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- PDB-9jt8: Chito oligosaccharide deacetylase from vibrio campbellii (VhCOD) ... -

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Basic information

Entry
Database: PDB / ID: 9jt8
TitleChito oligosaccharide deacetylase from vibrio campbellii (VhCOD) in complex with Triacetyl-Chitotriose (GlcNAc)3
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
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: 2.85 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: To be published
Title: Chito oligosaccharide deacetylase from vibrio campbellii (VhCOD) in complex with Triacetyl-Chitotriose (GlcNAc)3
Authors: Sirikan, P. / Wipa, S. / Tamo, F. / Robinson, R.C.
History
DepositionOct 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)135,5229
Polymers133,5693
Non-polymers1,9536
Water1267
1
A: NodB homology domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1743
Polymers44,5231
Non-polymers6512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-29 kcal/mol
Surface area16390 Å2
MethodPISA
2
B: NodB homology domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1743
Polymers44,5231
Non-polymers6512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-24 kcal/mol
Surface area16130 Å2
MethodPISA
3
C: NodB homology domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1743
Polymers44,5231
Non-polymers6512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-25 kcal/mol
Surface area16300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.881, 107.881, 260.731
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

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


Mass: 44522.875 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-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.: 3
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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.28 Å3/Da / Density % sol: 62.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2M Sodium iodide, 0.1M 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: 0.99764 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99764 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 40877 / % possible obs: 99.9 % / Redundancy: 16 % / CC1/2: 0.978 / CC star: 0.994 / Rmerge(I) obs: 0.396 / Rpim(I) all: 0.098 / Rrim(I) all: 0.408 / Χ2: 1.242 / Net I/σ(I): 2.7 / Num. measured all: 655084
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.85-2.96.41.30320070.520.8270.5491.4180.708100
2.9-2.957.81.43620060.5440.840.5441.5380.695100
2.95-3.019.31.4220570.6610.8920.4851.5020.687100
3.01-3.0711.11.41620300.6720.8960.4371.4830.698100
3.07-3.1412.31.34320200.7320.9190.3941.40.731100
3.14-3.2113.71.28720130.7580.9280.3571.3360.725100
3.21-3.29151.14220280.7890.9390.3021.1810.793100
3.29-3.3815.81.07820570.8320.9530.2791.1130.825100
3.38-3.4816.20.91820360.8450.9570.2350.9480.996100
3.48-3.5918.20.81520130.90.9730.1960.8381.024100
3.59-3.7219.70.7320330.9360.9830.1670.7491.056100
3.72-3.8719.20.59920370.9570.9890.140.6151.129100
3.87-4.0418.30.48220110.9630.9910.1160.4961.234100
4.04-4.2620.60.39420650.9770.9940.0880.4041.261100
4.26-4.5220.50.30520450.9850.9960.0680.3121.39100
4.52-4.8720.50.25920530.9880.9970.0580.2651.439100
4.87-5.3620.30.25620720.9880.9970.0580.2621.345100
5.36-6.1419.30.24720520.9860.9960.0570.2541.243100
6.14-7.7318.40.1820970.9920.9980.0430.1851.60599.9
7.73-5017.20.15121450.9940.9980.0380.1563.51699.1

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
HKL-2000data scaling
XDSdata reduction
PHENIX(1.21.2_5419: 5419)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→29.24 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 2040 5.03 %
Rwork0.1818 --
obs0.1847 40553 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9407 0 123 7 9537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099803
X-RAY DIFFRACTIONf_angle_d1.00613454
X-RAY DIFFRACTIONf_dihedral_angle_d16.2863520
X-RAY DIFFRACTIONf_chiral_restr0.0551492
X-RAY DIFFRACTIONf_plane_restr0.0071760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.920.36341250.28832497X-RAY DIFFRACTION97
2.92-2.990.32061210.27772536X-RAY DIFFRACTION99
2.99-3.070.31731640.26072495X-RAY DIFFRACTION98
3.07-3.160.30491470.25372517X-RAY DIFFRACTION99
3.16-3.260.2781410.25492511X-RAY DIFFRACTION99
3.26-3.380.27911080.22712607X-RAY DIFFRACTION99
3.38-3.520.24621460.19472522X-RAY DIFFRACTION100
3.52-3.680.21671180.17912603X-RAY DIFFRACTION100
3.68-3.870.23921400.16982589X-RAY DIFFRACTION100
3.87-4.110.20371210.15852566X-RAY DIFFRACTION100
4.11-4.430.21341540.1352553X-RAY DIFFRACTION100
4.43-4.870.19161300.13712617X-RAY DIFFRACTION100
4.87-5.570.22051350.15822590X-RAY DIFFRACTION100
5.57-70.21881510.18282615X-RAY DIFFRACTION100
7.01-29.240.22371390.14832695X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 39.9659 Å / Origin y: 4.1179 Å / Origin z: -35.6751 Å
111213212223313233
T0.4532 Å2-0.0173 Å20.0116 Å2-0.3754 Å2-0.0111 Å2--0.4495 Å2
L0.1375 °20.0183 °20.0098 °2-0.4808 °2-0.3733 °2--0.8121 °2
S0.0188 Å °0.0007 Å °-0.0479 Å °-0.0029 Å °-0.0113 Å °-0.0311 Å °0.1374 Å °-0.0094 Å °-0 Å °
Refinement TLS groupSelection details: all

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