[English] 日本語
Yorodumi
- PDB-8wco: (S)-citramalyl-CoA lyase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8wco
Title(S)-citramalyl-CoA lyase
ComponentsProbable acyl-CoA lyase beta chain
KeywordsLYASE / (S)-citramalyl-CoA lyase
Function / homology
Function and homology information


oxaloacetate metabolic process / lyase activity / magnesium ion binding
Similarity search - Function
Citrate lyase beta subunit-like / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
ACETYL COENZYME *A / Probable acyl-CoA lyase beta chain
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHuang, Q. / Bao, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2024
Title: Structural and functional characterization of itaconyl-CoA hydratase and citramalyl-CoA lyase involved in itaconate metabolism of Pseudomonas aeruginosa.
Authors: Huang, Q. / Duan, C. / Ma, H. / Nong, C. / Zheng, Q. / Zhou, J. / Zhao, N. / Mou, X. / Liu, T. / Zou, S. / Yang, N. / Tong, A. / Qin, W. / Bao, R.
History
DepositionSep 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable acyl-CoA lyase beta chain
B: Probable acyl-CoA lyase beta chain
C: Probable acyl-CoA lyase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6046
Polymers87,1753
Non-polymers2,4293
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, trimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12020 Å2
ΔGint-37 kcal/mol
Surface area31610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.874, 79.144, 121.515
Angle α, β, γ (deg.)90.000, 102.040, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-410-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and resid 1 through 275)
d_3ens_1(chain "C" and resid 1 through 275)

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 1 - 275 / Label seq-ID: 1 - 275

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC

-
Components

#1: Protein Probable acyl-CoA lyase beta chain


Mass: 29058.328 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA0883 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I562
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.25 M K2HPO4, 22% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.6→39.79 Å / Num. obs: 26786 / % possible obs: 97.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 26.02 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.1
Reflection shellResolution: 2.6→2.67 Å / Num. unique obs: 3101 / CC1/2: 0.912

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→39.79 Å / SU ML: 0.384 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.3996
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2658 1993 7.44 %
Rwork0.2069 24792 -
obs0.2114 26785 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.52 Å2
Refinement stepCycle: LAST / Resolution: 2.6→39.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6126 0 153 44 6323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00986387
X-RAY DIFFRACTIONf_angle_d1.24568697
X-RAY DIFFRACTIONf_chiral_restr0.0797990
X-RAY DIFFRACTIONf_plane_restr0.01621149
X-RAY DIFFRACTIONf_dihedral_angle_d15.94882337
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.701618522925
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.633504051405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.29621390.24731799X-RAY DIFFRACTION97.73
2.67-2.740.3131510.24681741X-RAY DIFFRACTION97.28
2.74-2.820.37961320.24991707X-RAY DIFFRACTION94.5
2.82-2.910.3351340.25091736X-RAY DIFFRACTION96.64
2.91-3.010.32481450.25171798X-RAY DIFFRACTION98.68
3.01-3.130.3251430.27721773X-RAY DIFFRACTION98.21
3.13-3.280.30251420.2451782X-RAY DIFFRACTION98.62
3.28-3.450.28541460.21741771X-RAY DIFFRACTION96.57
3.45-3.660.25351420.20571741X-RAY DIFFRACTION97.26
3.66-3.950.24771430.18571801X-RAY DIFFRACTION98.73
3.95-4.340.22871480.16621774X-RAY DIFFRACTION98.16
4.34-4.970.18631430.14711769X-RAY DIFFRACTION95.79
4.97-6.260.23841420.17991806X-RAY DIFFRACTION98.48
6.26-39.790.22081430.1851794X-RAY DIFFRACTION95.28

+
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