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- PDB-8y97: Crystal structure of a heterooligomeric aminotransferase from Ser... -

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Basic information

Entry
Database: PDB / ID: 8y97
TitleCrystal structure of a heterooligomeric aminotransferase from Serratia sp. ATCC 39006, PMP-bound form
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
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / 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: 2.83 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

Downloads & links

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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)149,5416
Polymers149,0454
Non-polymers4962
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13820 Å2
ΔGint-95 kcal/mol
Surface area44300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.465, 180.934, 183.306
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-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H13N2O5P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 57.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: dipotassium hydrogenphosphate, sodium dihydrogenphosphate, lithium sulfate, CAPS

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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 S 6M / Detector: PIXEL / Date: Nov 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.83→48.63 Å / Num. obs: 42789 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.055 / Rrim(I) all: 0.142 / Χ2: 1.02 / Net I/σ(I): 14.2
Reflection shellResolution: 2.83→2.94 Å / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.95 / Num. measured all: 30199 / Num. unique obs: 4430 / CC1/2: 0.786 / Rpim(I) all: 0.392 / Rrim(I) all: 1.029 / Χ2: 1 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→48.63 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.909 / SU B: 16.4 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R: 1.555 / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2569 2056 4.8 %RANDOM
Rwork0.22815 ---
obs0.22953 40666 99.95 %-
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: 55.58 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å20 Å20 Å2
2--0.53 Å2-0 Å2
3----2.89 Å2
Refinement stepCycle: 1 / Resolution: 2.83→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9642 0 32 48 9722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0129897
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169490
X-RAY DIFFRACTIONr_angle_refined_deg0.8681.82413401
X-RAY DIFFRACTIONr_angle_other_deg0.3231.75421839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.21351230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.534549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.819101699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0410.21497
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211524
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022242
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_it1.4735.6524935
X-RAY DIFFRACTIONr_mcbond_other1.4725.6534935
X-RAY DIFFRACTIONr_mcangle_it2.58410.166160
X-RAY DIFFRACTIONr_mcangle_other2.58410.166161
X-RAY DIFFRACTIONr_scbond_it1.2815.7734962
X-RAY DIFFRACTIONr_scbond_other1.2815.7744963
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.32910.6067242
X-RAY DIFFRACTIONr_long_range_B_refined4.32553.0710708
X-RAY DIFFRACTIONr_long_range_B_other4.32553.0710708
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.83→2.903 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 164 -
Rwork0.318 2956 -
obs--100 %

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