[English] 日本語
Yorodumi
- PDB-5mzx: Crystal structure of the decarboxylase AibA/AibB in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mzx
TitleCrystal structure of the decarboxylase AibA/AibB in complex with 4'-diphospho pantetheine
Components(Glutaconate CoA-transferase family, subunit ...) x 2
KeywordsLYASE / decarboxylase / CoA transferase like fold / coenzyme A
Function / homologyCoA-transferase activity / Coenzyme A transferase family I / Coenzyme A transferase / Coenzyme A transferase / NagB/RpiA transferase-like / 4'-diphospho pantetheine / ACETATE ION / Glutaconate CoA-transferase family, subunit B / Glutaconate CoA-transferase family, subunit A
Function and homology information
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsBock, T. / Luxenburger, E. / Hoffmann, J. / Schuetza, V. / Feiler, C. / Mueller, R. / Blankenfeldt, W.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: AibA/AibB Induces an Intramolecular Decarboxylation in Isovalerate Biosynthesis by Myxococcus xanthus.
Authors: Bock, T. / Luxenburger, E. / Hoffmann, J. / Schutza, V. / Feiler, C. / Muller, R. / Blankenfeldt, W.
History
DepositionFeb 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutaconate CoA-transferase family, subunit A
C: Glutaconate CoA-transferase family, subunit A
D: Glutaconate CoA-transferase family, subunit B
B: Glutaconate CoA-transferase family, subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,80515
Polymers109,2974
Non-polymers1,50711
Water7,945441
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14400 Å2
ΔGint-77 kcal/mol
Surface area32650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.546, 93.392, 90.044
Angle α, β, γ (deg.)90.000, 103.930, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Glutaconate CoA-transferase family, subunit ... , 2 types, 4 molecules ACDB

#1: Protein Glutaconate CoA-transferase family, subunit A


Mass: 28367.838 Da / Num. of mol.: 2 / Mutation: K191A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (strain DK 1622) (bacteria)
Strain: DK 1622 / Gene: MXAN_4264 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1D4I4
#2: Protein Glutaconate CoA-transferase family, subunit B


Mass: 26280.871 Da / Num. of mol.: 2 / Mutation: E200A, E201A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (strain DK 1622) (bacteria)
Strain: DK 1622 / Gene: MXAN_4265 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1D4I3

-
Non-polymers , 4 types, 452 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-4PS / 4'-diphospho pantetheine / N~3~-[(2R)-2-hydroxy-4-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}-3,3-dimethylbutanoyl]-N-(2-sulfanylethyl)-beta-alaninamide


Mass: 438.328 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H24N2O10P2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.085 M sodium acetate, 0.17 M ammonium acetate, 15 % glycerol, 25 % PEG4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→46.831 Å / Num. obs: 72195 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 24.59 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.118 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2-2.045.70.880.739199.8
9.8-46.836.70.0380.999198.9

-
Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5MZW

5mzw


Resolution: 2→46.831 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.63
RfactorNum. reflection% reflection
Rfree0.1965 3654 5.06 %
Rwork0.1644 --
obs0.166 72153 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.74 Å2 / Biso mean: 30.7134 Å2 / Biso min: 14.37 Å2
Refinement stepCycle: final / Resolution: 2→46.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7454 0 135 441 8030
Biso mean--40.9 32.15 -
Num. residues----1007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037833
X-RAY DIFFRACTIONf_angle_d0.610719
X-RAY DIFFRACTIONf_chiral_restr0.0441250
X-RAY DIFFRACTIONf_plane_restr0.0041415
X-RAY DIFFRACTIONf_dihedral_angle_d9.8034810
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.02630.26411490.217425862735
2.0263-2.05410.28781260.220826342760
2.0541-2.08340.28411240.212526592783
2.0834-2.11450.26781340.204926002734
2.1145-2.14760.24741580.199826452803
2.1476-2.18280.22621350.190225962731
2.1828-2.22040.22051420.180826512793
2.2204-2.26080.21451450.176925882733
2.2608-2.30430.2461510.17526302781
2.3043-2.35130.21291400.172226162756
2.3513-2.40240.22161540.170326262780
2.4024-2.45830.17141430.164926372780
2.4583-2.51980.21191410.161326062747
2.5198-2.58790.19061480.157326232771
2.5879-2.6640.22111260.159726832809
2.664-2.750.21371480.163225872735
2.75-2.84830.22341490.158326162765
2.8483-2.96230.17581410.162126422783
2.9623-3.09710.18791270.166126702797
3.0971-3.26040.17921200.16526342754
3.2604-3.46460.20521210.171326772798
3.4646-3.7320.1741550.166126222777
3.732-4.10740.18271550.148426432798
4.1074-4.70120.14881380.127926552793
4.7012-5.92120.15631420.151526662808
5.9212-46.84380.20531420.165627072849

+
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