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- PDB-6k20: Structure of Apo YdiU -

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Basic information

Entry
Database: PDB / ID: 6k20
TitleStructure of Apo YdiU
ComponentsProtein adenylyltransferase SelO
KeywordsTRANSFERASE
Function / homology
Function and homology information


AMPylase activity / protein adenylylation / protein adenylyltransferase / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / magnesium ion binding / ATP binding
Similarity search - Function
: / Protein adenylyltransferase SelO / Protein adenylyltransferase SelO
Similarity search - Domain/homology
Protein adenylyltransferase SelO / Protein nucleotidyltransferase SelO
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsLi, B. / Yang, Y. / Ma, Y.
CitationJournal: To Be Published
Title: Structure of Apo-YdiU
Authors: Li, B.
History
DepositionMay 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein adenylyltransferase SelO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5042
Polymers54,4801
Non-polymers241
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-6 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.526, 117.352, 147.789
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Protein adenylyltransferase SelO


Mass: 54480.004 Da / Num. of mol.: 1 / Mutation: C272S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ydiU
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A024L327, UniProt: P77649*PLUS, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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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: 3.38 Å3/Da / Density % sol: 63.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 10% peg200, 0.1M Bistris pH9.0, 18%PEG 8,000

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.58→29.34 Å / Num. obs: 22642 / % possible obs: 93.6 % / Redundancy: 1 % / Net I/σ(I): 20.5
Reflection shellResolution: 2.58→2.69 Å / Num. unique obs: 2275

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Processing

Software
NameVersionClassification
PHENIX(1.15.1_3469: ???)refinement
HKL-3000data collection
HKL-3000data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→27.891 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.63
RfactorNum. reflection% reflection
Rfree0.2193 1159 5.12 %
Rwork0.184 --
obs0.1858 22620 93.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.58→27.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3737 0 1 161 3899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053832
X-RAY DIFFRACTIONf_angle_d0.6665201
X-RAY DIFFRACTIONf_dihedral_angle_d4.6192264
X-RAY DIFFRACTIONf_chiral_restr0.041550
X-RAY DIFFRACTIONf_plane_restr0.005685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5764-2.69350.25211060.22642217X-RAY DIFFRACTION78
2.6935-2.83540.29991230.22322655X-RAY DIFFRACTION92
2.8354-3.01290.25281410.22072674X-RAY DIFFRACTION95
3.0129-3.24520.27871490.21962668X-RAY DIFFRACTION94
3.2452-3.57110.21971470.19982708X-RAY DIFFRACTION94
3.5711-4.08650.21911620.16672690X-RAY DIFFRACTION95
4.0865-5.14330.17671600.15032833X-RAY DIFFRACTION97
5.1433-27.89260.19291710.16973016X-RAY DIFFRACTION99

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