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- PDB-7nni: Crystal structure of Mycobacterium tuberculosis ArgC apoenzyme -

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Basic information

Entry
Database: PDB / ID: 7nni
TitleCrystal structure of Mycobacterium tuberculosis ArgC apoenzyme
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
N-acetyl-gamma-glutamyl-phosphate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.544 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 24, 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


Theoretical massNumber of molelcules
Total (without water)72,9712
Polymers72,9712
Non-polymers00
Water10,034557
1
A: N-acetyl-gamma-glutamyl-phosphate reductase
B: N-acetyl-gamma-glutamyl-phosphate reductase

A: N-acetyl-gamma-glutamyl-phosphate reductase
B: 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
crystal symmetry operation2_555-x,y,-z1
Buried area14370 Å2
ΔGint-87 kcal/mol
Surface area43360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.688, 77.991, 88.292
Angle α, β, γ (deg.)90.000, 127.520, 90.000
Int Tables number5
Space group name H-MC121

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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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 557 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.28 %
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: 0.9688 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9688 Å / Relative weight: 1
ReflectionResolution: 1.54→68.454 Å / Num. obs: 110883 / % possible obs: 99.9 % / Redundancy: 4.9 % / CC1/2: 0.986 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.101 / Rrim(I) all: 0.229 / Net I/σ(I): 5.4
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
1.54-1.634.61.46674721161030.4650.7521.6541.399.9
4.88-68.454.70.1261678936060.9820.060.1411.799.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.01 Å68.45 Å
Translation5.01 Å68.45 Å

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Processing

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

2i3a

2nqt


Resolution: 1.544→68.45 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2083 5473 4.96 %
Rwork0.1846 104902 -
obs0.1857 110375 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.95 Å2 / Biso mean: 17.6598 Å2 / Biso min: 7.05 Å2
Refinement stepCycle: final / Resolution: 1.544→68.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4989 0 0 557 5546
Biso mean---27.77 -
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 (%)
1.544-1.56120.32721740.3272323493
1.5612-1.57950.30681810.3068344497
1.5795-1.59880.34741610.3015343098
1.5988-1.6190.32751710.287346899
1.619-1.64030.30881960.2697348199
1.6403-1.66280.26452020.2546343599
1.6628-1.68660.28491960.24823461100
1.6866-1.71170.2511560.23733555100
1.7117-1.73850.23581850.22743517100
1.7385-1.7670.22861800.22263475100
1.767-1.79750.24252040.21873456100
1.7975-1.83010.2392020.21843500100
1.8301-1.86540.24771740.22153525100
1.8654-1.90340.26481910.21343506100
1.9034-1.94480.21521750.18873503100
1.9448-1.99010.23621800.17953489100
1.9901-2.03980.19911710.18163505100
2.0398-2.0950.19111910.16943512100
2.095-2.15660.20471740.16833520100
2.1566-2.22630.22021830.17143518100
2.2263-2.30580.18241710.16853519100
2.3058-2.39820.19321720.17433515100
2.3982-2.50730.19131990.17413520100
2.5073-2.63950.21072090.17073481100
2.6395-2.80490.19581810.17373534100
2.8049-3.02140.17671990.16833523100
3.0214-3.32550.1781860.1643513100
3.3255-3.80670.1761700.15123569100
3.8067-4.79580.1641520.14463581100
4.7958-68.450.19291870.1789361399

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