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

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Basic information

Entry
Database: PDB / ID: 7nnr
TitleCrystal structure of Mycobacterium tuberculosis ArgC in complex with xanthene-9-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
9~{H}-xanthene-9-carboxylic acid / N-acetyl-gamma-glutamyl-phosphate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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

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Assembly

Deposited unit
A: N-acetyl-gamma-glutamyl-phosphate reductase
B: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8426
Polymers72,9712
Non-polymers8714
Water12,088671
1
A: N-acetyl-gamma-glutamyl-phosphate reductase
B: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules

A: N-acetyl-gamma-glutamyl-phosphate reductase
B: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,68312
Polymers145,9414
Non-polymers1,7428
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area15540 Å2
ΔGint-83 kcal/mol
Surface area42430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.709, 78.227, 87.636
Angle α, β, γ (deg.)90.000, 127.510, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-802-

HOH

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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.: 2
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-UJQ / 9~{H}-xanthene-9-carboxylic acid


Mass: 226.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 671 / 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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris pH 5.5 17% PEG Smear High (PEGs 6K, 8K, 10K) 75 mM phosphate/citrate buffer pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.7→69.51 Å / Num. obs: 81979 / % possible obs: 99 % / Redundancy: 5.1 % / Biso Wilson estimate: 12.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.017 / Rrim(I) all: 0.038 / Net I/σ(I): 29.3 / Num. measured all: 417201 / Scaling rejects: 1
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
1.7-1.7340.1061559739450.9880.0580.12110.289.6
9-69.514.60.02127215870.9990.0110.02453.699.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.01 Å40.1 Å
Translation5.01 Å40.1 Å

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Processing

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

2i3a

2nqt


Resolution: 1.7→40.57 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1675 4077 4.97 %
Rwork0.1512 77884 -
obs0.1521 81961 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 48.52 Å2 / Biso mean: 15.8245 Å2 / Biso min: 5.21 Å2
Refinement stepCycle: final / Resolution: 1.7→40.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4918 0 62 675 5655
Biso mean--25.41 25.92 -
Num. residues----688
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.720.16641350.1541237087
1.72-1.740.2171280.1633250994
1.74-1.760.19991230.1629266198
1.76-1.790.18291180.1581269799
1.79-1.810.19781410.1578268499
1.81-1.840.20431390.1533265299
1.84-1.860.17541300.1557274299
1.86-1.890.20261270.15882697100
1.89-1.920.21491280.1525267799
1.92-1.960.16261500.1475270699
1.96-1.990.17591730.1517263799
1.99-2.030.1731580.15142659100
2.03-2.070.161440.14592713100
2.07-2.120.16991530.15172676100
2.12-2.170.15011270.15012715100
2.17-2.220.18471520.15152682100
2.22-2.280.16421360.1462713100
2.28-2.350.16741240.1522722100
2.35-2.420.20931090.15962746100
2.42-2.510.20651620.15912701100
2.51-2.610.15441380.15442711100
2.61-2.730.1681280.1522719100
2.73-2.870.18791200.15862756100
2.87-3.050.19231230.15642720100
3.05-3.290.15121270.15122719100
3.29-3.620.14551440.14552734100
3.62-4.140.13971740.13212708100
4.14-5.220.14371880.12992706100
5.22-40.570.16791780.1679275299

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