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

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Basic information

Entry
Database: PDB / ID: 7nlo
TitleCrystal structure of Mycobacterium tuberculosis ArgB in complex with L-arginine
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
ARGININE / Acetylglutamate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.82 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)31,6584
Polymers31,2131
Non-polymers4453
Water2,306128
1
A: Acetylglutamate kinase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)189,94524
Polymers187,2786
Non-polymers2,66718
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_676x-y+1,-y+2,-z+11
crystal symmetry operation6_766-x+2,-x+y+1,-z+11
Buried area18050 Å2
ΔGint-58 kcal/mol
Surface area63220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.298, 175.298, 70.537
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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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-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 3.34 Å3/Da / Density % sol: 63.19 %
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: May 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.82→63.97 Å / Num. obs: 37098 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 39.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.015 / Rrim(I) all: 0.046 / Net I/σ(I): 23.9 / Num. measured all: 372764 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1 / % possible all: 99.9

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.82-1.9210.11.02753930.8950.3441.083
5.76-63.979.40.032370980.9990.0110.034

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.87 Å63.97 Å
Translation6.87 Å63.97 Å

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Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
PHASER2.6.0phasing
PHENIX1.1refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AP9

2ap9


Resolution: 1.82→63.969 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2031 1838 4.96 %
Rwork0.1876 35220 -
obs0.1884 37058 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.4 Å2 / Biso mean: 56.2741 Å2 / Biso min: 31.93 Å2
Refinement stepCycle: final / Resolution: 1.82→63.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2116 0 29 128 2273
Biso mean--63.27 56.68 -
Num. residues----289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072176
X-RAY DIFFRACTIONf_angle_d0.8592963
X-RAY DIFFRACTIONf_chiral_restr0.058365
X-RAY DIFFRACTIONf_plane_restr0.005381
X-RAY DIFFRACTIONf_dihedral_angle_d14.4641295
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.82-1.86920.33821370.33822693
1.8692-1.92420.31051510.29792696
1.9242-1.98630.24391400.24392656
1.9863-2.05730.30681520.2282679
2.0573-2.13970.231400.20642705
2.1397-2.23710.211090.19082703
2.2371-2.3550.23121530.18742706
2.355-2.50260.22811190.19362717
2.5026-2.69580.24571660.20392687
2.6958-2.96710.24611640.21252697
2.9671-3.39640.22811340.20832728
3.3964-4.2790.17991380.1752741
4.279-63.9690.15291350.15292812
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)
13.68881.47181.4613.42421.54422.21330.13940.03550.003-0.1974-0.0357-0.20410.1290.0284-0.0880.42290.02880.03840.37480.12030.4592121.3344147.164330.7713
24.3583-4.3312-0.63114.47850.88984.9694-0.0311-0.1423-0.55440.6820.05160.62180.23660.0939-0.06810.4249-0.04-0.07420.35450.10320.6721117.9393138.889436.7675
31.8055-0.12690.04112.94381.15041.917-0.05160.32760.0255-0.1976-0.20140.1135-0.0171-0.05870.25390.38130.02670.00720.42090.02910.3721107.7111123.541325.4381
43.09551.2457-1.4611.71240.39921.5715-0.08850.2943-0.2763-0.18940.0986-0.34870.21990.1626-0.0350.51280.0711-0.070.46920.07970.4896122.1654136.321517.3554
53.7708-0.50430.75525.5257-2.41825.8176-0.17450.5481-0.4765-0.74850.1385-0.04480.66670.29340.04170.81850.03210.01190.6350.02540.534120.4879135.152110.1708
62.2311.0375-0.65713.35630.46412.70980.04840.43650.3469-0.52560.09970.05080.10910.1165-0.2070.48270.055-0.04630.37570.11740.47121.9252142.696922.6307
73.96680.3747-0.33843.73273.78864.0153-0.5452-0.3535-0.5131-0.03950.39240.46810.19860.35280.13270.57170.0643-0.04710.50760.01070.6492122.5659147.226421.3928
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 42 )A6 - 42
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 59 )A43 - 59
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 192 )A60 - 192
4X-RAY DIFFRACTION4chain 'A' and (resid 193 through 230 )A193 - 230
5X-RAY DIFFRACTION5chain 'A' and (resid 231 through 260 )A231 - 260
6X-RAY DIFFRACTION6chain 'A' and (resid 261 through 294 )A261 - 294
7X-RAY DIFFRACTION7chain 'A' and (resid 301 through 301 )A301

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