	100
2.61-2.69	0.2078	252	0.162	4912	X-RAY DIFFRACTION	100
2.69-2.79	0.1982	262	0.1682	4886	X-RAY DIFFRACTION	100
2.79-2.9	0.2059	216	0.1674	4946	X-RAY DIFFRACTION	100
2.9-3.03	0.2083	278	0.1739	4867	X-RAY DIFFRACTION	100
3.03-3.19	0.1948	243	0.1728	4931	X-RAY DIFFRACTION	100
3.19-3.39	0.1943	301	0.167	4880	X-RAY DIFFRACTION	100
3.39-3.65	0.1697	260	0.1505	4912	X-RAY DIFFRACTION	100
3.65-4.02	0.1636	239	0.1386	4985	X-RAY DIFFRACTION	100
4.02-4.6	0.1532	291	0.1247	4971	X-RAY DIFFRACTION	100
4.6-5.79	0.1675	261	0.1477	5034	X-RAY DIFFRACTION	100
5.79-29.68	0.1567	272	0.1632	5250	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Origin x: 29.277 Å / Origin y: -13.4046 Å / Origin z: -34.7973 Å

	11	12	13	21	22	23	31	32	33
T	0.109 Å²	-0.0035 Å²	0.016 Å²	-	0.1132 Å²	-0.0035 Å²	-	-	0.121 Å²
L	0.0774 °²	-0.0516 °²	-0.0404 °²	-	0.1422 °²	0.1008 °²	-	-	0.0914 °²
S	-0.0147 Å °	-0.0167 Å °	0.0021 Å °	0.0116 Å °	0.0187 Å °	-0.0264 Å °	0.031 Å °	0.0145 Å °	0 Å °

Refinement TLS group

Selection details: all

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