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- PDB-9jt0: Chito oligosaccharide deacetylase from vibrio campbellii (VhCOD) ... -

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Basic information

Entry
Database: PDB / ID: 9jt0
TitleChito oligosaccharide deacetylase from vibrio campbellii (VhCOD) complex with Chitobiose
ComponentsNodB homology domain-containing protein
KeywordsHYDROLASE / 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
: / NodB homology domain profile. / Carbohydrate-binding module family 5/12 / NodB homology domain / Polysaccharide deacetylase / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycoside hydrolase/deacetylase, beta/alpha-barrel
Similarity search - Domain/homology
NodB homology domain-containing protein
Similarity search - Component
Biological speciesVibrio campbellii ATCC BAA-1116 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSirikan, P. / Tamo, F. / Robinson, R.C. / Wipa, S.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Vidyasirimedhi Institute of Science and Technology (VISTEC) Thailand
CitationJournal: 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
DepositionOct 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NodB homology domain-containing protein
B: NodB homology domain-containing protein
C: NodB homology domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,73010
Polymers134,0403
Non-polymers6907
Water7,458414
1
A: NodB homology domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7914
Polymers44,6801
Non-polymers1113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-38 kcal/mol
Surface area16880 Å2
MethodPISA
2
B: NodB homology domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1703
Polymers44,6801
Non-polymers4902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-26 kcal/mol
Surface area16610 Å2
MethodPISA
3
C: NodB homology domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7683
Polymers44,6801
Non-polymers882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-38 kcal/mol
Surface area16740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.852, 107.852, 260.618
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11C-618-

HOH

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Components

#1: Protein NodB homology domain-containing protein / Chito oligosaccharide deacetylase


Mass: 44680.070 Da / Num. of mol.: 3
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-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / 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.: 414 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion / pH: 6.5
Details: 0.2M Sodium fluoride, 0.1M Bis-tris propane pH 6.5, 20% W/V PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9997 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9997 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 82477 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.814 / Rmerge(I) obs: 0.151 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
2.6-2.676.4141060.9680.9920.1170.560.468
2.67-2.755.70.47241050.9750.9940.1010.4830.477
2.75-2.835.70.37941240.9840.9960.0810.3870.505
2.83-2.945.70.29440930.9890.9970.0630.3010.537
2.94-3.055.80.25241120.9920.9980.0540.2580.581
3.05-3.195.80.20241290.9950.9990.0430.2070.641
3.19-3.365.80.1641310.9960.9990.0340.1630.759
3.36-3.575.80.12741270.9970.9990.0270.130.989
3.57-3.855.80.10741310.99810.0230.1091.158
3.85-4.235.80.09241380.99810.020.0941.375
4.23-4.845.80.08341750.99810.0180.0841.626
4.84-5.85.90.08341790.99810.0180.0851.577

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data scaling
XDSdata reduction
PHENIX(1.18.2_3874: 5419)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.31 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2174 3287 4.83 %
Rwork0.1796 --
obs0.1814 68103 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9412 0 35 414 9861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079717
X-RAY DIFFRACTIONf_angle_d0.85513331
X-RAY DIFFRACTIONf_dihedral_angle_d16.0443345
X-RAY DIFFRACTIONf_chiral_restr0.0511455
X-RAY DIFFRACTIONf_plane_restr0.0061755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.31521400.252762X-RAY DIFFRACTION100
2.44-2.470.29911370.24382805X-RAY DIFFRACTION100
2.47-2.510.28361540.24162769X-RAY DIFFRACTION100
2.51-2.560.28831540.23432798X-RAY DIFFRACTION100
2.56-2.60.2681340.22962782X-RAY DIFFRACTION100
2.6-2.650.27871500.22612776X-RAY DIFFRACTION100
2.65-2.710.2871370.23182835X-RAY DIFFRACTION100
2.71-2.770.28891530.22742812X-RAY DIFFRACTION100
2.77-2.830.25921260.22772825X-RAY DIFFRACTION100
2.83-2.90.28271520.2252762X-RAY DIFFRACTION100
2.9-2.980.24171760.21942771X-RAY DIFFRACTION100
2.98-3.070.29131350.22522840X-RAY DIFFRACTION100
3.07-3.170.24951470.22382823X-RAY DIFFRACTION100
3.17-3.280.26891380.22212795X-RAY DIFFRACTION100
3.28-3.410.25331130.20882824X-RAY DIFFRACTION100
3.41-3.570.22061160.17872855X-RAY DIFFRACTION100
3.57-3.750.2111490.1682813X-RAY DIFFRACTION100
3.75-3.990.19831510.15582845X-RAY DIFFRACTION100
3.99-4.30.16971380.13742821X-RAY DIFFRACTION100
4.3-4.730.16321420.12432831X-RAY DIFFRACTION100
4.73-5.410.15461430.14022863X-RAY DIFFRACTION100
5.41-6.80.19111480.15522872X-RAY DIFFRACTION100
6.8-29.310.16671540.14622937X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 22.9063 Å / Origin y: -18.1225 Å / Origin z: 36.8257 Å
111213212223313233
T0.3009 Å20.02 Å20.0239 Å2-0.4584 Å20.0284 Å2--0.4499 Å2
L0.1198 °2-0.1271 °2-0.1403 °2-0.1626 °20.1622 °2--1.1824 °2
S-0.0396 Å °0.0018 Å °-0.0041 Å °-0.0278 Å °-0.019 Å °-0.0129 Å °0.072 Å °0.2647 Å °-0 Å °
Refinement TLS groupSelection details: all

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