[English] 日本語
Yorodumi
- PDB-5yge: ArgA complexed with AceCoA and glutamate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yge
TitleArgA complexed with AceCoA and glutamate
ComponentsAmino-acid acetyltransferase
KeywordsTRANSFERASE / acetyltransferase / arginine biosynthesis / glutamate / acetyl coenzyme A
Function / homology
Function and homology information


amino-acid N-acetyltransferase / L-glutamate N-acetyltransferase activity / L-arginine biosynthetic process via ornithine / N-acetyltransferase activity / L-arginine biosynthetic process / protein homotetramerization / protein homodimerization activity / cytoplasm
Similarity search - Function
Acetyltransferase NSI-like / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
ACETYL COENZYME *A / CACODYLIC ACID / GLUTAMIC ACID / Amino-acid acetyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.039 Å
AuthorsYang, X. / Wu, L. / Ran, Y. / Xu, A. / Zhang, B. / Yang, X. / Zhang, R. / Rao, Z. / Li, J.
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Crystal structure of l-glutamate N-acetyltransferase ArgA from Mycobacterium tuberculosis
Authors: Yang, X. / Wu, L. / Ran, Y. / Xu, A. / Zhang, B. / Yang, X. / Zhang, R. / Rao, Z. / Li, J.
History
DepositionSep 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 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: Amino-acid acetyltransferase
B: Amino-acid acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,62410
Polymers39,1592
Non-polymers2,4658
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-12 kcal/mol
Surface area15600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.728, 73.728, 187.231
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-387-

HOH

-
Components

#1: Protein Amino-acid acetyltransferase / N-acetylglutamate synthase / NAGS


Mass: 19579.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: argA, Rv2747 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O33289, amino-acid N-acetyltransferase
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CAD / CACODYLIC ACID / HYDROXYDIMETHYLARSINE OXIDE


Mass: 137.997 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H7AsO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 3.35 Å3/Da / Density % sol: 63.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.08 M sodium cacodylate, pH6.2, 0.16 M magnesium acetate tetrahydrate, 12% (w/v) PEG10000, 20% (w/v) glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97624 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2.039→50 Å / Num. obs: 33893 / % possible obs: 99.9 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.037 / Rrim(I) all: 0.109 / Χ2: 0.909 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.04-2.087.80.46316370.9210.1730.4960.93599.5
2.08-2.118.10.45816840.9360.1680.4890.89799.8
2.11-2.158.20.35616390.9630.130.380.868100
2.15-2.28.10.32316480.9690.1180.3440.84999.8
2.2-2.258.20.30616690.9710.1120.3260.916100
2.25-2.38.10.26716640.9740.0990.2851.045100
2.3-2.358.30.23716660.9810.0860.2520.852100
2.35-2.428.40.19616560.9840.0710.2090.858100
2.42-2.498.40.17816740.9880.0650.190.869100
2.49-2.578.50.16616710.9910.060.1770.839100
2.57-2.668.60.15716820.990.0560.1670.863100
2.66-2.778.60.13416790.9940.0480.1420.879100
2.77-2.898.80.11916900.9940.0420.1270.88699.9
2.89-3.058.80.116990.9950.0350.1070.87100
3.05-3.248.90.08816990.9960.0310.0930.886100
3.24-3.498.70.0817010.9950.0290.0850.99100
3.49-3.848.40.07517280.9960.0270.081.085100
3.84-4.3980.06817410.9970.0260.0731.072100
4.39-5.5480.06417660.9970.0240.0680.95399.8
5.54-507.70.05419000.9970.0210.0580.78599.2

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.039→36.17 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.11
RfactorNum. reflection% reflection
Rfree0.2209 1717 5.09 %
Rwork0.1968 --
obs0.1981 33763 99.77 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 22.352 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso max: 124.01 Å2 / Biso mean: 28.18 Å2 / Biso min: 6.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.1041 Å20 Å20 Å2
2--0.1041 Å2-0 Å2
3----0.2082 Å2
Refinement stepCycle: final / Resolution: 2.039→36.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2653 0 16 178 2847
Biso mean--62.24 33.14 -
Num. residues----340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012847
X-RAY DIFFRACTIONf_angle_d1.2413894
X-RAY DIFFRACTIONf_chiral_restr0.07442
X-RAY DIFFRACTIONf_plane_restr0.005480
X-RAY DIFFRACTIONf_dihedral_angle_d16.4121045
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0395-2.09950.29051540.24982565271998
2.0995-2.16720.28011400.21826262766100
2.1672-2.24470.24131160.216426222738100
2.2447-2.33460.30271460.219226182764100
2.3346-2.44080.22591410.204226382779100
2.4408-2.56940.22821360.213226422778100
2.5694-2.73040.26861510.215126492800100
2.7304-2.94110.25891270.220926902817100
2.9411-3.23690.22751440.215526752819100
3.2369-3.70490.20861540.192826852839100
3.7049-4.66620.15971670.155227312898100
4.6662-36.17530.19991410.1782905304699

+
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