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- PDB-6jix: The cyrstal structure of taurine:2-oxoglutarate aminotransferase ... -

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Basic information

Entry
Database: PDB / ID: 6jix
TitleThe cyrstal structure of taurine:2-oxoglutarate aminotransferase from Bifidobacterium kashiwanohense, in complex with PLP and glutamate
Componentstaurine:2-oxoglutarate aminotransferase
KeywordsTRANSFERASE / aminotransferase / pyridoxal 5' phosphate / glutamate / 2-oxoglutarate
Function / homology
Function and homology information


transaminase activity / pyridoxal phosphate binding
Similarity search - Function
Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / PYRIDOXAL-5'-PHOSPHATE / Uncharacterized protein
Similarity search - Component
Biological speciesBifidobacterium kashiwanohense PV20-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.647 Å
AuthorsLi, M. / Lin, L. / Zhang, Y. / Yuchi, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31870049 China
CitationJournal: Biochem.J. / Year: 2019
Title: Biochemical and structural investigation of taurine:2-oxoglutarate aminotransferase fromBifidobacterium kashiwanohense.
Authors: Li, M. / Wei, Y. / Yin, J. / Lin, L. / Zhou, Y. / Hua, G. / Cao, P. / Ang, E.L. / Zhao, H. / Yuchi, Z. / Zhang, Y.
History
DepositionFeb 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 2.0Feb 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_site / struct_site_gen
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: taurine:2-oxoglutarate aminotransferase
A: taurine:2-oxoglutarate aminotransferase
C: taurine:2-oxoglutarate aminotransferase
D: taurine:2-oxoglutarate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,54916
Polymers199,3834
Non-polymers2,16612
Water6,575365
1
B: taurine:2-oxoglutarate aminotransferase
D: taurine:2-oxoglutarate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7748
Polymers99,6922
Non-polymers1,0836
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11350 Å2
ΔGint-72 kcal/mol
Surface area27290 Å2
MethodPISA
2
A: taurine:2-oxoglutarate aminotransferase
C: taurine:2-oxoglutarate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7748
Polymers99,6922
Non-polymers1,0836
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11150 Å2
ΔGint-74 kcal/mol
Surface area27420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.390, 164.544, 109.240
Angle α, β, γ (deg.)90.000, 105.810, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 1 through 3 and (name N...
21(chain B and ((resid 1 through 3 and (name N...
31(chain C and (resid 1 through 270 or (resid 271...
41(chain D and (resid 1 through 28 or (resid 29...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLUGLU(chain A and ((resid 1 through 3 and (name N...AB1 - 33 - 5
12METMETASPASP(chain A and ((resid 1 through 3 and (name N...AB1 - 4473 - 449
13METMETASPASP(chain A and ((resid 1 through 3 and (name N...AB1 - 4473 - 449
14METMETASPASP(chain A and ((resid 1 through 3 and (name N...AB1 - 4473 - 449
15METMETASPASP(chain A and ((resid 1 through 3 and (name N...AB1 - 4473 - 449
21METMETGLUGLU(chain B and ((resid 1 through 3 and (name N...BA1 - 33 - 5
22METMETCYSCYS(chain B and ((resid 1 through 3 and (name N...BA1 - 4463 - 448
23METMETCYSCYS(chain B and ((resid 1 through 3 and (name N...BA1 - 4463 - 448
24METMETCYSCYS(chain B and ((resid 1 through 3 and (name N...BA1 - 4463 - 448
25METMETCYSCYS(chain B and ((resid 1 through 3 and (name N...BA1 - 4463 - 448
31METMETVALVAL(chain C and (resid 1 through 270 or (resid 271...CC1 - 2703 - 272
32LYSLYSLYSLYS(chain C and (resid 1 through 270 or (resid 271...CC271273
33METMETCYSCYS(chain C and (resid 1 through 270 or (resid 271...CC1 - 4463 - 448
34METMETCYSCYS(chain C and (resid 1 through 270 or (resid 271...CC1 - 4463 - 448
35METMETCYSCYS(chain C and (resid 1 through 270 or (resid 271...CC1 - 4463 - 448
36METMETCYSCYS(chain C and (resid 1 through 270 or (resid 271...CC1 - 4463 - 448
41METMETVALVAL(chain D and (resid 1 through 28 or (resid 29...DD1 - 283 - 30
42LYSLYSLYSLYS(chain D and (resid 1 through 28 or (resid 29...DD2931
43METMETCYSCYS(chain D and (resid 1 through 28 or (resid 29...DD1 - 4463 - 448

