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- PDB-8y98: Crystal structure of a heterooligomeric aminotransferase from Ser... -

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Basic information

Entry
Database: PDB / ID: 8y98
TitleCrystal structure of a heterooligomeric aminotransferase from Serratia sp. ATCC 39006, PPE-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
Chem-PGU / 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: 2.31 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
B: DegT/DnrJ/EryC1/StrS family aminotransferase
C: DegT/DnrJ/EryC1/StrS aminotransferase
D: DegT/DnrJ/EryC1/StrS aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,8016
Polymers149,0454
Non-polymers7572
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12770 Å2
ΔGint-97 kcal/mol
Surface area44540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.978, 181.170, 182.531
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-PGU / N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-glutamic acid


Mass: 378.272 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N2O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.94 Å3/Da / Density % sol: 58.14 %
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: Feb 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.31→48.98 Å / Num. obs: 77803 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.047 / Rrim(I) all: 0.124 / Χ2: 1.01 / Net I/σ(I): 14 / Num. measured all: 520607
Reflection shellResolution: 2.31→2.36 Å / % possible obs: 98.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.922 / Num. measured all: 27335 / Num. unique obs: 4444 / CC1/2: 0.772 / Rpim(I) all: 0.399 / Rrim(I) all: 1.008 / Χ2: 0.97 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→45.86 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.446 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22318 3862 5 %RANDOM
Rwork0.1934 ---
obs0.19486 73862 99.39 %-
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: 52.749 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å2-0 Å20 Å2
2--1.41 Å20 Å2
3----2.52 Å2
Refinement stepCycle: 1 / Resolution: 2.31→45.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9742 0 50 423 10215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01210069
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169612
X-RAY DIFFRACTIONr_angle_refined_deg0.831.82413645
X-RAY DIFFRACTIONr_angle_other_deg0.3011.75222134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5351254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.02547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.95101718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0380.21520
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211734
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022282
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_it1.2895.5325013
X-RAY DIFFRACTIONr_mcbond_other1.2885.5325013
X-RAY DIFFRACTIONr_mcangle_it2.229.9396262
X-RAY DIFFRACTIONr_mcangle_other2.229.946263
X-RAY DIFFRACTIONr_scbond_it1.3875.7085056
X-RAY DIFFRACTIONr_scbond_other1.3875.7095057
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4410.4687382
X-RAY DIFFRACTIONr_long_range_B_refined4.16451.8811373
X-RAY DIFFRACTIONr_long_range_B_other4.12851.9111281
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.31→2.37 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 299 -
Rwork0.274 5239 -
obs--98.17 %

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