[English] 日本語
Yorodumi
- PDB-9jt8: Chito oligosaccharide deacetylase from vibrio campbellii (VhCOD) ... -

+
Open data


ID or keywords:

Loading...

-
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 / 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: 2.85 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: 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 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 8, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more