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- PDB-8y96: Crystal structure of a heterooligomeric aminotransferase from Ser... -

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Basic information

Entry
Database: PDB / ID: 8y96
TitleCrystal structure of a heterooligomeric aminotransferase from Serratia sp. ATCC 39006
Components
  • DegT/DnrJ/EryC1/StrS aminotransferase
  • DegT/DnrJ/EryC1/StrS family aminotransferase
KeywordsTRANSFERASE / Aminotransferase / Heterooligomer / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


polysaccharide biosynthetic process / transaminase activity / pyridoxal phosphate binding
Similarity search - Function
DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS family aminotransferase
Similarity search - Component
Biological speciesSerratia sp. ATCC 39006 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsPramono, H. / Yoshida, A. / Nishiyama, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17H06168 Japan
Japan Society for the Promotion of Science (JSPS)22H00355 Japan
CitationJournal: Febs Lett. / Year: 2025
Title: Crystal structure of a novel heterooligomeric aminotransferase from Serratia sp. ATCC 39006 provides insights into function.
Authors: Pramono, H. / Yoshida, A. / Hirashima, Y. / Sone, Y. / Terada, T. / Kosono, S. / Nishiyama, M.
History
DepositionFeb 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DegT/DnrJ/EryC1/StrS family aminotransferase
C: DegT/DnrJ/EryC1/StrS aminotransferase
B: DegT/DnrJ/EryC1/StrS family aminotransferase
D: DegT/DnrJ/EryC1/StrS aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,2376
Polymers149,0454
Non-polymers1922
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13250 Å2
ΔGint-133 kcal/mol
Surface area44100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.688, 181.029, 182.777
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 DegT/DnrJ/EryC1/StrS family aminotransferase


Mass: 49897.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia sp. ATCC 39006 (bacteria) / Gene: CWC46_09295, Ser39006_009300 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2I5TIB4
#2: Protein DegT/DnrJ/EryC1/StrS aminotransferase


Mass: 24625.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia sp. ATCC 39006 (bacteria) / Gene: CWC46_09290, Ser39006_009295 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2I5T5Y7
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.92 Å3/Da / Density % sol: 57.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: ammonium sulfate, MES

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.84→48.76 Å / Num. obs: 42411 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.049 / Rrim(I) all: 0.127 / Χ2: 1.02 / Net I/σ(I): 14.9 / Num. measured all: 279584
Reflection shellResolution: 2.84→2.95 Å / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.773 / Num. measured all: 29180 / Num. unique obs: 4402 / CC1/2: 0.778 / Rpim(I) all: 0.323 / Rrim(I) all: 0.839 / Χ2: 1 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→45.74 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.897 / SU B: 15.525 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R: 1.6 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25853 2100 5 %RANDOM
Rwork0.20429 ---
obs0.20696 40244 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 56.245 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å2-0 Å2-0 Å2
2--0.12 Å20 Å2
3---0.51 Å2
Refinement stepCycle: 1 / Resolution: 2.84→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9626 0 10 84 9720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0129857
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169440
X-RAY DIFFRACTIONr_angle_refined_deg0.9671.82213347
X-RAY DIFFRACTIONr_angle_other_deg0.3491.75221725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03851228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.976547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33101686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0450.21495
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211483
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022241
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.265.6954927
X-RAY DIFFRACTIONr_mcbond_other2.2535.6964927
X-RAY DIFFRACTIONr_mcangle_it3.78610.2336150
X-RAY DIFFRACTIONr_mcangle_other3.78610.2336151
X-RAY DIFFRACTIONr_scbond_it2.1565.8914930
X-RAY DIFFRACTIONr_scbond_other2.1575.8944923
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.70610.7867186
X-RAY DIFFRACTIONr_long_range_B_refined5.88352.9210792
X-RAY DIFFRACTIONr_long_range_B_other5.88252.9310786
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.84→2.913 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 144 -
Rwork0.281 2939 -
obs--99.97 %

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