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- PDB-8xhk: Crystal structure of alpha-Oxoamine Synthase Alb29 with PLP cofactor -

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Basic information

Entry
Database: PDB / ID: 8xhk
TitleCrystal structure of alpha-Oxoamine Synthase Alb29 with PLP cofactor
ComponentsAminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
KeywordsTRANSFERASE / complex / PLP / 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
PYRIDOXAL-5'-PHOSPHATE / Chem-PLR / 8-amino-7-oxononanoate synthase
Similarity search - Component
Biological speciesStreptomyces albogriseolus 1-36 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 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 18, 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
C: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
A: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
B: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
D: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
E: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
F: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,77412
Polymers257,3336
Non-polymers1,4416
Water32418
1
C: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
A: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2724
Polymers85,7782
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-40 kcal/mol
Surface area27920 Å2
MethodPISA
2
B: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
E: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2584
Polymers85,7782
Non-polymers4802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-40 kcal/mol
Surface area27250 Å2
MethodPISA
3
D: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
F: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2444
Polymers85,7782
Non-polymers4662
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-33 kcal/mol
Surface area27740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.110, 110.590, 354.667
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein
Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme / Alpha-Oxoamine Synthase


Mass: 42888.883 Da / Num. of mol.: 6 / Mutation: S87G
Source method: isolated from a genetically manipulated source
Details: GenBank ID is QHB15350.1
Source: (gene. exp.) Streptomyces albogriseolus 1-36 (bacteria)
Gene: alb29 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6B9KSL0
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PLR / (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / 4'-DEOXYPYRIDOXINE PHOSPHATE


Mass: 233.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H12NO5P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 293.15 K / Method: liquid diffusion
Details: 0.03M MgCl2, 0.03M CaCl2, 0.1M MES-Imidazole, pH 6.5, 20% Glycerol, 10%(w/v)PEG4000

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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 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 62296 / % possible obs: 99.51 % / Redundancy: 11.8 % / Biso Wilson estimate: 66.41 Å2 / CC1/2: 0.99 / CC star: 1 / Rmerge(I) obs: 0.09468 / Rpim(I) all: 0.02891 / Rrim(I) all: 0.09909 / Net I/σ(I): 18.78
Reflection shellResolution: 2.79→2.89 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.9972 / Mean I/σ(I) obs: 2.82 / Num. unique obs: 6367 / CC1/2: 0.906 / CC star: 0.975 / Rpim(I) all: 0.2993 / % possible all: 99.58

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Processing

Software
NameVersionClassification
REFMAC5.0.32refinement
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8I7U

8i7u


Resolution: 2.79→25.19 Å / SU ML: 0.4227 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1778
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2549 3202 5.15 %
Rwork0.2035 58939 -
obs0.2063 62141 95.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.12 Å2
Refinement stepCycle: LAST / Resolution: 2.79→25.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17844 0 90 18 17952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001918263
X-RAY DIFFRACTIONf_angle_d0.487424739
X-RAY DIFFRACTIONf_chiral_restr0.0412792
X-RAY DIFFRACTIONf_plane_restr0.00363211
X-RAY DIFFRACTIONf_dihedral_angle_d12.87626600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.830.40391380.31542679X-RAY DIFFRACTION99.47
2.83-2.880.32451440.28912564X-RAY DIFFRACTION99.63
2.88-2.920.34271510.26862642X-RAY DIFFRACTION99.61
2.92-2.970.35841390.23922634X-RAY DIFFRACTION99.6
2.97-3.030.29531330.2342604X-RAY DIFFRACTION99.31
3.03-3.090.32261370.24492651X-RAY DIFFRACTION99.57
3.09-3.150.35961350.25782630X-RAY DIFFRACTION99.5
3.15-3.220.36051620.26072626X-RAY DIFFRACTION99.68
3.22-3.290.36581260.26452660X-RAY DIFFRACTION99.61
3.29-3.370.3631490.24252622X-RAY DIFFRACTION99.71
3.37-3.420.3002850.24861446X-RAY DIFFRACTION98.97
3.47-3.570.2591430.2252555X-RAY DIFFRACTION99.78
3.57-3.680.30911320.222127X-RAY DIFFRACTION80.68
3.68-3.810.27281450.20992662X-RAY DIFFRACTION99.86
3.81-3.960.24931160.20212037X-RAY DIFFRACTION77.33
3.96-4.140.23851500.18732687X-RAY DIFFRACTION99.93
4.14-4.360.22331460.18122675X-RAY DIFFRACTION99.82
4.36-4.630.20621480.16272689X-RAY DIFFRACTION99.89
4.63-4.990.20381420.16852694X-RAY DIFFRACTION99.68
4.99-5.480.23891530.18872693X-RAY DIFFRACTION99.86
5.48-6.270.25541460.20642717X-RAY DIFFRACTION99.79
6.27-7.860.22311330.19222796X-RAY DIFFRACTION99.83
7.86-25.190.17871490.16832849X-RAY DIFFRACTION97.81

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