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- PDB-6u1q: Crystal Structure of VpsO (VC0937) Kinase domain -

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Basic information

Entry
Database: PDB / ID: 6u1q
TitleCrystal Structure of VpsO (VC0937) Kinase domain
ComponentsVpsO
KeywordsBIOSYNTHETIC PROTEIN / Kinase / polysaccharide synthesis / auto-phosphorylation / tyrosine kinase
Function / homology
Function and homology information


polysaccharide biosynthetic process / extracellular polysaccharide biosynthetic process / lipopolysaccharide biosynthetic process / protein tyrosine kinase activity / membrane => GO:0016020 / ATP binding / plasma membrane
Similarity search - Function
Tyrosine kinase, G-rich domain / G-rich domain on putative tyrosine kinase / Exopolysaccharide synthesis protein / Polysaccharide chain length determinant N-terminal domain / Chain length determinant protein / AAA domain / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
O-PHOSPHOTYROSINE / VpsO / Exopolysaccharide biosynthesis protein, putative
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsTripathi, S.M. / Schwechheimer, C. / Herbert, K. / Porcella, M.E. / Brown, E.R. / Yildiz, F.H. / Rubin, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Plos Pathog. / Year: 2020
Title: A tyrosine phosphoregulatory system controls exopolysaccharide biosynthesis and biofilm formation in Vibrio cholerae.
Authors: Schwechheimer, C. / Hebert, K. / Tripathi, S. / Singh, P.K. / Floyd, K.A. / Brown, E.R. / Porcella, M.E. / Osorio, J. / Kiblen, J.T.M. / Pagliai, F.A. / Drescher, K. / Rubin, S.M. / Yildiz, F.H.
History
DepositionAug 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VpsO
B: VpsO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0414
Polymers51,5192
Non-polymers5222
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-17 kcal/mol
Surface area18430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.430, 171.430, 44.390
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 508 through 710 or resid 801))
21(chain B and (resid 508 through 576 or (resid 577...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAASNASN(chain A and (resid 508 through 710 or resid 801))AA508 - 7106 - 208
12PTRPTRPTRPTR(chain A and (resid 508 through 710 or resid 801))AC801
21ALAALAARGARG(chain B and (resid 508 through 576 or (resid 577...BB508 - 5766 - 74
22LYSLYSLYSLYS(chain B and (resid 508 through 576 or (resid 577...BB57775
23ALAALAASNASN(chain B and (resid 508 through 576 or (resid 577...BB508 - 7106 - 208
24ALAALAASNASN(chain B and (resid 508 through 576 or (resid 577...BB508 - 7106 - 208
25ALAALAASNASN(chain B and (resid 508 through 576 or (resid 577...BB508 - 7106 - 208
26ALAALAASNASN(chain B and (resid 508 through 576 or (resid 577...BB508 - 7106 - 208

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Components

#1: Protein VpsO


Mass: 25759.268 Da / Num. of mol.: 2 / Mutation: E519A, R522, R525A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: vpsO / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S1ZT94, UniProt: Q9KTG5*PLUS
#2: Chemical ChemComp-PTR / O-PHOSPHOTYROSINE / PHOSPHONOTYROSINE


Type: L-peptide linking / Mass: 261.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12NO6P / Feature type: SUBJECT OF INVESTIGATION
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: 3.63 Å3/Da / Density % sol: 66.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium thiocyanate, pH 6.9, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.87→44.39 Å / Num. obs: 17506 / % possible obs: 100 % / Redundancy: 4.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.096 / Net I/σ(I): 9.2
Reflection shellResolution: 2.87→3.03 Å / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2518 / CC1/2: 0.73

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JLV

4jlv


Resolution: 2.87→42.858 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.23
RfactorNum. reflection% reflection
Rfree0.2283 810 4.77 %
Rwork0.1749 --
obs0.1775 16990 97.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.85 Å2 / Biso mean: 74.2976 Å2 / Biso min: 30.55 Å2
Refinement stepCycle: final / Resolution: 2.87→42.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3121 0 34 0 3155
Biso mean--118.73 --
Num. residues----411
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1240X-RAY DIFFRACTION9.161TORSIONAL
12B1240X-RAY DIFFRACTION9.161TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8701-3.04990.36861330.2743248691
3.0499-3.28530.291150.2316260394
3.2853-3.61580.24071230.1827272098
3.6158-4.13860.23611320.1697274599
4.1386-5.21280.19571480.14142770100
5.2128-42.8580.20931590.16942856100
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)
19.56357.27362.09167.51394.28014.8533-0.73330.68310.0759-0.40670.45510.5896-0.1496-0.26920.31160.41050.1447-0.03310.60030.16680.516338.028682.19814.7805
26.713-3.2053-0.02845.3766-0.32974.43960.02070.05430.6631-0.21490.06350.1095-0.9231-0.2101-0.06560.63880.0467-0.08390.35340.02880.390342.1447101.15720.0195
35.80744.02980.12199.6935-1.89742.41670.08610.7803-0.893-0.10470.8668-1.36390.21640.3501-0.82780.42030.0516-0.03880.4669-0.01530.509349.76488.0288-0.6654
44.38654.93861.75266.31091.38871.050.2544-0.24630.75420.5148-0.60070.95130.02330.06470.51770.53820.09110.15170.71660.00310.519731.009375.42738.4598
55.7191-1.9387-1.023.9303-1.41735.85970.2370.0730.4769-0.24380.158-0.12770.1517-0.6024-0.42030.3210.00660.10950.6199-0.0190.489222.801466.452511.8612
69.1504-2.1266-1.89614.32040.47296.0280.5019-0.24880.8801-0.01480.09030.4034-0.6061-0.9679-0.5950.38390.10620.12020.84360.03940.68069.874871.605314.499
74.4784-1.81221.76126.5468-0.30149.0158-0.1934-0.9733-0.13570.32560.3050.47130.2946-0.2546-0.11280.3823-0.08160.09180.79430.00440.405624.650359.118122.0011
86.9693-2.3895-2.8073.3025-2.00996.93930.51180.2490.27710.45930.4253-0.1595-0.15690.2362-0.6630.3621-0.01330.14610.4142-0.1340.494630.503162.765315.6543
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 504 through 532 )A504 - 532
2X-RAY DIFFRACTION2chain 'A' and (resid 533 through 697 )A533 - 697
3X-RAY DIFFRACTION3chain 'A' and (resid 698 through 711 )A698 - 711
4X-RAY DIFFRACTION4chain 'B' and (resid 508 through 532 )B508 - 532
5X-RAY DIFFRACTION5chain 'B' and (resid 533 through 563 )B533 - 563
6X-RAY DIFFRACTION6chain 'B' and (resid 564 through 653 )B564 - 653
7X-RAY DIFFRACTION7chain 'B' and (resid 654 through 697 )B654 - 697
8X-RAY DIFFRACTION8chain 'B' and (resid 698 through 710 )B698 - 710

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