[English] 日本語
Yorodumi
- PDB-8yfp: Chito oligosaccharide deacetylase from vibrio campbellii (VhCOD) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8yfp
TitleChito oligosaccharide deacetylase from vibrio campbellii (VhCOD)
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: 2.45 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: Structural and functional of Chito oligosaccharide deacetylase of Vibrio cambellii
Authors: Sirikan, P. / Wipa, S. / Tamo, F. / Robinson, R.C.
History
DepositionFeb 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)91,4929
Polymers91,1922
Non-polymers3007
Water4,378243
1
A: NodB homology domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7505
Polymers45,5961
Non-polymers1544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-37 kcal/mol
Surface area16920 Å2
MethodPISA
2
B: NodB homology domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7424
Polymers45,5961
Non-polymers1463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-37 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.061, 209.061, 209.061
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

-
Components

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


Mass: 45596.020 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: Chemical ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 4.28 Å3/Da / Density % sol: 70.58 % / Description: Hexagonal crytal
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.06M Divalent (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride), 0.1M buffer system2 (1M Sodium HEPES, MOPS (acid) pH 7.5, 35% precipitant mix 4 (25% v/v MPD, 25% PEG 100, 25% w/v PEG 3350)

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9997 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9997 Å / Relative weight: 1
ReflectionResolution: 2.45→19.933 Å / Num. obs: 55208 / % possible obs: 99 % / Redundancy: 20 % / Biso Wilson estimate: 33.23 Å2 / CC1/2: 0.971 / CC star: 0.993 / Rpim(I) all: 0.045 / Rrim(I) all: 0.208 / Net I/σ(I): 19
Reflection shellResolution: 2.8→6.75 Å / Num. unique obs: 37317 / CC1/2: 0.971 / CC star: 0.993 / Rpim(I) all: 0.182 / Rrim(I) all: 0.848

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→19.93 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2188 2799 5.07 %
Rwork0.1952 --
obs0.1964 55208 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6256 0 7 243 6506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076457
X-RAY DIFFRACTIONf_angle_d0.8998860
X-RAY DIFFRACTIONf_dihedral_angle_d20.1122218
X-RAY DIFFRACTIONf_chiral_restr0.054965
X-RAY DIFFRACTIONf_plane_restr0.0051168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.50.29251120.24692579X-RAY DIFFRACTION98
2.5-2.540.27051390.23042615X-RAY DIFFRACTION100
2.54-2.590.26511090.21592651X-RAY DIFFRACTION100
2.59-2.640.24851420.20362589X-RAY DIFFRACTION100
2.64-2.70.26471580.21492612X-RAY DIFFRACTION100
2.7-2.760.23931310.20872611X-RAY DIFFRACTION100
2.76-2.830.25631410.21022596X-RAY DIFFRACTION100
2.83-2.910.2211560.20692565X-RAY DIFFRACTION100
2.91-2.990.22371390.20842624X-RAY DIFFRACTION100
2.99-3.090.26251460.20432604X-RAY DIFFRACTION100
3.09-3.20.21541340.20482593X-RAY DIFFRACTION100
3.2-3.330.2181490.21222620X-RAY DIFFRACTION100
3.33-3.480.19371430.18952638X-RAY DIFFRACTION100
3.48-3.660.21311340.19012590X-RAY DIFFRACTION100
3.66-3.890.23151410.17532631X-RAY DIFFRACTION100
3.89-4.180.2011230.17842643X-RAY DIFFRACTION100
4.19-4.60.18811490.16082633X-RAY DIFFRACTION100
4.6-5.260.18171500.18642634X-RAY DIFFRACTION100
5.26-6.580.23791480.21612661X-RAY DIFFRACTION100
6.59-19.930.20661550.19312720X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -10.1185 Å / Origin y: 28.892 Å / Origin z: -41.5108 Å
111213212223313233
T0.3643 Å2-0.0686 Å2-0.0349 Å2-0.3322 Å20.0649 Å2--0.3482 Å2
L0.7501 °2-0.1813 °2-0.1765 °2-0.6103 °20.0899 °2--0.2622 °2
S0.0678 Å °-0.1512 Å °-0.0073 Å °0.0598 Å °-0.0732 Å °-0.0278 Å °0.0014 Å °0.0396 Å °0.0001 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