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- PDB-7nm0: Crystal structure of Mycobacterium tuberculosis ArgB in complex w... -

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Basic information

Entry
Database: PDB / ID: 7nm0
TitleCrystal structure of Mycobacterium tuberculosis ArgB in complex with 1-(2,6-dihydroxyphenyl)ethan-1-one.
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
1-[2,6-bis(oxidanyl)phenyl]ethanone / Acetylglutamate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.281 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 23, 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)31,6195
Polymers31,2131
Non-polymers4064
Water25214
1
A: Acetylglutamate kinase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)189,71630
Polymers187,2786
Non-polymers2,43824
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 area20110 Å2
ΔGint-215 kcal/mol
Surface area63640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.345, 174.345, 72.096
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-

9EQ

21A-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-9EQ / 1-[2,6-bis(oxidanyl)phenyl]ethanone


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3 / 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: 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: 3.38 Å3/Da / Density % sol: 63.59 %
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: 2.28→87.17 Å / Num. obs: 18982 / % possible obs: 99 % / Redundancy: 9 % / Biso Wilson estimate: 62.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.017 / Rrim(I) all: 0.05 / Net I/σ(I): 22.3 / Num. measured all: 170194
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.28-2.49.30.9552583727710.8920.331.0112.2
7.21-87.178.40.0354646490.9990.0110.03266.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.86 Å87.17 Å
Translation6.86 Å87.17 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: 2.281→43.586 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2253 982 5.18 %
Rwork0.1929 17984 -
obs0.1946 18966 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159 Å2 / Biso mean: 84.2765 Å2 / Biso min: 46.59 Å2
Refinement stepCycle: final / Resolution: 2.281→43.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2117 0 25 14 2156
Biso mean--95.11 65.15 -
Num. residues----291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082172
X-RAY DIFFRACTIONf_angle_d0.9822964
X-RAY DIFFRACTIONf_chiral_restr0.058365
X-RAY DIFFRACTIONf_plane_restr0.006382
X-RAY DIFFRACTIONf_dihedral_angle_d15.8391276
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.281-2.40090.32961350.27292568100
2.4009-2.55130.32091320.25942583100
2.5513-2.74820.27481310.2567243795
2.7482-3.02470.29511520.24362586100
3.0247-3.46220.31481450.2421252598
3.4622-4.36140.2181440.18232620100
4.3614-43.5860.17161430.15672665100
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)
17.88360.05745.03626.76650.98043.38550.24150.35921.0726-0.2913-0.0221-0.5977-0.17540.824-0.21940.5749-0.06650.15730.77450.10591.033837.90893.022334.0331
26.88044.22440.51413.45521.47277.3060.0647-0.09380.09950.2296-0.289-0.61180.26360.55170.1030.47190.05870.05930.44980.19270.724829.4912-14.212733.4858
32.6658-0.91050.22825.22011.2861.55670.22470.63820.1426-0.2759-0.24870.0050.07290.07740.01010.4940.13280.05850.54820.09070.47921.3947-29.970726.2634
41.48182.02010.75595.4807-0.48972.1032-0.14210.33120.4079-0.12160.0360.4232-0.3132-0.21310.070.56790.21930.05260.58180.0850.649817.9092-19.005124.4165
52.48481.03890.26731.88041.72053.7199-0.16560.58640.0546-0.58980.302-0.5388-0.09450.5994-0.09820.85590.08620.15670.71510.19870.895935.5985-13.893516.3609
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 161 )A60 - 161
4X-RAY DIFFRACTION4chain 'A' and (resid 162 through 213 )A162 - 213
5X-RAY DIFFRACTION5chain 'A' and (resid 214 through 294 )A214 - 294

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