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- PDB-7not: Crystal structure of Mycobacterium tuberculosis ArgC in complex w... -

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Basic information

Entry
Database: PDB / ID: 7not
TitleCrystal structure of Mycobacterium tuberculosis ArgC in complex with nicotinamide adenine dinucleotide phosphate (NADP+) and 5-Methoxy-3-indoleacetic 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 / arginine biosynthetic process / NADP+ binding / NAD binding / protein dimerization activity / cytoplasm
Similarity search - Function
N-acetyl-gamma-glutamyl-phosphate reductase, type 1 / N-acetyl-gamma-glutamyl-phosphate reductase, active site / N-acetyl-gamma-glutamyl-phosphate reductase active site. / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
(5-methoxy-1H-indol-3-yl)acetic acid / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / N-acetyl-gamma-glutamyl-phosphate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 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 25, 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)285,49314
Polymers283,1858
Non-polymers2,3086
Water2,486138
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)143,90010
Polymers141,5924
Non-polymers2,3086
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16300 Å2
ΔGint-100 kcal/mol
Surface area42700 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)141,5924
Polymers141,5924
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14080 Å2
ΔGint-93 kcal/mol
Surface area42980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.400, 132.000, 124.550
Angle α, β, γ (deg.)90.000, 97.060, 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: 35398.121 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: argC, Rv1652, MTCY06H11.17 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WPZ9, N-acetyl-gamma-glutamyl-phosphate reductase
#2: Chemical
ChemComp-MYI / (5-methoxy-1H-indol-3-yl)acetic acid / 5-methoxy-indole acetate


Mass: 205.210 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.35 Å3/Da / Density % sol: 47.56 %
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: 2.54→63.91 Å / Num. obs: 87548 / % possible obs: 99.3 % / Redundancy: 5.3 % / CC1/2: 0.986 / Rmerge(I) obs: 0.235 / Rpim(I) all: 0.11 / Rrim(I) all: 0.26 / Net I/σ(I): 7.3 / Num. measured all: 463192 / Scaling rejects: 2218
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
2.54-2.615.62.3533639264860.3171.0822.5980.899.9
11.36-63.915.20.05551909930.990.0270.06226.196.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHASER2.8.2phasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I3A, 2NQT

2i3a

2nqt


Resolution: 2.54→58.436 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2776 4348 4.97 %
Rwork0.2016 83144 -
obs0.2053 87492 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.01 Å2 / Biso mean: 54.9656 Å2 / Biso min: 29.62 Å2
Refinement stepCycle: final / Resolution: 2.54→58.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19806 0 156 138 20100
Biso mean--60.39 50.54 -
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 (%)
2.54-2.56890.33461300.28952746100
2.5689-2.59910.35721380.2932810100
2.5991-2.63080.37911390.29822768100
2.6308-2.66410.35461660.29292746100
2.6641-2.69910.3651500.28082801100
2.6991-2.73610.34371450.27482726100
2.7361-2.77520.35951520.2752813100
2.7752-2.81660.34351300.26982737100
2.8166-2.86060.37311360.2818280499
2.8606-2.90750.36151470.28562770100
2.9075-2.95770.39421560.2923274899
2.9577-3.01150.35691390.29942780100
3.0115-3.06940.38541520.2949279899
3.0694-3.1320.37571410.299273599
3.132-3.20010.38821420.2942279199
3.2001-3.27460.37011480.2691274899
3.2746-3.35640.3261480.2423275499
3.3564-3.44720.29461450.21332793100
3.4472-3.54860.29291440.2199276999
3.5486-3.66310.25951330.2104277299
3.6631-3.7940.31571660.1937277299
3.794-3.94590.26491490.1733275799
3.9459-4.12540.27731330.1638276599
4.1254-4.34290.2161520.1519276299
4.3429-4.61490.18271440.1442277099
4.6149-4.9710.22461390.1477275499
4.971-5.47090.22921390.1621278799
5.4709-6.26180.23631480.1818279399
6.2618-7.88610.24811560.1667278599
7.8861-58.4360.20421410.1578279097

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