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

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Basic information

Entry
Database: PDB / ID: 9jen
TitleChito oligosaccharide deacetylase from vibrio campbellii (VhCOD) complex Tetraacetyl-Chitotetraose Oligosaccharide (GlcNAc)4
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
ACETATE ION / NodB homology domain-containing protein
Similarity search - Component
Biological speciesVibrio campbellii ATCC BAA-1116 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
DepositionSep 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,98510
Polymers89,0462
Non-polymers9398
Water13,709761
1
A: NodB homology domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6704
Polymers44,5231
Non-polymers1473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-38 kcal/mol
Surface area16850 Å2
MethodPISA
2
B: NodB homology domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3156
Polymers44,5231
Non-polymers7925
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-38 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.343, 102.927, 77.285
Angle α, β, γ (deg.)90.00, 110.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 3 molecules AB

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


Mass: 44522.875 Da / Num. of mol.: 2
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-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 585.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1b_1-5_2*N]/1-2-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpN]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 768 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 761 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium iodide, 0.1 M Bis-Tris propane pH 8.5, 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: 0.97622 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 103025 / % possible obs: 97.2 % / Redundancy: 3.5 % / CC1/2: 0.831 / CC star: 0.953 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.033 / Rrim(I) all: 0.063 / Net I/σ(I): 12.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.78-1.823.40.85450370.8330.9530.2710.5190.84396.2
1.82-1.863.40.35950700.8790.9670.220.4220.84895.7
1.86-1.93.50.2850610.9190.9790.1710.3290.86396.3
1.9-1.963.50.2251340.9470.9860.1340.2590.88596.8
1.96-2.013.50.17351570.9640.9910.1050.2030.997
2.01-2.083.50.13451070.9780.9940.0820.1570.91197.1
2.08-2.153.50.1151560.9840.9960.0670.1290.91597.5
2.15-2.243.50.08852040.9870.9970.0540.1040.9298.1
2.24-2.343.60.07651920.9890.9970.0460.0890.90498.3
2.34-2.463.60.06452410.9910.9980.0390.0750.90698.9
2.46-2.623.70.05452550.9930.9980.0320.0630.85999.2
2.62-2.823.80.04852560.9930.9980.0290.0560.8999.5
2.82-3.113.80.0452900.9960.9990.0240.0460.83899.5
3.11-3.553.80.03553010.9960.9990.0210.0410.80699.4
3.55-4.483.80.03253140.9970.9990.0190.0370.72999.8
4.48-503.70.0353240.9970.9990.0180.0350.60698.3

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data scaling
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→29.06 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1975 4813 5.09 %
Rwork0.1694 --
obs0.1708 94523 89.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6262 0 56 761 7079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066495
X-RAY DIFFRACTIONf_angle_d0.7938910
X-RAY DIFFRACTIONf_dihedral_angle_d14.2462234
X-RAY DIFFRACTIONf_chiral_restr0.053977
X-RAY DIFFRACTIONf_plane_restr0.0051173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.2571610.2321069X-RAY DIFFRACTION32
1.67-1.690.2558670.23961335X-RAY DIFFRACTION40
1.69-1.710.2988790.22441604X-RAY DIFFRACTION48
1.71-1.730.25721110.23411987X-RAY DIFFRACTION60
1.73-1.760.2691290.23512467X-RAY DIFFRACTION74
1.76-1.780.2631500.23482839X-RAY DIFFRACTION83
1.78-1.810.22651450.22672979X-RAY DIFFRACTION90
1.81-1.830.28021670.22023060X-RAY DIFFRACTION91
1.83-1.860.23831970.2043122X-RAY DIFFRACTION94
1.86-1.890.22751720.19623193X-RAY DIFFRACTION95
1.89-1.920.22911730.19143203X-RAY DIFFRACTION97
1.92-1.960.18951820.18733234X-RAY DIFFRACTION96
1.96-20.21611530.17963254X-RAY DIFFRACTION97
2-2.040.20951870.17143231X-RAY DIFFRACTION97
2.04-2.080.20941970.17033242X-RAY DIFFRACTION97
2.08-2.130.17181780.16613252X-RAY DIFFRACTION98
2.13-2.180.22381680.16933260X-RAY DIFFRACTION98
2.18-2.240.18851640.16173331X-RAY DIFFRACTION98
2.24-2.310.211630.16723307X-RAY DIFFRACTION98
2.31-2.380.21161790.16843293X-RAY DIFFRACTION99
2.38-2.470.21011880.16943306X-RAY DIFFRACTION99
2.47-2.570.20621770.17633317X-RAY DIFFRACTION99
2.57-2.680.20551770.16943336X-RAY DIFFRACTION99
2.68-2.820.18961990.17513309X-RAY DIFFRACTION99
2.82-30.18851750.16483344X-RAY DIFFRACTION99
3-3.230.19981860.16993353X-RAY DIFFRACTION99
3.23-3.560.20291540.15543372X-RAY DIFFRACTION99
3.56-4.070.1591650.14123374X-RAY DIFFRACTION100
4.07-5.120.1511810.1323382X-RAY DIFFRACTION100
5.13-29.060.16751890.16413355X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -8.708 Å / Origin y: 23.4211 Å / Origin z: 12.5503 Å
111213212223313233
T0.0309 Å20.0151 Å20.0023 Å2-0.025 Å20.0248 Å2--0.0357 Å2
L1.0969 °20.3914 °2-0.0702 °2-1.1568 °20.3103 °2--0.7097 °2
S0.0464 Å °-0.0316 Å °-0.0057 Å °0.1083 Å °-0.0511 Å °0.0543 Å °0.0737 Å °-0.0333 Å °0.0016 Å °
Refinement TLS groupSelection details: all

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