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

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Basic information

Entry
Database: PDB / ID: 7nln
TitleCrystal structure of Mycobacterium tuberculosis ArgB in complex with N-acetyl-glutamate
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
N-ACETYL-L-GLUTAMATE / Acetylglutamate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 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
B: Acetylglutamate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9907
Polymers62,4262
Non-polymers5655
Water5,801322
1
A: Acetylglutamate kinase
B: Acetylglutamate kinase
hetero molecules

A: Acetylglutamate kinase
B: Acetylglutamate kinase
hetero molecules

A: Acetylglutamate kinase
B: Acetylglutamate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,97121
Polymers187,2786
Non-polymers1,69415
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area17460 Å2
ΔGint-53 kcal/mol
Surface area61490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.244, 100.244, 124.526
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 6:46 or resseq 48:77 or resseq...
21(chain B and (resseq 6:46 or resseq 48:77 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 6:46 or resseq 48:77 or resseq...A6 - 46
121(chain A and (resseq 6:46 or resseq 48:77 or resseq...A48 - 77
131(chain A and (resseq 6:46 or resseq 48:77 or resseq...A79 - 82
141(chain A and (resseq 6:46 or resseq 48:77 or resseq...A83
151(chain A and (resseq 6:46 or resseq 48:77 or resseq...A5 - 294
161(chain A and (resseq 6:46 or resseq 48:77 or resseq...A5 - 294
171(chain A and (resseq 6:46 or resseq 48:77 or resseq...A5 - 294
181(chain A and (resseq 6:46 or resseq 48:77 or resseq...A5 - 294
211(chain B and (resseq 6:46 or resseq 48:77 or resseq...B6 - 46
221(chain B and (resseq 6:46 or resseq 48:77 or resseq...B48 - 77
231(chain B and (resseq 6:46 or resseq 48:77 or resseq...B79 - 84
241(chain B and (resseq 6:46 or resseq 48:77 or resseq...B0
251(chain B and (resseq 6:46 or resseq 48:77 or resseq...B6 - 294
261(chain B and (resseq 6:46 or resseq 48:77 or resseq...B6 - 294
271(chain B and (resseq 6:46 or resseq 48:77 or resseq...B6 - 294
281(chain B and (resseq 6:46 or resseq 48:77 or resseq...B6 - 294
291(chain B and (resseq 6:46 or resseq 48:77 or resseq...B6 - 294
2101(chain B and (resseq 6:46 or resseq 48:77 or resseq...B6 - 294
2111(chain B and (resseq 6:46 or resseq 48:77 or resseq...B6 - 294
2121(chain B and (resseq 6:46 or resseq 48:77 or resseq...B6 - 294

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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.: 2
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-NLG / N-ACETYL-L-GLUTAMATE


Mass: 189.166 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 1000 mM Potassium sodium tartrate 100 mM Imidazole/HCl pH 8.0 200 mM Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.919→124.53 Å / Num. obs: 54187 / % possible obs: 99.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 32.83 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.022 / Rrim(I) all: 0.074 / Net I/σ(I): 19.6
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
1.92-2.025.20.5954076478790.8130.2850.6622.599.6
6.07-124.5311.60.0472049517740.9990.0140.0546100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.41 Å86.81 Å
Translation7.41 Å86.81 Å

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Processing

Software
NameVersionClassification
PHENIX1.1refinement
Aimless0.5.15data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AP9

