[English] 日本語
Yorodumi
- PDB-8k6h: Crystal structure of e.coli cyanase complex with cyanate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8k6h
TitleCrystal structure of e.coli cyanase complex with cyanate
ComponentsCyanate hydratase
KeywordsLYASE / enzyme / substrate complex
Function / homology
Function and homology information


cyanate catabolic process / cyanase / cyanate hydratase activity / DNA binding
Similarity search - Function
: / Cyanate hydratase, N-terminal / Cyanate lyase, C-terminal / Cyanate hydratase / Cyanate lyase, C-terminal domain superfamily / Cyanate lyase C-terminal domain / Cyanate lyase C-terminal domain, Cyanate hydratase / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
cyanic acid / Cyanate hydratase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKim, J. / Nam, K.H. / Cho, Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1A2C301335711 Korea, Republic Of
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural mechanism of Escherichia coli cyanase.
Authors: Kim, J. / Kim, Y. / Park, J. / Nam, K.H. / Cho, Y.
History
DepositionJul 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyanate hydratase
B: Cyanate hydratase
C: Cyanate hydratase
D: Cyanate hydratase
E: Cyanate hydratase
F: Cyanate hydratase
G: Cyanate hydratase
H: Cyanate hydratase
I: Cyanate hydratase
J: Cyanate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,64445
Polymers174,81310
Non-polymers2,83235
Water34,9131938
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area69610 Å2
ΔGint-736 kcal/mol
Surface area47250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.136, 81.066, 81.065
Angle α, β, γ (deg.)70.51, 76.37, 65.26
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Cyanate hydratase / Cyanase / Cyanate hydrolase / Cyanate lyase


Mass: 17481.266 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: cynS, cnt, b0340, JW0331 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00816, cyanase
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-0NM / cyanic acid


Mass: 43.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CHNO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1938 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.3
Details: 50mM Tris-Cl (pH 7.3), 50 mM potassium phosphate, 2.5 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 237769 / % possible obs: 87.8 % / Redundancy: 3.9 % / CC1/2: 0.97 / Rmerge(I) obs: 0.13 / Net I/σ(I): 19.39
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.41 / Num. unique obs: 11830 / CC1/2: 0.86

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
MxDCdata collection
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→49.01 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 18.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1839 1998 8.4 %
Rwork0.1615 --
obs0.1617 237412 87.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11970 0 155 1938 14063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612414
X-RAY DIFFRACTIONf_angle_d0.91716785
X-RAY DIFFRACTIONf_dihedral_angle_d6.0561680
X-RAY DIFFRACTIONf_chiral_restr0.0551971
X-RAY DIFFRACTIONf_plane_restr0.0092135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.23661380.211216296X-RAY DIFFRACTION85
1.54-1.580.23841350.196315870X-RAY DIFFRACTION83
1.58-1.630.20971430.179716858X-RAY DIFFRACTION88
1.63-1.680.21841470.16817249X-RAY DIFFRACTION90
1.68-1.740.1781450.164917167X-RAY DIFFRACTION89
1.74-1.810.19821420.169116737X-RAY DIFFRACTION87
1.81-1.890.2021340.172815730X-RAY DIFFRACTION82
1.89-1.990.18171480.161617505X-RAY DIFFRACTION91
1.99-2.110.2011470.160717231X-RAY DIFFRACTION90
2.11-2.280.19231440.155217054X-RAY DIFFRACTION89
2.28-2.510.16471380.159716240X-RAY DIFFRACTION85
2.51-2.870.18321500.166317705X-RAY DIFFRACTION92
2.87-3.610.18851390.153516393X-RAY DIFFRACTION85
3.61-49.010.15531480.150817379X-RAY DIFFRACTION90

+
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