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- PDB-5z0q: Crystal Structure of OvoB -

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Basic information

Entry
Database: PDB / ID: 5z0q
TitleCrystal Structure of OvoB
ComponentsAminotransferase, class I and IITransaminase
KeywordsTRANSFERASE / Ovothiol A / biosynthesis / C-S lyase / aminotransferase / PLP coenzyme / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


transaminase activity / biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Putative C-S lyase / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...Putative C-S lyase / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Aminotransferase, class I and II
Similarity search - Component
Biological speciesErwinia tasmaniensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsCai, Y.J. / Huang, P. / Wu, L. / Zhou, J.H. / Liu, P.H.
CitationJournal: Org. Lett. / Year: 2018
Title: In Vitro Reconstitution of the Remaining Steps in Ovothiol A Biosynthesis: C-S Lyase and Methyltransferase Reactions.
Authors: Naowarojna, N. / Huang, P. / Cai, Y. / Song, H. / Wu, L. / Cheng, R. / Li, Y. / Wang, S. / Lyu, H. / Zhang, L. / Zhou, J. / Liu, P.
History
DepositionDec 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Aminotransferase, class I and II
A: Aminotransferase, class I and II
B: Aminotransferase, class I and II
D: Aminotransferase, class I and II
E: Aminotransferase, class I and II
F: Aminotransferase, class I and II
G: Aminotransferase, class I and II
H: Aminotransferase, class I and II
I: Aminotransferase, class I and II
J: Aminotransferase, class I and II
K: Aminotransferase, class I and II
L: Aminotransferase, class I and II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)528,55224
Polymers525,58612
Non-polymers2,96612
Water0
1
C: Aminotransferase, class I and II
E: Aminotransferase, class I and II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0924
Polymers87,5982
Non-polymers4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-27 kcal/mol
Surface area28830 Å2
MethodPISA
2
A: Aminotransferase, class I and II
I: Aminotransferase, class I and II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0924
Polymers87,5982
Non-polymers4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-25 kcal/mol
Surface area28640 Å2
MethodPISA
3
B: Aminotransferase, class I and II
K: Aminotransferase, class I and II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0924
Polymers87,5982
Non-polymers4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-30 kcal/mol
Surface area28770 Å2
MethodPISA
4
D: Aminotransferase, class I and II
G: Aminotransferase, class I and II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0924
Polymers87,5982
Non-polymers4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-28 kcal/mol
Surface area28870 Å2
MethodPISA
5
F: Aminotransferase, class I and II
J: Aminotransferase, class I and II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0924
Polymers87,5982
Non-polymers4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-29 kcal/mol
Surface area28520 Å2
MethodPISA
6
H: Aminotransferase, class I and II
L: Aminotransferase, class I and II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0924
Polymers87,5982
Non-polymers4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-33 kcal/mol
Surface area29120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.123, 133.590, 165.703
Angle α, β, γ (deg.)89.39, 84.58, 86.56
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Aminotransferase, class I and II / Transaminase / OvoB


Mass: 43798.848 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia tasmaniensis (strain DSM 17950 / CIP 109463 / Et1/99) (bacteria)
Strain: DSM 17950 / CIP 109463 / Et1/99 / Gene: ETA_14770 / Production host: Escherichia coli (E. coli) / References: UniProt: B2VJB8
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H10NO6P

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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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: PEG 8000, sodium cacodylate, calcium acetate, glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.77→50 Å / Num. obs: 125870 / % possible obs: 96.7 % / Redundancy: 3.8 % / Net I/σ(I): 7.05
Reflection shellResolution: 2.77→2.82 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DGT

4dgt


Resolution: 2.77→42.973 Å / SU ML: 0.39 / Cross valid method: NONE / σ(F): 1.97 / Phase error: 29.9
RfactorNum. reflection% reflection
Rfree0.2669 5826 4.92 %
Rwork0.2096 --
obs0.2125 118344 90.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.77→42.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36073 0 0 0 36073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00236951
X-RAY DIFFRACTIONf_angle_d0.51350110
X-RAY DIFFRACTIONf_dihedral_angle_d14.9922057
X-RAY DIFFRACTIONf_chiral_restr0.045359
X-RAY DIFFRACTIONf_plane_restr0.0046604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7318-2.76290.3678740.31921645X-RAY DIFFRACTION39
2.7629-2.79540.42171120.29752412X-RAY DIFFRACTION59
2.7954-2.82940.37021500.29722709X-RAY DIFFRACTION66
2.8294-2.86520.38971690.29543214X-RAY DIFFRACTION76
2.8652-2.90290.3341750.29243528X-RAY DIFFRACTION83
2.9029-2.94270.37532020.27983560X-RAY DIFFRACTION88
2.9427-2.98470.32962120.26873723X-RAY DIFFRACTION90
2.9847-3.02930.35192040.26353835X-RAY DIFFRACTION91
3.0293-3.07660.34441820.2653809X-RAY DIFFRACTION92
3.0766-3.1270.32531990.26753843X-RAY DIFFRACTION93
3.127-3.18090.36622050.25423953X-RAY DIFFRACTION94
3.1809-3.23870.31842270.25313942X-RAY DIFFRACTION95
3.2387-3.3010.31331920.25263909X-RAY DIFFRACTION95
3.301-3.36840.32341810.24553982X-RAY DIFFRACTION95
3.3684-3.44160.29782260.24253997X-RAY DIFFRACTION96
3.4416-3.52160.31821710.23013972X-RAY DIFFRACTION96
3.5216-3.60960.28112240.22693958X-RAY DIFFRACTION95
3.6096-3.70720.28931950.20363903X-RAY DIFFRACTION94
3.7072-3.81620.27471960.19914092X-RAY DIFFRACTION98
3.8162-3.93930.24332030.19244104X-RAY DIFFRACTION98
3.9393-4.080.24152230.18664067X-RAY DIFFRACTION98
4.08-4.24320.23542150.1814069X-RAY DIFFRACTION98
4.2432-4.43610.24042070.17634105X-RAY DIFFRACTION98
4.4361-4.66970.23982170.17384062X-RAY DIFFRACTION98
4.6697-4.96190.24781850.17974100X-RAY DIFFRACTION98
4.9619-5.34440.23932130.18324049X-RAY DIFFRACTION96
5.3444-5.8810.24471900.19284058X-RAY DIFFRACTION97
5.881-6.72920.24591770.20344115X-RAY DIFFRACTION99
6.7292-8.46740.18732310.16664036X-RAY DIFFRACTION97
8.4674-42.97860.18512690.16323767X-RAY DIFFRACTION92

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