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- PDB-6u78: Rv3722c in complex with glutamic acid -

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Basic information

Entry
Database: PDB / ID: 6u78
TitleRv3722c in complex with glutamic acid
ComponentsAminotransferase
KeywordsTRANSFERASE / Aminotransferase / Pyridoxal phosphate / Complex / 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
GLUTAMIC ACID / PYRIDOXAL-5'-PHOSPHATE / Aminotransferase / Aspartate aminotransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMandyoli, L. / Sacchettini, J.C.
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
DepositionAug 31, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,84712
Polymers189,4274
Non-polymers1,4208
Water1,946108
1
A: Aminotransferase
C: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2084
Polymers94,7142
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-16 kcal/mol
Surface area30840 Å2
MethodPISA
2
B: Aminotransferase
D: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6398
Polymers94,7142
Non-polymers9266
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-37 kcal/mol
Surface area30450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.784, 173.691, 173.515
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Aminotransferase / Aspartate transaminase


Mass: 47356.754 Da / Num. of mol.: 4
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, Transferases

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Non-polymers , 5 types, 116 molecules

#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 3.61 Å3/Da / Density % sol: 65.89 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium acetate, pH 4.5, 200 mM lithium sulfate, 50% PEG400

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 15, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→48.33 Å / Num. obs: 82156 / % possible obs: 99.76 % / Redundancy: 7.5 % / Biso Wilson estimate: 34.04 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.148 / Net I/σ(I): 9.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 8067 / CC1/2: 0.81 / % possible all: 99.36

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Processing

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

5c6u


Resolution: 2.6→48.33 Å / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 20.5456
RfactorNum. reflection% reflection
Rfree0.2146 3949 4.81 %
Rwork0.1928 --
obs0.1941 82156 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.04 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12927 0 58 108 13093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002413300
X-RAY DIFFRACTIONf_angle_d0.556918109
X-RAY DIFFRACTIONf_chiral_restr0.04041992
X-RAY DIFFRACTIONf_plane_restr0.00432375
X-RAY DIFFRACTIONf_dihedral_angle_d4.12337906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.650.30291740.26263835X-RAY DIFFRACTION94.93
2.65-2.690.30631810.24583872X-RAY DIFFRACTION95.04
2.69-2.740.29241990.24053897X-RAY DIFFRACTION94.7
2.74-2.80.24891620.23773834X-RAY DIFFRACTION95.71
2.8-2.860.24891980.22873883X-RAY DIFFRACTION95.1
2.86-2.930.27211980.22523872X-RAY DIFFRACTION95.02
2.93-30.25522060.21913847X-RAY DIFFRACTION94.89
3-3.080.23552210.20993873X-RAY DIFFRACTION94.53
3.08-3.170.21511830.20743880X-RAY DIFFRACTION95.47
3.17-3.280.20981780.20553914X-RAY DIFFRACTION95.58
3.28-3.390.23852000.19893876X-RAY DIFFRACTION94.98
3.39-3.530.23372180.19443891X-RAY DIFFRACTION94.67
3.53-3.690.20551720.19553922X-RAY DIFFRACTION95.8
3.69-3.880.19621850.18443895X-RAY DIFFRACTION95.37
3.88-4.130.18232140.17233912X-RAY DIFFRACTION94.65
4.13-4.450.1922100.16033915X-RAY DIFFRACTION94.57
4.45-4.890.17451940.15563944X-RAY DIFFRACTION95.24
4.89-5.60.18272110.17143974X-RAY DIFFRACTION94.91
5.6-7.050.19592380.18643964X-RAY DIFFRACTION94.22
7.05-46.570.1921980.17824196X-RAY DIFFRACTION95.21

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