[English] 日本語
Yorodumi
- PDB-6add: The crystal structure of Rv2747 from Mycobacterium tuberculosis i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6add
TitleThe crystal structure of Rv2747 from Mycobacterium tuberculosis in complex with CoA and NLQ
ComponentsAmino-acid acetyltransferase
KeywordsTRANSFERASE / Acetyl transferase / Mycobacterium tuberculosis / Rv2747
Function / homology
Function and homology information


methione N-acyltransferase activity / amino-acid N-acetyltransferase / acetyl-CoA:L-glutamate N-acetyltransferase activity / arginine biosynthetic process via ornithine / N-acetyltransferase activity / protein homotetramerization / protein homodimerization activity / cytoplasm
Similarity search - Function
Amino-acid N-acetyltransferase / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
COENZYME A / N~2~-ACETYL-L-GLUTAMINE / Amino-acid acetyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.301 Å
AuthorsDas, U. / Singh, E. / Pal, R.K. / Tiruttani Subhramanyam, U.K. / Gourinath, S. / Srinivasan, A.
Funding support India, 1items
OrganizationGrant numberCountry
India
CitationJournal: Int. J. Biol. Macromol. / Year: 2019
Title: Structural insights into the substrate binding mechanism of novel ArgA from Mycobacterium tuberculosis
Authors: Das, U. / Singh, E. / Dharavath, S. / Tiruttani Subhramanyam, U.K. / Pal, R.K. / Vijayan, R. / Menon, S. / Kumar, S. / Gourinath, S. / Srinivasan, A.
History
DepositionJul 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.3Nov 22, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
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)43,2776
Polymers41,3662
Non-polymers1,9114
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-23 kcal/mol
Surface area15040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.385, 82.385, 114.899
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 10 through 60 or (resid 61...
21(chain B and resid 10 through 174)

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROGLYGLY(chain A and (resid 10 through 60 or (resid 61...AA10 - 6010 - 60
12LYSLYSLYSLYS(chain A and (resid 10 through 60 or (resid 61...AA6161
13ASPASPLEULEU(chain A and (resid 10 through 60 or (resid 61...AA7 - 1747 - 174
14ASPASPLEULEU(chain A and (resid 10 through 60 or (resid 61...AA7 - 1747 - 174
15ASPASPLEULEU(chain A and (resid 10 through 60 or (resid 61...AA7 - 1747 - 174
16ASPASPLEULEU(chain A and (resid 10 through 60 or (resid 61...AA7 - 1747 - 174
21PROPROLEULEU(chain B and resid 10 through 174)BB10 - 17410 - 174

-
Components

#1: Protein Amino-acid acetyltransferase


Mass: 20682.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: Rv2747 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O33289, amino-acid N-acetyltransferase
#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NLQ / N~2~-ACETYL-L-GLUTAMINE / N-ACETYL-L-GLUTAMINE


Type: L-peptide linking / Mass: 188.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H12N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: PEG

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→35 Å / Num. obs: 18183 / % possible obs: 99.8 % / Redundancy: 18.6 % / Biso Wilson estimate: 37.17 Å2 / CC1/2: 0.9955 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.019 / Net I/σ(I): 41.74
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.517 / Num. unique obs: 875 / CC1/2: 0.981 / Rpim(I) all: 0.121

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
PHASER2.8.0phasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YO2

5yo2


Resolution: 2.301→26.552 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2448 939 5.21 %RANDOM
Rwork0.2047 17081 --
obs0.2067 18020 99.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.2 Å2 / Biso mean: 40.4581 Å2 / Biso min: 19.62 Å2
Refinement stepCycle: final / Resolution: 2.301→26.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2627 0 122 151 2900
Biso mean--57.68 38.72 -
Num. residues----334
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1004X-RAY DIFFRACTION2.011TORSIONAL
12B1004X-RAY DIFFRACTION2.011TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3009-2.42220.23631300.205923902520100
2.4222-2.57380.26041420.225324112553100
2.5738-2.77230.27671250.250724132538100
2.7723-3.0510.32111480.25182397254599
3.051-3.49160.26451320.22892416254899
3.4916-4.39580.2561260.20972419254597
4.3958-26.5540.18311360.154226352771100
Refinement TLS params.Method: refined / Origin x: -20.1258 Å / Origin y: 24.0162 Å / Origin z: -3.7592 Å
111213212223313233
T0.2108 Å2-0.0432 Å20.018 Å2-0.2234 Å20.0146 Å2--0.2082 Å2
L1.0719 °2-0.2143 °20.289 °2-0.3946 °2-0.1292 °2--0.6588 °2
S0.1033 Å °-0.1825 Å °-0.0547 Å °0.0264 Å °0.0227 Å °0.0385 Å °-0.0958 Å °-0.0671 Å °0.0078 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA7 - 174
2X-RAY DIFFRACTION1allB10 - 175
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allD1 - 2
5X-RAY DIFFRACTION1allS1 - 152

+
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