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- PDB-7nn7: Crystal structure of Mycobacterium tuberculosis ArgB in complex w... -

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Basic information

Entry
Database: PDB / ID: 7nn7
TitleCrystal structure of Mycobacterium tuberculosis ArgB in complex with dimethyl 5-hydroxyisophthalate.
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
dimethyl 5-oxidanylbenzene-1,3-dicarboxylate / Acetylglutamate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.172 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 24, 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)31,6775
Polymers31,2131
Non-polymers4644
Water43224
1
A: Acetylglutamate kinase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)190,06430
Polymers187,2786
Non-polymers2,78624
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-158 kcal/mol
Surface area63330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.156, 174.156, 72.057
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-

98W

21A-304-

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-98W / dimethyl 5-oxidanylbenzene-1,3-dicarboxylate


Mass: 210.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 24 / 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: 63.49 %
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: 2.17→65.02 Å / Num. obs: 21728 / % possible obs: 98.3 % / Redundancy: 8.9 % / Biso Wilson estimate: 59.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.02 / Rrim(I) all: 0.059 / Net I/σ(I): 19.1 / Num. measured all: 193857
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
2.17-2.298.70.8632560629580.8390.3080.9172.393
6.87-65.028.50.04563757460.9980.0160.04843.599.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.85 Å65.02 Å
Translation6.85 Å65.02 Å

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Processing

Software
NameVersionClassification
PHENIX1.1refinement
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: 2.172→44.707 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 1126 5.18 %
Rwork0.1882 20592 -
obs0.1907 21718 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.35 Å2 / Biso mean: 76.1188 Å2 / Biso min: 45.4 Å2
Refinement stepCycle: final / Resolution: 2.172→44.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2119 0 29 24 2172
Biso mean--85.46 64.13 -
Num. residues----291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092178
X-RAY DIFFRACTIONf_angle_d0.9652971
X-RAY DIFFRACTIONf_chiral_restr0.063365
X-RAY DIFFRACTIONf_plane_restr0.006383
X-RAY DIFFRACTIONf_dihedral_angle_d14.711280
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.172-2.27080.29831170.2697237992
2.2708-2.39050.27451560.23172599100
2.3905-2.54030.27021180.2322619100
2.5403-2.73640.27531460.2475248896
2.7364-3.01170.29171410.23752638100
3.0117-3.44740.28551600.2342253898
3.4474-4.34270.23631390.17672635100
4.3427-44.7070.1881490.15112696100
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)
13.68570.37673.8855.92591.57074.47410.15280.68570.7827-0.18920.0337-0.6877-0.42651.0538-0.18970.5182-0.08210.13790.64760.11190.807237.65883.181233.6658
26.65072.56231.93185.29220.06367.750.1236-0.01910.32390.2063-0.2991-0.15690.07820.75880.18520.46570.06790.07870.43420.17690.597129.444-14.028733.4013
33.0175-0.72380.63953.8959-0.95180.9670.19020.6325-0.0355-0.4379-0.1622-0.08620.26770.1136-0.06420.55210.13970.05880.6028-0.00430.461426.2364-34.082625.8097
41.39230.78191.53544.95776.7559.03110.19410.0727-0.0531.0086-0.46050.1240.5856-0.13040.13990.61870.12180.02260.49440.11290.520522.1487-28.676534.7538
52.22820.58030.47633.9976-0.2912.51740.11390.52660.3368-0.3058-0.05590.27750.0749-0.0515-0.09670.57130.17830.04180.58180.10650.544417.2111-22.585422.6943
65.2507-4.93212.75667.66630.2574.94760.2860.9743-0.0881-0.4316-0.3285-0.9582-0.41120.566-0.0420.98070.14180.10371.12680.04561.102644.438-16.403714.3098
76.14981.41381.80669.05164.10924.89610.10141.3176-0.2051-1.3922-0.1667-1.4638-0.14851.5949-0.00691.18970.0880.361.04050.19260.754934.8977-15.8597.3321
83.8083-4.24250.03634.7325-0.51152.47180.27780.6036-0.5976-1.70790.09810.42361.0038-0.275-0.23631.08040.09430.08410.83960.08970.868628.9781-19.107313.4289
91.83761.36570.91432.24470.94756.24920.12970.26240.2195-0.22250.0813-0.1068-0.19310.5323-0.18160.66770.11910.09290.62310.18920.815934.0191-9.411522.6835
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 213 )A121 - 213
6X-RAY DIFFRACTION6chain 'A' and (resid 214 through 230 )A214 - 230
7X-RAY DIFFRACTION7chain 'A' and (resid 231 through 245 )A231 - 245
8X-RAY DIFFRACTION8chain 'A' and (resid 246 through 260 )A246 - 260
9X-RAY DIFFRACTION9chain 'A' and (resid 261 through 294 )A261 - 294

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