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- PDB-7npj: Crystal structure of Mycobacterium tuberculosis ArgC in complex w... -

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Basic information

Entry
Database: PDB / ID: 7npj
TitleCrystal structure of Mycobacterium tuberculosis ArgC in complex with 6-phenoxy-3-pyridinamine
ComponentsN-acetyl-gamma-glutamyl-phosphate reductase
KeywordsOXIDOREDUCTASE / ArgC / N-acetyl-gamma-glutamyl-phosphate reductase / NAGPR / Arginine biosynthesis
Function / homology
Function and homology information


N-acetyl-gamma-glutamyl-phosphate reductase / N-acetyl-gamma-glutamyl-phosphate reductase activity / L-arginine biosynthetic process / NADP+ binding / NAD binding / cytoplasm
Similarity search - Function
: / N-acetyl-gamma-glutamyl-phosphate reductase, type 1 / N-acetyl-gamma-glutamyl-phosphate reductase, active site / Semialdehyde dehydrogenase, dimerisation domain / N-acetyl-gamma-glutamyl-phosphate reductase active site. / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
6-phenoxy-3-pyridinamine / N-acetyl-gamma-glutamyl-phosphate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsGupta, P. / Mendes, V. / 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 27, 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: N-acetyl-gamma-glutamyl-phosphate reductase
B: N-acetyl-gamma-glutamyl-phosphate reductase
C: N-acetyl-gamma-glutamyl-phosphate reductase
D: N-acetyl-gamma-glutamyl-phosphate reductase
E: N-acetyl-gamma-glutamyl-phosphate reductase
F: N-acetyl-gamma-glutamyl-phosphate reductase
G: N-acetyl-gamma-glutamyl-phosphate reductase
H: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,0699
Polymers291,8828
Non-polymers1861
Water00
1
A: N-acetyl-gamma-glutamyl-phosphate reductase
B: N-acetyl-gamma-glutamyl-phosphate reductase
C: N-acetyl-gamma-glutamyl-phosphate reductase
D: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,1275
Polymers145,9414
Non-polymers1861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13840 Å2
ΔGint-100 kcal/mol
Surface area42800 Å2
MethodPISA
2
E: N-acetyl-gamma-glutamyl-phosphate reductase
F: N-acetyl-gamma-glutamyl-phosphate reductase
G: N-acetyl-gamma-glutamyl-phosphate reductase
H: N-acetyl-gamma-glutamyl-phosphate reductase


Theoretical massNumber of molelcules
Total (without water)145,9414
Polymers145,9414
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12920 Å2
ΔGint-103 kcal/mol
Surface area46300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.340, 132.813, 122.819
Angle α, β, γ (deg.)90.000, 90.120, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
N-acetyl-gamma-glutamyl-phosphate reductase / AGPR / N-acetyl-glutamate semialdehyde dehydrogenase / NAGSA dehydrogenase


Mass: 36485.305 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: argC, Rv1652, MTCY06H11.17 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WPZ9, N-acetyl-gamma-glutamyl-phosphate reductase
#2: Chemical ChemComp-UKK / 6-phenoxy-3-pyridinamine / 6-phenoxypyridin-3-amine


Mass: 186.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10N2O / Feature type: SUBJECT OF INVESTIGATION
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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris pH 7 17% PEG Smear High 70 mM phosphate/citrate pH 5.6 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.81→71.24 Å / Num. obs: 65900 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 79.25 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.059 / Rrim(I) all: 0.14 / Net I/σ(I): 6.9 / Num. measured all: 353903 / Scaling rejects: 390
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
2.81-2.885.51.8132640848070.3210.8422.0061100
12.57-71.245.30.06141267760.9760.0290.06815.899.7

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
PHASER2.8.2phasing
xia2data reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I3A, 2NQT

2i3a

2nqt


Resolution: 2.81→69.59 Å / SU ML: 0.63 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 38.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3246 3175 4.82 %
Rwork0.2375 62659 -
obs0.2417 65834 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 199.22 Å2 / Biso mean: 84.7941 Å2 / Biso min: 29.28 Å2
Refinement stepCycle: final / Resolution: 2.81→69.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18603 0 14 0 18617
Biso mean--73.09 --
Num. residues----2752
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.81-2.850.44251300.43242528265893
2.85-2.890.44331470.366327022849100
2.89-2.940.40541490.334927302879100
2.94-2.990.43481520.320426972849100
2.99-3.050.34611300.311227132843100
3.05-3.110.42191560.319427322888100
3.11-3.170.4141590.330527292888100
3.17-3.240.40361310.318927052836100
3.24-3.310.40691500.303826932843100
3.31-3.40.39311690.27926842853100
3.4-3.490.34411020.285127722874100
3.49-3.590.4593890.286627442833100
3.59-3.710.35821280.258627542882100
3.71-3.840.35481490.259727462895100
3.84-3.990.35241300.25927092839100
3.99-4.170.38151260.24727542880100
4.17-4.390.3451300.225327442874100
4.39-4.670.28591410.208527272868100
4.67-5.030.28561380.20427442882100
5.03-5.540.33571330.205827652898100
5.54-6.340.29691740.218127072881100
6.34-7.980.23111290.183127642893100
7.98-69.590.22131330.174228162949100
Refinement TLS params.Method: refined / Origin x: 19.798 Å / Origin y: -5.4102 Å / Origin z: 44.6798 Å
111213212223313233
T0.2245 Å2-0.0659 Å2-0.0382 Å2-0.3935 Å2-0.058 Å2--0.346 Å2
L-0.106 °2-0.2171 °2-0.2587 °2-0.2697 °20.1358 °2--0.692 °2
S-0.0206 Å °-0.0598 Å °0.0328 Å °0.0038 Å °-0.0294 Å °-0.0985 Å °0.0096 Å °-0.0084 Å °0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA9 - 352
2X-RAY DIFFRACTION1allB9 - 352
3X-RAY DIFFRACTION1allB401
4X-RAY DIFFRACTION1allC9 - 352
5X-RAY DIFFRACTION1allD9 - 352
6X-RAY DIFFRACTION1allE9 - 352
7X-RAY DIFFRACTION1allF9 - 352
8X-RAY DIFFRACTION1allG9 - 352
9X-RAY DIFFRACTION1allH9 - 352

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