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- PDB-9cf4: Crystal structure of the dimeric transaminase DoeD from C. salexi... -

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Basic information

Entry
Database: PDB / ID: 9cf4
TitleCrystal structure of the dimeric transaminase DoeD from C. salexigens DSM 3043.
Components(Aminotransferase) x 2
KeywordsTRANSFERASE / Transaminase / L-2 / 4-diaminobutyric acid / ectoine
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / pyridoxal phosphate binding / cytosol
Similarity search - Function
: / 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 / Aminotransferase
Similarity search - Component
Biological speciesChromohalobacter israelensis DSM 3043 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 Å
AuthorsSkogvold, A.C. / Brakestad, H.T. / Erlandsen, H. / Leiros, I.
Funding support Norway, 1items
OrganizationGrant numberCountry
Not funded Norway
CitationJournal: Febs J. / Year: 2025
Title: Crystal structure and biochemical analysis of the dimeric transaminase DoeD provides insights into ectoine degradation.
Authors: Skogvold, A.C.A. / Brakestad, H.T. / Erlandsen, H. / Leiros, I.
History
DepositionJun 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 18, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminotransferase
B: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,7568
Polymers103,0482
Non-polymers7086
Water21,3301184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12780 Å2
ΔGint-76 kcal/mol
Surface area29660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.383, 94.102, 219.984
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1191-

HOH

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Components

#1: Protein Aminotransferase


Mass: 51638.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromohalobacter israelensis DSM 3043 (bacteria)
Strain: C. salexigens DSM 3043 / Gene: Csal_2724 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q1QTY7, Transferases; Transferring nitrogenous groups; Transaminases
#2: Protein Aminotransferase


Mass: 51410.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromohalobacter israelensis DSM 3043 (bacteria)
Strain: C. salexigens DSM 3043 / Gene: Csal_2724 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: Transferases; Transferring nitrogenous groups; Transaminases
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1184 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.67 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M TRIS pH 8, 19.28 % (w/v) PEG 6000 and 0.3 M MgCl2
Temp details: Minimum light exposure

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.499→35.913 Å / Num. obs: 136251 / % possible obs: 99.72 % / Redundancy: 10.2 % / Rpim(I) all: 0.02988 / Net I/σ(I): 17.2
Reflection shellResolution: 1.499→1.553 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 1.93 / Num. unique obs: 13274 / Rpim(I) all: 0.3451 / % possible all: 98.12

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.499→35.913 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1512 2290 1.68 %0.1512
Rwork0.1124 ---
obs0.113 136228 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.499→35.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7076 0 60 1184 8320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087454
X-RAY DIFFRACTIONf_angle_d1.10110112
X-RAY DIFFRACTIONf_dihedral_angle_d18.0462717
X-RAY DIFFRACTIONf_chiral_restr0.0781074
X-RAY DIFFRACTIONf_plane_restr0.0061344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.499-1.53130.2611360.19028020X-RAY DIFFRACTION96
1.5313-1.56690.23371400.1688314X-RAY DIFFRACTION100
1.5669-1.60610.23911260.14838338X-RAY DIFFRACTION100
1.6061-1.64950.19761660.14028300X-RAY DIFFRACTION100
1.6495-1.69810.17691350.13048298X-RAY DIFFRACTION100
1.6981-1.75290.18541470.12258312X-RAY DIFFRACTION100
1.7529-1.81550.1761410.11488351X-RAY DIFFRACTION100
1.8155-1.88820.17011520.10938369X-RAY DIFFRACTION100
1.8882-1.97420.14981350.10858355X-RAY DIFFRACTION100
1.9742-2.07820.16261410.09718390X-RAY DIFFRACTION100
2.0782-2.20840.12361360.09178365X-RAY DIFFRACTION100
2.2084-2.37890.13931540.09168386X-RAY DIFFRACTION100
2.3789-2.61820.14371210.09698474X-RAY DIFFRACTION100
2.6182-2.99690.11291470.10038446X-RAY DIFFRACTION100
2.9969-3.77520.12431510.10198509X-RAY DIFFRACTION100
3.7752-35.9130.15661620.13068711X-RAY DIFFRACTION100

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