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- PDB-4azv: Co-crystal structure of WbdD and kinase inhibitor GW435821x. -

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Basic information

Entry
Database: PDB / ID: 4azv
TitleCo-crystal structure of WbdD and kinase inhibitor GW435821x.
ComponentsWBDDWorld Blood Donor Day
KeywordsTRANSFERASE / METHYLTRANSFERASE
Function / homology
Function and homology information


3-O-phospho-polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol 3-phospho-methyltransferase / polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol kinase / O antigen biosynthetic process / methyltransferase activity / methylation / protein kinase activity / phosphorylation / ATP binding / plasma membrane
Similarity search - Function
Methyltransferase domain / Methyltransferase domain / Vaccinia Virus protein VP39 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Methyltransferase domain / Methyltransferase domain / Vaccinia Virus protein VP39 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain / Protein kinase-like domain superfamily / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / O-antigen chain terminator bifunctional methyltransferase/kinase WbdD
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.291 Å
AuthorsHagelueken, G. / Huang, H. / Naismith, J.H.
CitationJournal: Mol.Microbiol. / Year: 2012
Title: Structure of Wbdd; a Bifunctional Kinase and Methyltransferase that Regulates the Chain Length of the O Antigen in Escherichia Coli O9A.
Authors: Hagelueken, G. / Huang, H. / Clarke, B.R. / Lebl, T. / Whitfield, C. / Naismith, J.H.
History
DepositionJun 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Feb 6, 2013Group: Atomic model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WBDD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8817
Polymers65,0631
Non-polymers8186
Water0
1
A: WBDD
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)790,57484
Polymers780,75612
Non-polymers9,81872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation8_555-z,x,-y1
Buried area44190 Å2
ΔGint-757.2 kcal/mol
Surface area204950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.320, 159.320, 159.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein WBDD / World Blood Donor Day


Mass: 65063.023 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-556
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Gene: ORF708 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q47592
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.51 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.24→112.8 Å / Num. obs: 10923 / % possible obs: 99.9 % / Observed criterion σ(I): 2.6 / Redundancy: 5.9 % / Biso Wilson estimate: 84.09 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.5

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.291→112.656 Å / SU ML: 0.81 / σ(F): 1.36 / Phase error: 24.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2653 499 4.8 %
Rwork0.2225 --
obs0.2245 10374 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.4 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.291→112.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3595 0 48 0 3643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083790
X-RAY DIFFRACTIONf_angle_d1.3565167
X-RAY DIFFRACTIONf_dihedral_angle_d15.5421389
X-RAY DIFFRACTIONf_chiral_restr0.092548
X-RAY DIFFRACTIONf_plane_restr0.007674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2907-3.62190.28281330.24782437X-RAY DIFFRACTION100
3.6219-4.1460.2671170.21312442X-RAY DIFFRACTION100
4.146-5.22360.23371360.1872445X-RAY DIFFRACTION100
5.2236-112.72230.28311130.24372551X-RAY DIFFRACTION100

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