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

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Basic information

Entry
Database: PDB / ID: 7nlp
TitleCrystal structure of Mycobacterium tuberculosis ArgB in complex with L-canavanine
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
L-CANAVANINE / Acetylglutamate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.213 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)31,4853
Polymers31,2131
Non-polymers2722
Water19811
1
A: Acetylglutamate kinase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)188,91118
Polymers187,2786
Non-polymers1,63312
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 area19340 Å2
ΔGint-138 kcal/mol
Surface area63070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.058, 174.058, 71.154
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-GGB / L-CANAVANINE / L-2-AMINO-4-(GUANIDINOOXY)BUTYRIC ACID


Type: L-peptide linking / Mass: 176.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.32 Å3/Da / Density % sol: 62.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion
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: Feb 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.21→87.03 Å / Num. obs: 20426 / % possible obs: 98.9 % / Redundancy: 7.6 % / Biso Wilson estimate: 48.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.024 / Rrim(I) all: 0.066 / Net I/σ(I): 14.6 / Num. measured all: 154874
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
2.21-2.337.20.5312011628110.9510.2080.5722.294
7-87.037.10.0349166950.9990.0120.03238.399.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.84 Å87.03 Å
Translation6.84 Å87.03 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: 2.213→64.346 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 35.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2409 981 4.81 %
Rwork0.2051 19417 -
obs0.207 20398 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.8 Å2 / Biso mean: 68.6298 Å2 / Biso min: 38.25 Å2
Refinement stepCycle: final / Resolution: 2.213→64.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2100 0 17 11 2128
Biso mean--79.63 58.48 -
Num. residues----292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082151
X-RAY DIFFRACTIONf_angle_d1.0142937
X-RAY DIFFRACTIONf_chiral_restr0.062367
X-RAY DIFFRACTIONf_plane_restr0.006378
X-RAY DIFFRACTIONf_dihedral_angle_d16.0571265
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.213-2.32960.40021360.316259994
2.3296-2.47550.3311400.26012794100
2.4755-2.66670.28871220.25012781100
2.6667-2.9350.32011390.24232809100
2.935-3.35970.26591470.25582790100
3.3597-4.23280.21991560.195275699
4.2328-64.3460.1981410.16382888100
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)
13.26454.59564.57337.87794.65427.960.5360.63210.39720.0692-0.0236-0.42490.40790.8267-0.50570.52350.03150.04280.4480.01860.676437.77842.682233.526
25.53162.9891.70691.61631.06057.14640.1494-0.0737-0.16580.0992-0.1236-0.17970.38420.12730.00030.51440.0053-0.03010.35860.09910.792629.5232-14.22133.2685
31.5188-0.47590.19893.1310.84152.24750.00990.29170.07-0.1756-0.20410.1751-0.08-0.15390.2140.33150.03670.0020.41660.01010.531619.8617-28.04325.8458
43.24170.7463-1.91940.92490.62642.55130.14140.3201-0.0749-0.3309-0.1634-0.2241-0.00240.31970.01730.62530.0632-0.05670.60610.07910.77131.7368-16.130418.5511
52.2613-1.45370.42972.46691.98193.4749-0.47240.89470.32620.41590.4506-0.9289-0.564-0.46970.09720.90130.0617-0.00070.7590.08880.697338.004-10.841310.0702
66.4313-0.0282-1.5171.93450.12495.36620.14710.7423-0.0506-1.5918-0.3306-0.58121.160.23910.4721.00910.13860.08060.6767-0.00030.679331.7605-19.151111.6007
73.47233.61261.24584.09892.40515.33870.01810.38170.5669-0.27980.0238-0.1118-0.13330.4097-0.14330.52950.07420.00960.42430.1360.690634.0001-9.048522.8331
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 26 )A3 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 59 )A27 - 59
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 192 )A60 - 192
4X-RAY DIFFRACTION4chain 'A' and (resid 193 through 224 )A193 - 224
5X-RAY DIFFRACTION5chain 'A' and (resid 225 through 239 )A225 - 239
6X-RAY DIFFRACTION6chain 'A' and (resid 240 through 260 )A240 - 260
7X-RAY DIFFRACTION7chain 'A' and (resid 261 through 294 )A261 - 294

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