[English] 日本語
Yorodumi
- PDB-5mlk: Biotin dependent carboxylase AccA3 dimer from Mycobacterium tuber... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mlk
TitleBiotin dependent carboxylase AccA3 dimer from Mycobacterium tuberculosis (Rv3285)
ComponentsAcetyl-COA carboxylase
KeywordsLIGASE / Biotin dependant carboxylase / GRASP
Function / homology
Function and homology information


propionyl-CoA carboxylase activity / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / acetyl-CoA carboxylase activity / carbon fixation / cell wall / fatty acid biosynthetic process / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Rossmann fold - #20 ...Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Rossmann fold - #20 / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / ATP-grasp fold, B domain / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Carbamoyl-phosphate synthase subdomain signature 2. / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.939 Å
AuthorsBennett, M.D. / Hogbom, M.
CitationJournal: FEBS Open Bio / Year: 2017
Title: Crystal structure of the essential biotin-dependent carboxylase AccA3 from Mycobacterium tuberculosis.
Authors: Bennett, M. / Hogbom, M.
History
DepositionDec 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetyl-COA carboxylase
B: Acetyl-COA carboxylase


Theoretical massNumber of molelcules
Total (without water)130,9252
Polymers130,9252
Non-polymers00
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint10 kcal/mol
Surface area31420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.897, 85.206, 148.097
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Acetyl-COA carboxylase / / Probable bifunctional protein acetyl-/propionyl-coenzyme A carboxylase (Alpha chain) AccA3: biotin ...Probable bifunctional protein acetyl-/propionyl-coenzyme A carboxylase (Alpha chain) AccA3: biotin carboxylase + biotin carboxyl carrier protein (BCCP)


Mass: 65462.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: accA3, Rv3285, LH57_17955 / Production host: Escherichia coli (E. coli) / References: UniProt: P96890
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 1.88 Å3/Da / Density % sol: 34.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG 3350, 0.1M Bis-Tris pH 6.5 / Temp details: RT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97471 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97471 Å / Relative weight: 1
ReflectionResolution: 1.939→50 Å / Num. obs: 73716 / % possible obs: 99.8 % / Redundancy: 12.98 % / Rrim(I) all: 0.123 / Net I/σ(I): 19.04
Reflection shellResolution: 1.94→2.06 Å / Redundancy: 12.98 % / Mean I/σ(I) obs: 2.89 / CC1/2: 0.862 / Rrim(I) all: 0.973 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.939→45.412 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 3685 5 %
Rwork0.1885 --
obs0.1901 73710 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.939→45.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6369 0 0 411 6780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076508
X-RAY DIFFRACTIONf_angle_d1.0798846
X-RAY DIFFRACTIONf_dihedral_angle_d15.1482366
X-RAY DIFFRACTIONf_chiral_restr0.075980
X-RAY DIFFRACTIONf_plane_restr0.0051190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9386-1.96410.30991350.26472569X-RAY DIFFRACTION96
1.9641-1.9910.25391410.23222676X-RAY DIFFRACTION100
1.991-2.01940.27431390.22992638X-RAY DIFFRACTION100
2.0194-2.04960.29451400.22372655X-RAY DIFFRACTION100
2.0496-2.08160.24361400.21632683X-RAY DIFFRACTION100
2.0816-2.11570.23791400.20272665X-RAY DIFFRACTION100
2.1157-2.15220.26331400.19932651X-RAY DIFFRACTION100
2.1522-2.19140.25291410.19572687X-RAY DIFFRACTION100
2.1914-2.23350.22391410.19992675X-RAY DIFFRACTION100
2.2335-2.27910.25131390.20042652X-RAY DIFFRACTION100
2.2791-2.32860.25691410.1962663X-RAY DIFFRACTION100
2.3286-2.38280.23641410.20292687X-RAY DIFFRACTION100
2.3828-2.44240.25921420.20392690X-RAY DIFFRACTION100
2.4424-2.50840.25831410.19782694X-RAY DIFFRACTION100
2.5084-2.58220.27741410.19532662X-RAY DIFFRACTION100
2.5822-2.66560.23681400.20022674X-RAY DIFFRACTION100
2.6656-2.76080.2351440.19932725X-RAY DIFFRACTION100
2.7608-2.87130.20691400.1952666X-RAY DIFFRACTION100
2.8713-3.0020.23781420.20532696X-RAY DIFFRACTION100
3.002-3.16020.26191420.20772706X-RAY DIFFRACTION100
3.1602-3.35820.22741430.19792713X-RAY DIFFRACTION100
3.3582-3.61740.1791430.18242718X-RAY DIFFRACTION100
3.6174-3.98120.18941450.16172746X-RAY DIFFRACTION100
3.9812-4.55680.16561430.1462733X-RAY DIFFRACTION100
4.5568-5.73930.16141470.1572786X-RAY DIFFRACTION100
5.7393-45.4240.22071540.19022915X-RAY DIFFRACTION100

+
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