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- PDB-6add: The crystal structure of Rv2747 from Mycobacterium tuberculosis i... -

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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


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
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

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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)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

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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


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


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 289 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: 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

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Phasing

PhasingMethod: molecular replacement

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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

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