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- PDB-7nlw: Crystal structure of Mycobacterium tuberculosis ArgB in complex w... -

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Basic information

Entry
Database: PDB / ID: 7nlw
TitleCrystal structure of Mycobacterium tuberculosis ArgB in complex with 2-(5-methoxy-1H-indol-3-yl)acetonitrile
ComponentsAcetylglutamate kinase
KeywordsTRANSFERASE / ArgB / Acetylglutamate kinase
Function / homology
Function and homology information


acetylglutamate kinase / acetylglutamate kinase activity / arginine biosynthetic process via ornithine / L-arginine biosynthetic process / peptidoglycan-based cell wall / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
N-Acetyl-L-glutamate kinase, cyclic / Acetylglutamate kinase ArgB / Acetylglutamate kinase family / Glutamate/acetylglutamate kinase / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family
Similarity search - Domain/homology
2-(5-methoxy-1~{H}-indol-3-yl)ethanenitrile / Acetylglutamate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.32 Å
AuthorsMendes, V. / Thomas, S.E. / Cory-Wright, J. / Blundell, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1158806 United States
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: A fragment-based approach to assess the ligandability of ArgB, ArgC, ArgD and ArgF in the L-arginine biosynthetic pathway of Mycobacterium tuberculosis
Authors: Gupta, P. / Thomas, S.E. / Zaidan, S.A. / Pasillas, M.A. / Cory-Wright, J. / Sebastian-Perez, V. / Burgess, A. / Cattermole, E. / Meghir, C. / Abell, C. / Coyne, A.G. / Jacobs, W.R. / ...Authors: Gupta, P. / Thomas, S.E. / Zaidan, S.A. / Pasillas, M.A. / Cory-Wright, J. / Sebastian-Perez, V. / Burgess, A. / Cattermole, E. / Meghir, C. / Abell, C. / Coyne, A.G. / Jacobs, W.R. / Blundell, T.L. / Tiwari, S. / Mendes, V.
History
DepositionFeb 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetylglutamate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5914
Polymers31,2131
Non-polymers3783
Water724
1
A: Acetylglutamate kinase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)189,54824
Polymers187,2786
Non-polymers2,27018
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area19290 Å2
ΔGint-244 kcal/mol
Surface area64260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.350, 174.350, 72.785
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-301-

UOK

21A-301-

UOK

31A-303-

SO4

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Components

#1: Protein Acetylglutamate kinase / N-acetyl-L-glutamate 5-phosphotransferase / NAG kinase / NAGK


Mass: 31212.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: argB, Rv1654, MTCY06H11.19 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WQ01, acetylglutamate kinase
#2: Chemical ChemComp-UOK / 2-(5-methoxy-1~{H}-indol-3-yl)ethanenitrile


Mass: 186.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.41 Å3/Da / Density % sol: 63.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 9.5
Details: 1260 mM ammonium sulphate 100 mM CHES pH 9.5 200 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.32→87.18 Å / Num. obs: 18318 / % possible obs: 99.7 % / Redundancy: 8.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.026 / Rrim(I) all: 0.076 / Net I/σ(I): 14.8 / Num. measured all: 157958
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
2.32-2.459.21.192448926570.7540.421.2631.8100
7.34-87.188.40.05151816160.9980.0190.05532.699.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.87 Å65.56 Å
Translation6.87 Å65.56 Å

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
Aimless0.5.31data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AP9

2ap9


Resolution: 2.32→26.2 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2429 909 4.97 %
Rwork0.2111 17381 -
obs0.2127 18290 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.98 Å2 / Biso mean: 89.132 Å2 / Biso min: 58.39 Å2
Refinement stepCycle: final / Resolution: 2.32→26.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 24 4 2126
Biso mean--101.04 71.54 -
Num. residues----290
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.32-2.470.38861460.336228693015100
2.47-2.660.32371600.288928913051100
2.66-2.920.34111500.281728823032100
2.92-3.350.27491350.2729153050100
3.35-4.210.26621480.21522852300098
4.21-26.20.1951700.170129723142100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.93692.64465.07122.62172.7257.06460.4010.85350.9246-0.1291-0.2345-0.51890.25061.14790.08580.654-0.01690.10990.74020.18311.262137.73323.194534.09
28.10964.74172.18123.65813.57789.88940.1994-0.2954-0.5804-0.0105-0.2954-0.78540.62310.76750.12870.56590.07310.1280.59540.31880.944729.4764-14.150333.7069
32.8891-0.31560.43315.86711.33012.46640.22770.72910.1647-0.4343-0.23920.1034-0.00270.0059-0.00650.63350.18320.1420.65040.16860.609719.8176-27.443926.2449
44.3162.29850.15321.5641.21063.7153-0.23690.811-0.2036-0.52740.1364-0.81260.11940.72390.1610.98250.20140.24410.80250.2651.035834.593-13.680317.4501
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 26 )A4 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 59 )A27 - 59
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 203 )A60 - 203
4X-RAY DIFFRACTION4chain 'A' and (resid 204 through 293 )A204 - 293

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