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- PDB-8xha: Crystal structure of alpha-Oxoamine Synthase Alb29 with PLP cofac... -

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Basic information

Entry
Database: PDB / ID: 8xha
TitleCrystal structure of alpha-Oxoamine Synthase Alb29 with PLP cofactor and L-glutamate
Components8-amino-7-oxononanoate synthase
KeywordsTRANSFERASE / complex / PLP / L-glutamate / Dimer / alpha-Oxoamine Synthase
Function / homology
Function and homology information


8-amino-7-oxononanoate synthase / 8-amino-7-oxononanoate synthase activity / biotin biosynthetic process / transaminase activity / pyridoxal phosphate binding
Similarity search - Function
: / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-PGU / PYRIDOXAL-5'-PHOSPHATE / 8-amino-7-oxononanoate synthase
Similarity search - Component
Biological speciesStreptomyces albogriseolus 1-36 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsXu, M.J. / Zhang, D.K.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)No. 2022YFC2804100 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural and mechanistic investigations on CC bond forming alpha-oxoamine synthase allowing L-glutamate as substrate.
Authors: Zhang, D.K. / Song, K.Y. / Yan, Y.Q. / Zheng, J.T. / Xu, J. / Da, L.T. / Xu, M.J.
History
DepositionDec 17, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 8-amino-7-oxononanoate synthase
B: 8-amino-7-oxononanoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2844
Polymers86,6592
Non-polymers6252
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-36 kcal/mol
Surface area27240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.369, 117.369, 145.106
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-648-

HOH

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Components

#1: Protein 8-amino-7-oxononanoate synthase / alpha-oxoamine synthase


Mass: 43329.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: It was overpressed in E.coli. The sequence of organism Streptomyces albogriseolus 1-36 is not available, replaced by A0A6B9KSL0 temporarily.
Source: (gene. exp.) Streptomyces albogriseolus 1-36 (bacteria)
Gene: alb29 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A6B9KSL0, 8-amino-7-oxononanoate synthase
#2: 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.: 1 / Source method: obtained synthetically / Formula: C13H19N2O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 3.33 Å3/Da / Density % sol: 63.06 %
Crystal growTemperature: 293.15 K / Method: liquid diffusion / pH: 8.5
Details: 0.1 M Amino acid mix, 0.1 M Buffer system 3, pH8.5, 30% v/v Precipitant Mix2;

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 53844 / % possible obs: 99.94 % / Redundancy: 8.7 % / Biso Wilson estimate: 54.55 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.07795 / Rpim(I) all: 0.01793 / Rrim(I) all: 0.08002 / Net I/σ(I): 26.95
Reflection shellResolution: 2.27→2.351 Å / Rmerge(I) obs: 1.26 / Mean I/σ(I) obs: 2.44 / Num. unique obs: 5293 / CC1/2: 0.803 / CC star: 0.944 / Rsym value: 0.2869 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158)refinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→32.99 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2244 2663 4.95 %
Rwork0.1893 --
obs0.1911 53841 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→32.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6078 0 41 141 6260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066233
X-RAY DIFFRACTIONf_angle_d0.9058438
X-RAY DIFFRACTIONf_dihedral_angle_d14.1872268
X-RAY DIFFRACTIONf_chiral_restr0.053949
X-RAY DIFFRACTIONf_plane_restr0.0091094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.310.31471620.25772618X-RAY DIFFRACTION100
2.31-2.360.2811500.24892648X-RAY DIFFRACTION100
2.36-2.40.28191410.24992648X-RAY DIFFRACTION100
2.4-2.460.27931330.24192673X-RAY DIFFRACTION100
2.46-2.510.29011430.23472656X-RAY DIFFRACTION100
2.51-2.580.26151190.23912691X-RAY DIFFRACTION100
2.58-2.650.32371100.24952687X-RAY DIFFRACTION100
2.65-2.720.28451630.24842666X-RAY DIFFRACTION100
2.72-2.810.2781510.23572656X-RAY DIFFRACTION100
2.81-2.910.2541210.22762699X-RAY DIFFRACTION100
2.91-3.030.29711320.22622668X-RAY DIFFRACTION100
3.03-3.170.25881510.22442716X-RAY DIFFRACTION100
3.17-3.330.28221420.22732672X-RAY DIFFRACTION100
3.33-3.540.25231470.20632689X-RAY DIFFRACTION100
3.54-3.810.2041630.19042678X-RAY DIFFRACTION100
3.81-4.20.19651260.172724X-RAY DIFFRACTION100
4.2-4.80.18871370.15262750X-RAY DIFFRACTION100
4.8-6.040.20641350.16412759X-RAY DIFFRACTION100
6.05-32.990.16521370.14632880X-RAY DIFFRACTION100

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