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- PDB-6rl5: The first crystal structure of the DABA aminotransferase EctB in ... -

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Basic information

Entry
Database: PDB / ID: 6rl5
TitleThe first crystal structure of the DABA aminotransferase EctB in the ectoine biosynthesis pathway of the model organism Chromohalobacter salexigens DSM 3034
ComponentsDiaminobutyrate--2-oxoglutarate transaminase
KeywordsTRANSFERASE / Ectoine / DABA aminotransferase / osmoadaptation
Function / homology
Function and homology information


diaminobutyrate-pyruvate transaminase activity / diaminobutyrate-2-oxoglutarate transaminase / diaminobutyrate-2-oxoglutarate transaminase activity / ectoine biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Ectoine biosynthetic protein / 2,4-diaminobutyrate 4-transaminase / : / 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
PYRIDOXAL-5'-PHOSPHATE / Diaminobutyrate--2-oxoglutarate transaminase
Similarity search - Component
Biological speciesChromohalobacter salexigens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsHillier, H.T. / Altermark, B. / Leiros, I.
CitationJournal: Febs J. / Year: 2020
Title: The crystal structure of the tetrameric DABA-aminotransferase EctB, a rate-limiting enzyme in the ectoine biosynthesis pathway.
Authors: Hillier, H.T. / Altermark, B. / Leiros, I.
History
DepositionMay 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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: Diaminobutyrate--2-oxoglutarate transaminase
B: Diaminobutyrate--2-oxoglutarate transaminase
C: Diaminobutyrate--2-oxoglutarate transaminase
D: Diaminobutyrate--2-oxoglutarate transaminase
E: Diaminobutyrate--2-oxoglutarate transaminase
F: Diaminobutyrate--2-oxoglutarate transaminase
G: Diaminobutyrate--2-oxoglutarate transaminase
H: Diaminobutyrate--2-oxoglutarate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)378,66616
Polymers376,6898
Non-polymers1,9778
Water5,585310
1
A: Diaminobutyrate--2-oxoglutarate transaminase
B: Diaminobutyrate--2-oxoglutarate transaminase
C: Diaminobutyrate--2-oxoglutarate transaminase
D: Diaminobutyrate--2-oxoglutarate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,3338
Polymers188,3454
Non-polymers9894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27720 Å2
ΔGint-124 kcal/mol
Surface area47550 Å2
MethodPISA
2
E: Diaminobutyrate--2-oxoglutarate transaminase
F: Diaminobutyrate--2-oxoglutarate transaminase
G: Diaminobutyrate--2-oxoglutarate transaminase
H: Diaminobutyrate--2-oxoglutarate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,3338
Polymers188,3454
Non-polymers9894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27850 Å2
ΔGint-125 kcal/mol
Surface area47200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.055, 124.782, 145.416
Angle α, β, γ (deg.)90.00, 98.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Diaminobutyrate--2-oxoglutarate transaminase / DABA aminotransferase / Diaminobutyrate--2-oxoglutarate aminotransferase / L-2 / 4-diaminobutyric ...DABA aminotransferase / Diaminobutyrate--2-oxoglutarate aminotransferase / L-2 / 4-diaminobutyric acid transaminase


Mass: 47086.125 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Synthetic construct containing a 6xHIS C-terminal purification tag
Source: (gene. exp.) Chromohalobacter salexigens (strain DSM 3043 / ATCC BAA-138 / NCIMB 13768) (bacteria)
Strain: DSM 3043 / ATCC BAA-138 / NCIMB 13768 / Gene: ectB, Csal_1877 / Production host: Escherichia coli (E. coli) / Variant (production host): BL21*(DE3)
References: UniProt: Q9ZEU7, diaminobutyrate-2-oxoglutarate transaminase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.55 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M sodium malonate, 0.1M BisTris propane pH 6.5, 30% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.99187 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 26, 2018 / Details: toroidal mirror
RadiationMonochromator: Si (111) silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 2.45→49.073 Å / Num. obs: 136967 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rpim(I) all: 0.047 / Net I/σ(I): 10.6
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 6796 / Rpim(I) all: 1.07 / % possible all: 99.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIX(1.13_2998: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1sf2

1sf2


Resolution: 2.45→49.073 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.73
RfactorNum. reflection% reflection
Rfree0.2435 2703 1.97 %
Rwork0.1849 --
obs0.1861 136907 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.45→49.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25722 0 120 310 26152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00926404
X-RAY DIFFRACTIONf_angle_d0.99835668
X-RAY DIFFRACTIONf_dihedral_angle_d4.0916241
X-RAY DIFFRACTIONf_chiral_restr0.0553840
X-RAY DIFFRACTIONf_plane_restr0.0064701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.49460.37521340.34937058X-RAY DIFFRACTION100
2.4946-2.54250.38691310.3317105X-RAY DIFFRACTION100
2.5425-2.59440.38131410.32567047X-RAY DIFFRACTION99
2.5944-2.65080.33641510.30447054X-RAY DIFFRACTION99
2.6508-2.71250.37711340.30336841X-RAY DIFFRACTION96
2.7125-2.78030.33631540.28577100X-RAY DIFFRACTION99
2.7803-2.85550.36111540.27167060X-RAY DIFFRACTION100
2.8555-2.93950.31571390.25277085X-RAY DIFFRACTION100
2.9395-3.03440.3151480.25437131X-RAY DIFFRACTION100
3.0344-3.14280.31091590.23467085X-RAY DIFFRACTION99
3.1428-3.26860.31761290.22967035X-RAY DIFFRACTION99
3.2686-3.41730.28871480.21466971X-RAY DIFFRACTION98
3.4173-3.59750.2431430.18597082X-RAY DIFFRACTION99
3.5975-3.82280.23811360.15587125X-RAY DIFFRACTION99
3.8228-4.11780.2211350.1437050X-RAY DIFFRACTION98
4.1178-4.53190.17681300.13356967X-RAY DIFFRACTION97
4.5319-5.18710.181490.13187138X-RAY DIFFRACTION99
5.1871-6.53270.22471340.16677066X-RAY DIFFRACTION98
6.5327-49.08330.18011540.1417204X-RAY DIFFRACTION99

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