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

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Basic information

Entry
Database: PDB / ID: 7nlu
TitleCrystal structure of Mycobacterium tuberculosis ArgB in complex with 1-(1H-indol-3-yl)ethan-1-one
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
1-(1~{H}-indol-3-yl)ethanone / Acetylglutamate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.235 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)31,5644
Polymers31,2131
Non-polymers3513
Water25214
1
A: Acetylglutamate kinase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)189,38624
Polymers187,2786
Non-polymers2,10818
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-242 kcal/mol
Surface area63160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.487, 174.487, 71.730
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-302-

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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-5RN / 1-(1~{H}-indol-3-yl)ethanone


Mass: 159.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 63.46 %
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: 0.9763 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: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.235→64.8 Å / Num. obs: 20234 / % possible obs: 99.8 % / Redundancy: 8.9 % / Biso Wilson estimate: 60.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.018 / Rrim(I) all: 0.053 / Net I/σ(I): 20.2
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
2.235-2.369.11.0032662329290.90.3491.0632.4100
7.07-64.88.40.03256116710.9990.0110.03455.897.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.84 Å64.8 Å
Translation6.84 Å64.8 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: 2.235→26.532 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 988 4.89 %
Rwork0.1947 19220 -
obs0.1967 20208 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.69 Å2 / Biso mean: 77.7133 Å2 / Biso min: 44.77 Å2
Refinement stepCycle: final / Resolution: 2.235→26.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2102 0 22 14 2138
Biso mean--89.16 65.88 -
Num. residues----291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092166
X-RAY DIFFRACTIONf_angle_d1.1112958
X-RAY DIFFRACTIONf_chiral_restr0.062365
X-RAY DIFFRACTIONf_plane_restr0.006380
X-RAY DIFFRACTIONf_dihedral_angle_d16.271272
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2353-2.35310.3291330.29092724100
2.3531-2.50040.32061150.26442727100
2.5004-2.69330.31911490.24612748100
2.6933-2.9640.27261570.24132715100
2.964-3.39220.28271400.24472753100
3.3922-4.27090.25391550.192743100
4.2709-26.5320.17871390.1564281099
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)
19.88143.49214.89036.06952.8032.66480.23-0.16270.3204-0.20010.0525-0.3812-0.10230.4048-0.12180.578-0.01520.11880.70080.10110.993737.94082.931133.9266
25.81223.28590.60622.68942.28127.07930.1449-0.11530.39080.1857-0.1469-0.26670.1250.42990.01260.44080.05590.02940.40080.14340.675829.3271-14.066533.3831
32.08950.03720.534.27830.51732.06810.06760.44720.1612-0.2023-0.11510.19190.04970.0190.04430.48880.12810.02840.54380.05870.549720.2607-26.440125.4934
44.3087-0.2370.58816.04220.71943.115-0.21010.2754-0.7633-0.1914-0.2266-0.5056-0.27370.84860.27850.82130.14480.08550.9957-0.03571.172544.2709-16.622114.2476
51.86561.155-0.27372.69812.17046.1404-0.09670.45240.0968-0.61040.2126-0.4951-0.0980.4893-0.11730.7030.08950.0940.62380.17510.817332.9375-13.180116.8395
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 213 )A60 - 213
4X-RAY DIFFRACTION4chain 'A' and (resid 214 through 230 )A214 - 230
5X-RAY DIFFRACTION5chain 'A' and (resid 231 through 294 )A231 - 294

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