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- PDB-5yo2: The crystal structure of Rv2747 from Mycobacterium tuberculosis i... -

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Basic information

Entry
Database: PDB / ID: 5yo2
TitleThe crystal structure of Rv2747 from Mycobacterium tuberculosis in complex with Acetyl CoA and L-Arginine
ComponentsAmino-acid acetyltransferase
KeywordsTRANSFERASE / Acetyltransferase
Function / homology
Function and homology information


amino-acid N-acetyltransferase / L-glutamate N-acetyltransferase activity, acting on acetyl-CoA as donor / L-arginine biosynthetic process via ornithine / N-acetyltransferase activity / 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 / ARGININE / Amino-acid acetyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.997 Å
AuthorsSingh, E. / Tiruttani Subhramanyam, U.K. / Pal, R.K. / Srinivasan, A. / Gourinath, S. / Das, U.
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
DepositionOct 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 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 1.3Feb 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 1.4Mar 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amino-acid acetyltransferase
B: Amino-acid acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5265
Polymers41,3662
Non-polymers1,1603
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-21 kcal/mol
Surface area14810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.773, 79.773, 115.388
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12(chain A and (resid 9 through 23 or (resid 24...
22(chain B and (resid 9 through 106 or (resid 107...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain CC200
211chain FF200
112(chain A and (resid 9 through 23 or (resid 24...A9 - 23
122(chain A and (resid 9 through 23 or (resid 24...A24
132(chain A and (resid 9 through 23 or (resid 24...A6 - 173
142(chain A and (resid 9 through 23 or (resid 24...A6 - 173
152(chain A and (resid 9 through 23 or (resid 24...A6 - 173
162(chain A and (resid 9 through 23 or (resid 24...A6 - 173
212(chain B and (resid 9 through 106 or (resid 107...B9 - 106
222(chain B and (resid 9 through 106 or (resid 107...B107
232(chain B and (resid 9 through 106 or (resid 107...B9 - 174
242(chain B and (resid 9 through 106 or (resid 107...B9 - 174
252(chain B and (resid 9 through 106 or (resid 107...B9 - 174
262(chain B and (resid 9 through 106 or (resid 107...B9 - 174

NCS ensembles :
ID
1
2

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Components

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


Mass: 20682.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Genomic DNA
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: Rv2747 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O33289, amino-acid N-acetyltransferase
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: PEG

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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: Jul 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→46.75 Å / Num. obs: 7975 / % possible obs: 99.8 % / Redundancy: 22.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.044 / Rrim(I) all: 0.211 / Net I/σ(I): 18 / Num. measured all: 180968 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3-3.18230.912842712380.9670.1940.9314.298.8
8.99-46.7517.60.045628135610.0110.0464999.4

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.997→32.809 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2458 385 4.86 %
Rwork0.219 7530 -
obs0.2204 7915 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.41 Å2 / Biso mean: 47.1693 Å2 / Biso min: 28.37 Å2
Refinement stepCycle: final / Resolution: 2.997→32.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2581 0 133 0 2714
Biso mean--68.1 --
Num. residues----334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032713
X-RAY DIFFRACTIONf_angle_d0.6613700
X-RAY DIFFRACTIONf_chiral_restr0.043436
X-RAY DIFFRACTIONf_plane_restr0.003466
X-RAY DIFFRACTIONf_dihedral_angle_d15.8451595
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A12X-RAY DIFFRACTION6.439TORSIONAL
12B12X-RAY DIFFRACTION6.439TORSIONAL
21A1938X-RAY DIFFRACTION6.439TORSIONAL
22B1938X-RAY DIFFRACTION6.439TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9971-3.43040.30721270.24992435256299
3.4304-4.32040.24041340.216324562590100
4.3204-32.81110.22421240.207526392763100

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