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- PDB-7nn4: Crystal structure of Mycobacterium tuberculosis ArgD with prosthe... -

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Basic information

Entry
Database: PDB / ID: 7nn4
TitleCrystal structure of Mycobacterium tuberculosis ArgD with prosthetic group pyridoxal 5'-phosphate and 3-hydroxy-2-naphthoic acid.
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
3-hydroxynaphthalene-2-carboxylic acid / NITRATE ION / Acetylornithine aminotransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 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: Acetylornithine aminotransferase
B: Acetylornithine aminotransferase
C: Acetylornithine aminotransferase
D: Acetylornithine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,30310
Polymers165,3004
Non-polymers1,0036
Water25,6711425
1
A: Acetylornithine aminotransferase
B: Acetylornithine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0264
Polymers82,6502
Non-polymers3762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9450 Å2
ΔGint-64 kcal/mol
Surface area23570 Å2
MethodPISA
2
C: Acetylornithine aminotransferase
D: Acetylornithine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2776
Polymers82,6502
Non-polymers6274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9690 Å2
ΔGint-63 kcal/mol
Surface area23450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.190, 184.350, 71.300
Angle α, β, γ (deg.)90.000, 106.210, 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-BZJ / 3-hydroxynaphthalene-2-carboxylic acid


Mass: 188.179 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C11H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1425 / 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: 2.5 Å3/Da / Density % sol: 50.85 %
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: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.47→68.47 Å / Num. obs: 265823 / % possible obs: 97.4 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.021 / Rrim(I) all: 0.048 / Net I/σ(I): 16.5 / Num. measured all: 1192624 / Scaling rejects: 5
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
1.47-1.5130.81251854175100.50.5470.9871.286.7
6.57-68.475.10.01715841310910.0080.01954.299.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.2 Å68.47 Å
Translation4.2 Å68.47 Å

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.7.4data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.27data extraction
xia2data reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ADB

4adb


Resolution: 1.47→68.465 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1959 13042 4.91 %
Rwork0.1769 252719 -
obs0.1778 265761 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.33 Å2 / Biso mean: 24.1684 Å2 / Biso min: 11.75 Å2
Refinement stepCycle: final / Resolution: 1.47→68.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11344 0 74 1427 12845
Biso mean--30.78 33.48 -
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 (%)
1.47-1.48670.32713590.3033730683
1.4867-1.50420.30484260.2871757089
1.5042-1.52250.32834170.2862790091
1.5225-1.54180.31154160.2739786492
1.5418-1.56210.2744150.2726802793
1.5621-1.58350.27784320.2531816294
1.5835-1.60610.26394340.2436815795
1.6061-1.63010.25064250.2323832396
1.6301-1.65560.25244310.2377824396
1.6556-1.68270.24814000.2319846697
1.6827-1.71180.25824370.2282864999
1.7118-1.74290.25574320.21258565100
1.7429-1.77640.24644520.21778598100
1.7764-1.81270.24514380.20878621100
1.8127-1.85210.24414570.20258605100
1.8521-1.89520.22474590.19438545100
1.8952-1.94260.22184460.19278662100
1.9426-1.99510.21764330.19228623100
1.9951-2.05380.20624530.19418657100
2.0538-2.12010.20674410.18648604100
2.1201-2.19590.19614520.17388634100
2.1959-2.28380.20654920.17568598100
2.2838-2.38770.20074230.17188655100
2.3877-2.51360.21664150.17538669100
2.5136-2.67110.18864120.17118674100
2.6711-2.87740.18034220.17088679100
2.8774-3.16690.17724800.16088618100
3.1669-3.62520.16624400.15528675100
3.6252-4.56720.14894350.13318665100
4.5672-68.4650.15624680.15618705100

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