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- PDB-6u7a: Rv3722c in complex with kynurenine -

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Basic information

Entry
Database: PDB / ID: 6u7a
TitleRv3722c in complex with kynurenine
ComponentsAminotransferase
KeywordsTRANSFERASE / Aminotransferase / Mycobacterium tuberculosis
Function / homology
Function and homology information


aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / extracellular region
Similarity search - Function
Aspartate aminotransferase Ic / Aspartate amino-transferase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex ...Aspartate aminotransferase Ic / Aspartate amino-transferase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-hydroxyquinoline-2-carboxylic acid / PYRIDOXAL-5'-PHOSPHATE / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Chem-Q0P / Aminotransferase / Aspartate aminotransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsMandyoli, L. / Sacchettini, J.
CitationJournal: Nat Commun / Year: 2020
Title: Aspartate aminotransferase Rv3722c governs aspartate-dependent nitrogen metabolism in Mycobacterium tuberculosis.
Authors: Jansen, R.S. / Mandyoli, L. / Hughes, R. / Wakabayashi, S. / Pinkham, J.T. / Selbach, B. / Guinn, K.M. / Rubin, E.J. / Sacchettini, J.C. / Rhee, K.Y.
History
DepositionSep 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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: Aminotransferase
B: Aminotransferase
C: Aminotransferase
D: Aminotransferase
E: Aminotransferase
F: Aminotransferase
G: Aminotransferase
H: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)384,70342
Polymers378,8548
Non-polymers5,84934
Water18,8261045
1
A: Aminotransferase
B: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,52812
Polymers94,7142
Non-polymers1,81510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-13 kcal/mol
Surface area30600 Å2
MethodPISA
2
C: Aminotransferase
D: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,20111
Polymers94,7142
Non-polymers1,4879
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-26 kcal/mol
Surface area30810 Å2
MethodPISA
3
E: Aminotransferase
H: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0188
Polymers94,7142
Non-polymers1,3046
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-25 kcal/mol
Surface area30140 Å2
MethodPISA
4
F: Aminotransferase
G: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,95611
Polymers94,7142
Non-polymers1,2439
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-19 kcal/mol
Surface area30530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.398, 108.398, 321.344
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Aminotransferase / Aspartate transaminase


Mass: 47356.754 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: DKC2_3956, DSI35_31455, ERS007661_01687, ERS007663_01945, ERS007665_01586, ERS007670_01863, ERS007672_01473, ERS007679_00092, ERS007681_00098, ERS007688_00789, ERS007703_00081, ERS007720_02793, ...Gene: DKC2_3956, DSI35_31455, ERS007661_01687, ERS007663_01945, ERS007665_01586, ERS007670_01863, ERS007672_01473, ERS007679_00092, ERS007681_00098, ERS007688_00789, ERS007703_00081, ERS007720_02793, ERS007722_01790, ERS023446_00155, ERS024276_02601, ERS027646_02441, ERS027652_01615, ERS027653_01450, ERS027656_00154, ERS027666_02093, ERS031537_01226, ERS124361_00578, EUB07_12880, EUB11_07270, EUB16_18395, SAMEA2682835_06491, SAMEA2682864_02982, SAMEA2683035_02356
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E8TWE4, UniProt: O69689*PLUS

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Non-polymers , 8 types, 1079 molecules

#2: Chemical ChemComp-Q0P / (2S)-4-(2-aminophenyl)-2-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-4-oxobutanoic acid


Mass: 437.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N3O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical
ChemComp-KYA / 4-hydroxyquinoline-2-carboxylic acid / Kynurenic acid


Mass: 189.167 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H13N2O5P
#8: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1045 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.94 Å3/Da / Density % sol: 58.18 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 100 mM sodium phosphate dibasic / citric acid, 40% ethanol, 5% PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 2, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.22→48.361 Å / Num. obs: 178462 / % possible obs: 89.5 % / Redundancy: 7.5 % / Biso Wilson estimate: 30.89 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.138 / Net I/σ(I): 10.7
Reflection shellResolution: 2.223→2.228 Å / Num. unique obs: 7803 / CC1/2: 0.63

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5C6U

5c6u


Resolution: 2.22→32.46 Å / SU ML: 0.2683 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 24.5626
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.219 8909 4.99 %
Rwork0.1783 169553 -
obs0.1803 178462 85.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.9 Å2
Refinement stepCycle: LAST / Resolution: 2.22→32.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26019 0 357 1045 27421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009726998
X-RAY DIFFRACTIONf_angle_d1.298536721
X-RAY DIFFRACTIONf_chiral_restr0.08294022
X-RAY DIFFRACTIONf_plane_restr0.01064807
X-RAY DIFFRACTIONf_dihedral_angle_d13.003515995
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.240.2614770.24091386X-RAY DIFFRACTION20.94
2.24-2.270.2802870.24381575X-RAY DIFFRACTION24.01
2.27-2.30.27671090.25071827X-RAY DIFFRACTION27.66
2.3-2.330.29151170.23972206X-RAY DIFFRACTION33.67
2.33-2.360.30481510.25512937X-RAY DIFFRACTION43.41
2.36-2.390.28542070.24653646X-RAY DIFFRACTION55.94
2.39-2.420.30432310.24844715X-RAY DIFFRACTION70.81
2.42-2.460.30262860.25835788X-RAY DIFFRACTION86.56
2.46-2.50.32363470.25466367X-RAY DIFFRACTION96.59
2.5-2.540.28223440.24366584X-RAY DIFFRACTION99.13
2.54-2.580.27733380.23146689X-RAY DIFFRACTION99.93
2.58-2.630.31663460.2146590X-RAY DIFFRACTION100
2.63-2.680.25953280.20026638X-RAY DIFFRACTION99.99
2.68-2.730.23863760.20196606X-RAY DIFFRACTION100
2.73-2.790.22233080.20696682X-RAY DIFFRACTION100
2.79-2.860.24813860.2086623X-RAY DIFFRACTION100
2.86-2.930.25392960.1986692X-RAY DIFFRACTION99.99
2.93-3.010.26963420.19596650X-RAY DIFFRACTION100
3.01-3.10.23673440.19826605X-RAY DIFFRACTION100
3.1-3.20.24183180.19356625X-RAY DIFFRACTION100
3.2-3.310.22853380.18926618X-RAY DIFFRACTION100
3.31-3.440.23593360.18176643X-RAY DIFFRACTION100
3.44-3.60.19213660.16686627X-RAY DIFFRACTION100
3.6-3.790.21553620.16676579X-RAY DIFFRACTION99.99
3.79-4.030.18443900.15126657X-RAY DIFFRACTION99.9
4.03-4.340.18583240.14026660X-RAY DIFFRACTION99.96
4.34-4.770.1663760.13066575X-RAY DIFFRACTION99.94
4.77-5.460.16563820.13936582X-RAY DIFFRACTION99.9
5.46-6.870.19673950.16076549X-RAY DIFFRACTION99.94
6.87-32.460.17443020.14536632X-RAY DIFFRACTION99.07

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