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- PDB-7nn1: Crystal structure of Mycobacterium tuberculosis ArgD with prosthe... -

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Basic information

Entry
Database: PDB / ID: 7nn1
TitleCrystal structure of Mycobacterium tuberculosis ArgD with prosthetic group pyridoxal 5'-phosphate
ComponentsAcetylornithine aminotransferase
KeywordsTRANSFERASE / ArgD / N-acetylornithine aminotrasferase / AcOAT
Function / homology
Function and homology information


acetylornithine transaminase / N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity / L-arginine biosynthetic process / pyridoxal phosphate binding / identical protein binding / cytoplasm
Similarity search - Function
Acetylornithine/Succinylornithine transaminase family / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
NITRATE ION / Acetylornithine aminotransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.54 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 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

Downloads & links

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Assembly

Deposited unit
A: Acetylornithine aminotransferase
B: Acetylornithine aminotransferase
C: Acetylornithine aminotransferase
D: Acetylornithine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,5488
Polymers165,3004
Non-polymers2484
Water24,4461357
1
A: Acetylornithine aminotransferase
B: Acetylornithine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7744
Polymers82,6502
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9710 Å2
ΔGint-61 kcal/mol
Surface area23460 Å2
MethodPISA
2
C: Acetylornithine aminotransferase
D: Acetylornithine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7744
Polymers82,6502
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9640 Å2
ΔGint-61 kcal/mol
Surface area23450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.055, 184.265, 71.545
Angle α, β, γ (deg.)90.000, 106.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Acetylornithine aminotransferase / ACOAT


Mass: 41325.035 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: argD, Rv1655, MTCY06H11.20 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WPZ7, acetylornithine transaminase
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1357 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Bis-Tris Propane pH 8.5 18% PEG Smear High (PEGs 6K, 8K, 10K) 0.2 M ammonium nitrate 10 mM nickel chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.539→62.5 Å / Num. obs: 218441 / % possible obs: 91.7 % / Redundancy: 4.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.035 / Rrim(I) all: 0.081 / Net I/σ(I): 9.4
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
1.54-1.623.60.96775420209030.4380.5591.1241.160.2
4.87-62.550.0463813876180.9980.0220.0512099.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.18 Å62.5 Å
Translation4.18 Å62.5 Å

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.7.3data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ADB

4adb


Resolution: 1.54→46.812 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1988 10835 4.96 %
Rwork0.1771 207471 -
obs0.1781 218306 91.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.45 Å2 / Biso mean: 27.2946 Å2 / Biso min: 13.91 Å2
Refinement stepCycle: final / Resolution: 1.54→46.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11330 0 16 1363 12709
Biso mean--35.5 36.49 -
Num. residues----1564
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.54-1.55630.39132030.3803386751
1.5563-1.57460.37252180.3471425957
1.5746-1.59380.35852430.3467457961
1.5938-1.6140.32592560.3259506567
1.614-1.63520.35292780.3104550373
1.6352-1.65760.31293360.2904602880
1.6576-1.68130.31063840.2759680491
1.6813-1.70640.26873890.2571719295
1.7064-1.73310.29633810.2374724297
1.7331-1.76150.25773880.2316732597
1.7615-1.79190.27743720.2269748499
1.7919-1.82440.25594140.2192732098
1.8244-1.85950.24143830.2167744298
1.8595-1.89750.24454010.2128744799
1.8975-1.93870.24074100.2061739999
1.9387-1.98380.22283830.1998747099
1.9838-2.03350.23473820.1936744799
2.0335-2.08840.21253990.195747099
2.0884-2.14990.21643890.1859746799
2.1499-2.21930.2063770.1819747999
2.2193-2.29860.19323630.1793748999
2.2986-2.39060.22723900.1795745699
2.3906-2.49940.21143830.1783753099
2.4994-2.63120.20053610.1735750599
2.6312-2.7960.21143810.1757750599
2.796-3.01190.21423640.1703752699
3.0119-3.31490.17923840.1616753999
3.3149-3.79440.15733850.1489752699
3.7944-4.77980.13834100.1299752799
4.7798-46.8120.16074280.1512757999

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