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

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Basic information

Entry
Database: PDB / ID: 7nlr
TitleCrystal structure of Mycobacterium tuberculosis ArgB in complex with 2-phenyl-1H-imidazole
ComponentsAcetylglutamate kinase
KeywordsTRANSFERASE / ArgB Acetylglutamate kinase
Function / homology
Function and homology information


acetylglutamate kinase / acetylglutamate kinase activity / arginine biosynthetic process via ornithine / arginine biosynthetic process / peptidoglycan-based cell wall / phosphorylation / 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 / Amino acid kinase family / Acetylglutamate kinase-like superfamily
Similarity search - Domain/homology
2-phenyl-1H-imidazole / Acetylglutamate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.254 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

Downloads & links

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Assembly

Deposited unit
A: Acetylglutamate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5494
Polymers31,2131
Non-polymers3363
Water41423
1
A: Acetylglutamate kinase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)189,29624
Polymers187,2786
Non-polymers2,01818
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 area19070 Å2
ΔGint-232 kcal/mol
Surface area64410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.819, 173.819, 72.432
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-

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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PIY / 2-phenyl-1H-imidazole


Mass: 144.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.37 Å3/Da / Density % sol: 63.54 %
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: 2.25→86.91 Å / Num. obs: 19795 / % possible obs: 99.8 % / Redundancy: 10.1 % / Biso Wilson estimate: 60.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.017 / Rrim(I) all: 0.052 / Net I/σ(I): 23.1 / Num. measured all: 199430
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
2.25-2.3910.10.8613171431390.8430.2840.9072.398.9
6.76-86.919.50.02873947820.9990.010.02966.799.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.85 Å86.91 Å
Translation6.85 Å86.91 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: 2.254→52.19 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.214 921 4.65 %
Rwork0.1836 18870 -
obs0.185 19791 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.65 Å2 / Biso mean: 75.8657 Å2 / Biso min: 45 Å2
Refinement stepCycle: final / Resolution: 2.254→52.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2124 0 21 23 2168
Biso mean--96.09 65.11 -
Num. residues----291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082181
X-RAY DIFFRACTIONf_angle_d0.9082975
X-RAY DIFFRACTIONf_chiral_restr0.059365
X-RAY DIFFRACTIONf_plane_restr0.006384
X-RAY DIFFRACTIONf_dihedral_angle_d16.2461284
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2545-2.37330.29491350.2542262799
2.3733-2.5220.26951450.23222681100
2.522-2.71680.28871380.23792680100
2.7168-2.99010.26491310.21872667100
2.9901-3.42270.26461300.23012704100
3.4227-4.3120.21671280.17642715100
4.312-52.190.15521140.14732796100
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)
14.00890.24654.15866.92371.15464.65550.26040.55320.9555-0.2553-0.0875-0.8802-0.33771.2562-0.16490.5635-0.08360.15560.77470.05970.782137.7223.191233.9043
26.93173.35863.49032.12531.277.09730.48030.37740.0074-0.5953-0.4676-0.51780.55850.82360.00820.51290.10450.13420.54330.17070.540128.6186-15.784229.4546
37.039-2.152-0.08087.21383.73192.8345-0.0353-0.40650.10580.7184-0.1786-0.32810.18640.66830.18020.59910.0650.0230.56960.15320.68430.276-12.82637.334
41.7965-0.51480.20223.1782-0.6260.05160.06520.38730.032-0.2587-0.0491-0.05520.10770.1274-0.03590.59210.15140.0530.5826-0.00710.453226.156-34.109525.9966
51.55161.90211.49487.86897.57787.89980.12860.1294-0.03760.9351-0.39750.00620.69520.06330.08710.62980.15370.01650.48810.09210.486221.8493-29.492234.5045
63.01691.71331.89671.05080.23644.26010.19390.23440.18270.1798-0.26530.0710.5974-0.11710.01860.5820.13660.03910.4840.03130.548914.5788-21.820229.8068
72.7811-0.04313.22927.8072.25627.08170.58821.1439-0.3518-2.3196-0.5710.3521-0.25640.5004-0.20910.95260.23280.05720.92880.1470.541718.9182-31.243913.1568
81.59381.11920.14194.5738-0.59241.7366-0.06870.36540.3416-0.07740.0880.3638-0.1682-0.0861-0.02960.58660.19620.04690.56030.07650.552917.8779-18.897224.5857
95.5391-4.09830.92288.88820.50217.85940.28081.104-0.506-0.112-0.7715-0.623-0.94991.15610.51270.99620.23010.0911.20380.04551.088644.3975-16.134414.4378
104.4861-0.13880.20981.70981.93273.58510.01240.8588-0.1869-1.463-0.3581-1.0923-0.00641.29040.32611.37260.16890.32021.10020.18480.756534.776-15.72967.7309
115.5688-2.36321.32091.9908-2.05892.731-0.18520.4626-1.0676-1.23380.49290.3081.0612-0.1082-0.4131.10880.14970.130.72320.07110.770728.8865-18.792313.5752
122.19362.11511.65292.06411.68819.5657-0.13420.26940.2042-0.48160.2078-0.1806-0.41650.535-0.04060.6450.13030.09550.60410.17580.757434.0384-9.286522.9996
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 42 )A27 - 42
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 59 )A43 - 59
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 94 )A60 - 94
5X-RAY DIFFRACTION5chain 'A' and (resid 95 through 119 )A95 - 119
6X-RAY DIFFRACTION6chain 'A' and (resid 120 through 139 )A120 - 139
7X-RAY DIFFRACTION7chain 'A' and (resid 140 through 161 )A140 - 161
8X-RAY DIFFRACTION8chain 'A' and (resid 162 through 213 )A162 - 213
9X-RAY DIFFRACTION9chain 'A' and (resid 214 through 230 )A214 - 230
10X-RAY DIFFRACTION10chain 'A' and (resid 231 through 245 )A231 - 245
11X-RAY DIFFRACTION11chain 'A' and (resid 246 through 260 )A246 - 260
12X-RAY DIFFRACTION12chain 'A' and (resid 261 through 294 )A261 - 294

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