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- PDB-4azt: Co-crystal structure of WbdD and kinase inhibitor LY294002. -

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Basic information

Entry
Database: PDB / ID: 4azt
TitleCo-crystal structure of WbdD and kinase inhibitor LY294002.
ComponentsMETHYLTRANSFERASE WBDD
KeywordsTRANSFERASE
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 / ATP binding / plasma membrane
Similarity search - Function
Methyltransferase domain / Methyltransferase domain / Vaccinia Virus protein VP39 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...Methyltransferase domain / Methyltransferase domain / Vaccinia Virus protein VP39 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / 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
2-MORPHOLIN-4-YL-7-PHENYL-4H-CHROMEN-4-ONE / S-ADENOSYLMETHIONINE / O-antigen chain terminator bifunctional methyltransferase/kinase WbdD
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.34 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 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHYLTRANSFERASE WBDD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,60813
Polymers65,0631
Non-polymers1,54512
Water3,765209
1
A: METHYLTRANSFERASE WBDD
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)799,299156
Polymers780,75612
Non-polymers18,542144
Water21612
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 area61740 Å2
ΔGint-1426.4 kcal/mol
Surface area201600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.984, 158.984, 158.984
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-2111-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein METHYLTRANSFERASE WBDD


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) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q47592

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Non-polymers , 5 types, 221 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


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


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-LY2 / 2-MORPHOLIN-4-YL-7-PHENYL-4H-CHROMEN-4-ONE / 2-(4-MORPHOLINYL)-8-PHENYL-4H-1-BENZOPYRAN-4-ONE


Mass: 307.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 55.6 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5417
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.34→42.5 Å / Num. obs: 27997 / % possible obs: 99.3 % / Observed criterion σ(I): 2.4 / Redundancy: 8.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.1

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.34→112.42 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.906 / SU B: 11.451 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25517 1430 5.1 %RANDOM
Rwork0.18752 ---
obs0.19087 26528 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.78 Å2
Refinement stepCycle: LAST / Resolution: 2.34→112.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3535 0 92 209 3836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023777
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7841.9665151
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5675447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02224.158202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.20115605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.041527
X-RAY DIFFRACTIONr_chiral_restr0.1250.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212942
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.342→2.403 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 108 -
Rwork0.226 1681 -
obs--90.58 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.93120.267-0.08231.1472-0.35521.56420.0188-0.02620.0361-0.03370.03240.0137-0.0179-0.0339-0.05120.0640.0026-0.00140.1003-0.01580.07629.41-39.666-16.573
23.43620.12960.79711.4447-0.93962.6073-0.117-0.12590.10970.17360.0361-0.1902-0.24380.21550.0810.16310.0146-0.03280.1630.03570.126424.38-51.1855.688
30.9175-0.7591.17271.1071-0.41013.0287-0.0091-0.08240.0196-0.07170.11850.0415-0.2396-0.4342-0.10950.20150.0323-0.03530.28090.03750.115530.829-56.37630.053
44.00890.232311.523331.99167.46834.6736-0.00230.17630.29940.0831-1.35392.1431-0.07210.16151.35620.13090.2147-0.0620.5707-0.10040.354433.607-42.437.949
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 221
2X-RAY DIFFRACTION2A222 - 316
3X-RAY DIFFRACTION3A317 - 464
4X-RAY DIFFRACTION4A465 - 471

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