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

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Basic information

Entry
Database: PDB / ID: 7nlt
TitleCrystal structure of Mycobacterium tuberculosis ArgB in complex with 4-(4-methylpiperazin-1-yl)benzoic acid
ComponentsAcetylglutamate kinase
KeywordsTRANSFERASE / ArgB Acetylglutamate kinase
Function / homology
Function and homology information


acetylglutamate kinase / acetylglutamate kinase activity / L-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
4-(4-methylpiperazin-1-yl)benzoic acid / Acetylglutamate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.225 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)31,6254
Polymers31,2131
Non-polymers4123
Water28816
1
A: Acetylglutamate kinase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)189,75224
Polymers187,2786
Non-polymers2,47418
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 area18970 Å2
ΔGint-234 kcal/mol
Surface area63450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.627, 173.627, 71.992
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-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-14N / 4-(4-methylpiperazin-1-yl)benzoic acid


Mass: 220.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16N2O2 / 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.: 16 / 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: 3.35 Å3/Da / Density % sol: 63.23 %
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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.225→50.122 Å / Num. obs: 20440 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.021 / Rrim(I) all: 0.068 / Net I/σ(I): 18
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
2.23-2.3510.41.0053076029500.8660.3251.0562.2100
7.04-50.129.50.05165696890.9980.0180.05444.499.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.85 Å50.12 Å
Translation6.85 Å50.12 Å

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Processing

Software
NameVersionClassification
PHENIX1.1refinement
Aimless0.5.15data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AP9

2ap9


Resolution: 2.225→50.122 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 1000 4.89 %
Rwork0.1896 19432 -
obs0.1926 20432 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.73 Å2 / Biso mean: 80.8134 Å2 / Biso min: 48.16 Å2
Refinement stepCycle: final / Resolution: 2.225→50.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2125 0 26 16 2167
Biso mean--94.01 64.73 -
Num. residues----291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082189
X-RAY DIFFRACTIONf_angle_d0.9822987
X-RAY DIFFRACTIONf_chiral_restr0.065365
X-RAY DIFFRACTIONf_plane_restr0.006385
X-RAY DIFFRACTIONf_dihedral_angle_d17.0491293
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2253-2.34260.32211570.28022734
2.3426-2.48930.28371290.25432759
2.4893-2.68150.30921380.24662767
2.6815-2.95140.28961410.23392769
2.9514-3.37840.31521480.24142759
3.3784-4.2560.2541500.18582794
4.256-50.1220.211370.15172850
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)
13.2926-0.42745.02384.2750.64778.28340.45960.41870.9283-0.0282-0.2593-0.42810.17651.1842-0.11970.6046-0.07670.09730.78840.06670.842737.88823.061134.0415
24.1732.27411.7953.56580.11744.71910.19530.01080.2602-0.0173-0.2571-0.57840.36320.62120.05820.59730.11320.07070.5160.12870.734529.4911-14.185233.4368
32.2013-0.33130.64721.4771-0.61110.2340.14050.4577-0.0585-0.3473-0.16850.00480.12810.165-0.00460.69770.16060.06460.630.01970.535526.1564-34.015425.8232
40.45030.07310.01263.39774.39585.63430.02620.032-0.13050.7754-0.1874-0.23640.33460.01240.02670.70380.1305-0.02260.54470.05450.622222.0674-28.590734.7628
52.50771.19311.06890.70240.8814.20050.250.23080.36720.0649-0.1793-0.04110.2154-0.1827-0.01380.72510.12160.07590.51190.06350.690113.631-22.515728.704
61.54660.48912.91165.10420.47025.31080.8951.2472-0.5072-2.0584-1.18110.5163-0.2677-0.13530.13480.98610.30980.07891.01940.09450.69618.9525-31.071513.074
71.30631.89610.36184.4815-0.49131.5218-0.09270.37090.49030.10290.12930.5094-0.122-0.00950.00450.65250.19710.07680.60460.0860.669317.8862-18.804624.4175
87.9061-3.46822.04095.87460.96852.8955-0.08061.3632-0.1950.4541-0.465-0.8759-0.35860.72370.15530.92490.14920.10291.21890.06071.281344.2859-16.243314.1991
95.7988-2.10871.24864.90811.50012.3082-0.16071.1354-0.2837-1.1349-0.4782-0.58210.26811.46260.63731.4740.09210.36111.14050.13750.805334.6482-15.70157.4255
107.8959-3.97140.92212.4676-2.17848.22840.23590.4597-0.6875-1.81660.0799-0.22991.41240.4648-0.00741.12520.07580.14980.77410.02610.847528.5937-18.579113.5
111.92410.47350.47142.30491.13265.49060.03080.33750.2845-0.40030.0753-0.0313-0.06570.8784-0.040.76160.11190.08830.68660.17550.874733.967-9.284822.7454
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 94 )A60 - 94
4X-RAY DIFFRACTION4chain 'A' and (resid 95 through 120 )A95 - 120
5X-RAY DIFFRACTION5chain 'A' and (resid 121 through 139 )A121 - 139
6X-RAY DIFFRACTION6chain 'A' and (resid 140 through 161 )A140 - 161
7X-RAY DIFFRACTION7chain 'A' and (resid 162 through 213 )A162 - 213
8X-RAY DIFFRACTION8chain 'A' and (resid 214 through 230 )A214 - 230
9X-RAY DIFFRACTION9chain 'A' and (resid 231 through 245 )A231 - 245
10X-RAY DIFFRACTION10chain 'A' and (resid 246 through 260 )A246 - 260
11X-RAY DIFFRACTION11chain 'A' and (resid 261 through 294 )A261 - 294

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