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- PDB-6k8h: Crystal structure of an omega-transaminase from Sphaerobacter the... -

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Basic information

Entry
Database: PDB / ID: 6k8h
TitleCrystal structure of an omega-transaminase from Sphaerobacter thermophilus
ComponentsAminotransferase class-III
KeywordsTRANSFERASE / Transaminase / Thermostability / Transamination
Function / homology
Function and homology information


transaminase activity / pyridoxal phosphate binding
Similarity search - Function
Aminotransferase class-III / Aminotransferase class-III / 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 ...Aminotransferase class-III / Aminotransferase class-III / 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
Chem-PLR / Aminotransferase class-III
Similarity search - Component
Biological speciesSphaerobacter thermophilus DSM 20745 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPark, H.H. / Kwon, S.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2017M3A9D8062960 Korea, Republic Of
National Research Foundation (Korea)NRF-2018R1A2B3008541 Korea, Republic Of
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Structural insights into the enzyme specificity of a novel omega-transaminase from the thermophilic bacterium Sphaerobacter thermophilus.
Authors: Kwon, S. / Lee, J.H. / Kim, C.M. / Ha, H.J. / Lee, S.H. / Lee, C.S. / Jeon, J.H. / So, I. / Park, H.H.
History
DepositionJun 12, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionOct 9, 2019ID: 5D95
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.2Mar 25, 2020Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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

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Assembly

Deposited unit
A: Aminotransferase class-III
B: Aminotransferase class-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,8384
Polymers97,3722
Non-polymers4662
Water18,5731031
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10460 Å2
ΔGint-62 kcal/mol
Surface area28220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.064, 61.246, 185.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aminotransferase class-III / omega-transaminase


Mass: 48685.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphaerobacter thermophilus DSM 20745 (bacteria)
Strain: DSM 20745 / S 6022 / Gene: Sthe_0848 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D1C218
#2: Chemical ChemComp-PLR / (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / 4'-DEOXYPYRIDOXINE PHOSPHATE


Mass: 233.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12NO5P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1031 / Source method: isolated from a natural source / Formula: H2O
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: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate (pH 4.8), 1.2 M K2HPO4, 0.9 M NaH2PO4, 40% 2,5-hexanediol

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 63258 / % possible obs: 85.2 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 26.1
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.621 / Num. unique obs: 3017

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AO9

4ao9


Resolution: 1.9→29.849 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 16.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1938 3133 5.06 %
Rwork0.1556 --
obs0.1576 61941 83.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→29.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6605 0 30 1031 7666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076783
X-RAY DIFFRACTIONf_angle_d0.9439235
X-RAY DIFFRACTIONf_dihedral_angle_d15.452467
X-RAY DIFFRACTIONf_chiral_restr0.0591021
X-RAY DIFFRACTIONf_plane_restr0.0071243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92970.26371300.22012389X-RAY DIFFRACTION76
1.9297-1.96130.27751300.20282492X-RAY DIFFRACTION78
1.9613-1.99510.26181240.18952479X-RAY DIFFRACTION78
1.9951-2.03140.21641450.17922485X-RAY DIFFRACTION79
2.0314-2.07040.21321350.1722515X-RAY DIFFRACTION79
2.0704-2.11270.18841430.16242490X-RAY DIFFRACTION78
2.1127-2.15860.19521280.1542535X-RAY DIFFRACTION80
2.1586-2.20880.19311300.15012493X-RAY DIFFRACTION79
2.2088-2.2640.20771310.14962501X-RAY DIFFRACTION78
2.264-2.32520.20351180.14792528X-RAY DIFFRACTION79
2.3252-2.39360.20031390.15312504X-RAY DIFFRACTION79
2.3936-2.47090.21051210.15682528X-RAY DIFFRACTION78
2.4709-2.55910.22591340.15852501X-RAY DIFFRACTION78
2.5591-2.66150.20491300.15612531X-RAY DIFFRACTION79
2.6615-2.78260.2191490.16382587X-RAY DIFFRACTION80
2.7826-2.92910.19951470.16372659X-RAY DIFFRACTION83
2.9291-3.11250.17421620.16022800X-RAY DIFFRACTION87
3.1125-3.35250.1911480.15272954X-RAY DIFFRACTION91
3.3525-3.68930.17181600.14143045X-RAY DIFFRACTION93
3.6893-4.22190.16911570.13213143X-RAY DIFFRACTION96
4.2219-5.31430.14621860.13553214X-RAY DIFFRACTION98
5.3143-29.85230.19941860.16483435X-RAY DIFFRACTION99

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