2ap9


Resolution: 1.92→71.216 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1961 2745 5.07 %
Rwork0.1649 51405 -
obs0.1666 54150 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.06 Å2 / Biso mean: 42.9767 Å2 / Biso min: 20.09 Å2
Refinement stepCycle: final / Resolution: 1.92→71.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4227 0 38 322 4587
Biso mean--54.22 47.36 -
Num. residues----579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084336
X-RAY DIFFRACTIONf_angle_d1.0165908
X-RAY DIFFRACTIONf_chiral_restr0.098730
X-RAY DIFFRACTIONf_plane_restr0.006766
X-RAY DIFFRACTIONf_dihedral_angle_d16.2992563
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2420X-RAY DIFFRACTION7.801TORSIONAL
12B2420X-RAY DIFFRACTION7.801TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.92-1.95190.281200.2571255499
1.9519-1.98740.29141260.23362534100
1.9874-2.02560.26031370.20372590100
2.0256-2.0670.22071740.19552529100
2.067-2.11190.22121310.18192566100
2.1119-2.1610.24931280.1792582100
2.161-2.21510.20361120.17342595100
2.2151-2.2750.20881300.1752575100
2.275-2.34190.21381180.17232565100
2.3419-2.41750.22021540.17272556100
2.4175-2.50390.2161370.17432571100
2.5039-2.60420.22211380.17872546100
2.6042-2.72270.21081450.17792556100
2.7227-2.86630.25051510.18482582100
2.8663-3.04590.22341360.18362573100
3.0459-3.2810.2241220.18062595100
3.281-3.61120.22051220.16662592100
3.6112-4.13370.16771810.14562530100
4.1337-5.20780.13321200.12842614100
5.2078-71.2160.16611630.14952600100
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)
15.1752.20061.10796.04171.12842.1659-0.0076-0.12-0.24650.06690.1556-0.30790.00590.2103-0.14480.2825-0.0070.03060.2657-0.03870.2686-21.044412.5928-23.1769
21.30190.48270.48913.293-0.46530.8330.00550.2281-0.1282-0.9196-0.0794-0.14790.2530.19020.06640.40740.05190.05830.2931-0.01020.2861-34.502-9.8803-30.5907
32.45011.01220.39991.81680.42552.3328-0.01490.3177-0.0152-0.27390.0804-0.1120.03040.1256-0.04390.28030.02230.00220.2232-0.00160.2304-36.35880.5854-32.4078
42.82021.01692.63031.81660.37316.7758-0.07490.8814-0.1529-0.52650.3093-0.24970.10150.9473-0.1870.3921-0.03360.03020.4516-0.07980.2926-23.06276.6671-39.8683
53.57663.78595.3697.26054.09869.25360.3746-0.5092-0.24610.0176-0.20470.51080.4178-0.8678-0.12580.31780.03490.00140.28370.0280.3554-79.54926.0839-17.7875
64.5780.39281.30335.38691.08913.92090.13280.1784-0.0346-0.1121-0.0372-0.0260.1932-0.0864-0.07840.2047-0.00010.04220.21590.01770.2201-61.9159-1.7101-18.1184
73.6882-1.4569-0.47331.20120.79661.4471-0.2143-0.5787-0.37210.4260.20390.1660.25790.18110.00230.32840.01670.01750.27770.04540.2641-46.9637-12.7278-10.5865
89.7896-6.45575.53576.8784-4.67334.70530.22050.3076-0.3376-0.24-0.11970.01610.2360.3203-0.18310.23720.02120.02130.1971-0.01770.1922-46.6518-7.0223-19.2872
93.9170.64190.9170.90350.68144.4882-0.1564-0.21170.26170.25540.1728-0.1041-0.43960.3498-0.01770.2718-0.01330.01470.1559-0.02610.2208-44.7223.2175-13.1851
103.5457-0.9582-0.29942.0488-1.36464.789-0.3279-0.7425-0.25171.4995-0.00080.29880.04290.310.27570.55670.0270.06730.45420.00160.2982-42.6675-6.58212.7314
113.1835-0.194-0.7820.77030.32212.02980.0697-0.3109-0.07790.109-0.04340.06990.0173-0.0275-0.02960.307-0.0046-0.00880.2255-0.00570.246-55.9965-1.9586-6.3659
125.2939-0.6537-1.04873.8783-0.09356.7049-0.0493-0.5244-0.31580.269-0.00370.01610.27070.11830.01640.3528-0.00320.01620.3207-0.01060.211-61.5978-6.11965.0112
132.85130.31350.44622.44371.29126.69420.0101-0.23090.14080.17860.01990.2847-0.1237-0.4814-0.03660.25550.02540.04490.21860.01140.2896-68.6038-1.5709-7.2032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 59 )A5 - 59
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 94 )A60 - 94
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 230 )A95 - 230
4X-RAY DIFFRACTION4chain 'A' and (resid 231 through 294 )A231 - 294
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 26 )B6 - 26
6X-RAY DIFFRACTION6chain 'B' and (resid 27 through 59 )B27 - 59
7X-RAY DIFFRACTION7chain 'B' and (resid 60 through 94 )B60 - 94
8X-RAY DIFFRACTION8chain 'B' and (resid 95 through 120 )B95 - 120
9X-RAY DIFFRACTION9chain 'B' and (resid 121 through 139 )B121 - 139
10X-RAY DIFFRACTION10chain 'B' and (resid 140 through 161 )B140 - 161
11X-RAY DIFFRACTION11chain 'B' and (resid 162 through 230 )B162 - 230
12X-RAY DIFFRACTION12chain 'B' and (resid 231 through 260 )B231 - 260
13X-RAY DIFFRACTION13chain 'B' and (resid 261 through 294 )B261 - 294

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