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

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Basic information

Entry
Database: PDB / ID: 7nph
TitleCrystal structure of Mycobacterium tuberculosis ArgC in complex with 5-methoxy-1,3-benzoxazole-2-carboxylic acid
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
PHOSPHATE ION / 5-methoxy-1,3-benzoxazole-2-carboxylic acid / N-acetyl-gamma-glutamyl-phosphate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 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 26, 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)292,17110
Polymers291,8828
Non-polymers2882
Water32418
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)146,2296
Polymers145,9414
Non-polymers2882
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14000 Å2
ΔGint-95 kcal/mol
Surface area42570 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
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13950 Å2
ΔGint-98 kcal/mol
Surface area43780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.290, 132.780, 122.818
Angle α, β, γ (deg.)90.000, 90.170, 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-UKE / 5-methoxy-1,3-benzoxazole-2-carboxylic acid / 5-Methoxybenzo[d]oxazole-2-carboxylic acid


Mass: 193.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
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: 2.57→69.593 Å / Num. obs: 86043 / % possible obs: 100 % / Redundancy: 5.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.034 / Rrim(I) all: 0.082 / Net I/σ(I): 11
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
2.57-2.645.51.6393474663380.5220.7611.8121100
11.49-69.595.40.035544010160.9960.0160.03838.299

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
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: 2.57→69.59 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 38.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3137 4222 4.91 %
Rwork0.2392 81683 -
obs0.2428 85905 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.01 Å2 / Biso mean: 81.6685 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.57→69.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19202 0 19 18 19239
Biso mean--63.22 62.7 -
Num. residues----2752
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.57-2.5990.40811500.3448267099
2.599-2.62960.40071490.3592271199
2.6296-2.66170.41641470.33652718100
2.6617-2.69540.3851110.33522691100
2.6954-2.73080.38221320.32352741100
2.7308-2.76830.40981360.32812704100
2.7683-2.80780.41261530.3342729100
2.8078-2.84970.40031310.35132698100
2.8497-2.89420.4171550.32642692100
2.8942-2.94170.37971290.3272730100
2.9417-2.99240.44631540.3262694100
2.9924-3.04680.38181360.30762709100
3.0468-3.10540.37961310.30722750100
3.1054-3.16880.36511550.31532715100
3.1688-3.23770.36791270.30952724100
3.2377-3.3130.41181370.29242702100
3.313-3.39590.38471690.28572705100
3.3959-3.48770.40891470.2792717100
3.4877-3.59030.34651320.27832708100
3.5903-3.70620.41641640.25642719100
3.7062-3.83870.28641390.25782751100
3.8387-3.99230.32121510.24422693100
3.9923-4.1740.3151300.23712744100
4.174-4.39410.33031550.22192722100
4.3941-4.66930.28081420.20732727100
4.6693-5.02970.29121400.21482734100
5.0297-5.53570.25051150.21582781100
5.5357-6.33630.31430.22272738100
6.3363-7.98120.24071470.1882748100
7.9812-69.590.19481150.1605281899

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