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

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Basic information

Entry
Database: PDB / ID: 8xhd
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: 2.7 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)86,4854
Polymers85,8602
Non-polymers6252
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-41 kcal/mol
Surface area27030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.734, 117.734, 145.018
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

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Components

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


Mass: 42929.961 Da / Num. of mol.: 2 / Mutation: S87G
Source method: isolated from a genetically manipulated source
Details: 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.: 31 / 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: 3.36 Å3/Da / Density % sol: 63.45 %
Crystal growTemperature: 293.15 K / Method: liquid diffusion
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: 2.7→101.96 Å / Num. obs: 32498 / % possible obs: 100 % / Redundancy: 11.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.033 / Rrim(I) all: 0.113 / Χ2: 1.14 / Net I/σ(I): 20.3 / Num. measured all: 368062
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.274 / Num. unique obs: 3210 / CC1/2: 0.712 / CC star: 0.912 / Rpim(I) all: 0.389 / Rrim(I) all: 1.306 / Χ2: 0.95 / % possible all: 99.97

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8XHA

8xha


Resolution: 2.7→43.68 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2518 1638 5.05 %
Rwork0.2154 --
obs0.2172 32441 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→43.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6022 0 41 31 6094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026175
X-RAY DIFFRACTIONf_angle_d0.5418360
X-RAY DIFFRACTIONf_dihedral_angle_d12.5772244
X-RAY DIFFRACTIONf_chiral_restr0.041942
X-RAY DIFFRACTIONf_plane_restr0.0041084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.780.33951370.29682539X-RAY DIFFRACTION100
2.78-2.870.34321610.27512524X-RAY DIFFRACTION100
2.87-2.970.33461310.30412512X-RAY DIFFRACTION100
2.97-3.090.31281230.2822565X-RAY DIFFRACTION100
3.09-3.230.2931170.28492540X-RAY DIFFRACTION100
3.23-3.40.31761280.25892571X-RAY DIFFRACTION100
3.4-3.610.3011430.24722525X-RAY DIFFRACTION100
3.61-3.890.24771670.22342541X-RAY DIFFRACTION100
3.89-4.280.23971290.19752561X-RAY DIFFRACTION100
4.29-4.90.20081250.17792614X-RAY DIFFRACTION100
4.9-6.180.20391170.19712622X-RAY DIFFRACTION100
6.18-43.680.22371600.1722689X-RAY DIFFRACTION99

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