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Components

#1: Protein
taurine:2-oxoglutarate aminotransferase


Mass: 49845.758 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium kashiwanohense PV20-2 (bacteria)
Gene: AH68_00255
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0A7I435
#2: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.96 Å3/Da / Density % sol: 58.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M MES, pH 5.0, 0.2M ammonium chloride, 10% W/V PEG 6000, 0.5mM PLP, 100mM glutamate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 66599 / % possible obs: 98.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.071 / Rrim(I) all: 0.133 / Χ2: 0.487 / Net I/σ(I): 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.73.50.4933020.8370.3040.5780.44498.5
2.7-2.743.50.42433050.8420.2640.5010.4498.1
2.74-2.83.50.35232930.8940.220.4160.42198.4
2.8-2.853.50.35933140.8760.2260.4260.44698.6
2.85-2.923.50.31432740.910.1970.3720.44598.6
2.92-2.983.50.2933450.9160.1820.3430.44398.7
2.98-3.063.40.24333000.9510.1550.2890.43598.9
3.06-3.143.20.20133270.950.1330.2420.44898.9
3.14-3.233.20.18533320.9490.1240.2240.45898.7
3.23-3.343.30.1632880.9650.1040.1920.46398.9
3.34-3.463.60.1433520.9790.0860.1650.4899.1
3.46-3.63.60.1133430.9860.0680.1290.47999
3.6-3.763.60.09333350.9890.0580.110.51999.1
3.76-3.963.50.08133200.9920.0510.0960.52799.3
3.96-4.213.50.07233510.9930.0450.0860.52199.3
4.21-4.533.30.0633370.9930.0390.0710.57199.3
4.53-4.993.20.05433400.9950.0360.0650.5699
4.99-5.713.60.05933820.9950.0360.070.48899.4
5.71-7.193.50.06733540.9940.0420.0790.52499.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3247refinement
HKL-3000data scaling
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LH9

5lh9


Resolution: 2.647→44.289 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.2
RfactorNum. reflection% reflection
Rfree0.2269 1995 3 %
Rwork0.1669 --
obs0.1687 66583 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.18 Å2 / Biso mean: 31.6502 Å2 / Biso min: 12.19 Å2
Refinement stepCycle: final / Resolution: 2.647→44.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13704 0 236 365 14305
Biso mean--36.26 30.1 -
Num. residues----1785
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5392X-RAY DIFFRACTION5.615TORSIONAL
12B5392X-RAY DIFFRACTION5.615TORSIONAL
13C5392X-RAY DIFFRACTION5.615TORSIONAL
14D5392X-RAY DIFFRACTION5.615TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6471-2.71330.30851300.23194344447493
2.7133-2.78660.29511410.21454547468898
2.7866-2.86860.27951440.2164634477899
2.8686-2.96120.29731370.21694637477499
2.9612-3.0670.28171460.21624579472599
3.067-3.18980.26921410.19024619476099
3.1898-3.33490.25481440.19214603474799
3.3349-3.51070.25321480.18194646479499
3.5107-3.73050.22281450.16524616476199
3.7305-4.01840.21551460.14714665481199
4.0184-4.42240.18861400.13274630477099
4.4224-5.06160.17151420.12444665480799
5.0616-6.3740.21581480.14824683483199
6.374-44.29570.15481430.13664720486399

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