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- PDB-6u1p: Crystal structure of VpsU (VC0916) from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 6u1p
TitleCrystal structure of VpsU (VC0916) from Vibrio cholerae
ComponentsLow molecular weight phosphotyrosine protein phosphatase
KeywordsHYDROLASE / Phosphatase / VC0916 / dimer
Function / homologyProtein-tyrosine phosphatase, low molecular weight / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / Protein-tyrosine-phosphatase / Protein-tyrosine-phosphatase
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsTripathi, S.M. / Schwechheimer, C. / Herbert, K. / Osorio, J. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Low molecular weight phosphotyrosine protein phosphatase
B: Low molecular weight phosphotyrosine protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8434
Polymers37,6592
Non-polymers1842
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-54 kcal/mol
Surface area15010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.323, 80.323, 105.053
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 120 or (resid 121...
21(chain B and (resid 5 through 33 or (resid 34...

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
11GLYGLYGLUGLU(chain A and (resid 5 through 120 or (resid 121...AA5 - 1205 - 120
12LYSLYSLYSLYS(chain A and (resid 5 through 120 or (resid 121...AA121121
13GLYGLYGLNGLN(chain A and (resid 5 through 120 or (resid 121...AA5 - 1535 - 153
14GLYGLYGLNGLN(chain A and (resid 5 through 120 or (resid 121...AA5 - 1535 - 153
15GLYGLYGLNGLN(chain A and (resid 5 through 120 or (resid 121...AA5 - 1535 - 153
16GLYGLYGLNGLN(chain A and (resid 5 through 120 or (resid 121...AA5 - 1535 - 153
21GLYGLYLYSLYS(chain B and (resid 5 through 33 or (resid 34...BB5 - 335 - 33
22ARGARGARGARG(chain B and (resid 5 through 33 or (resid 34...BB3434
23GLYGLYGLUGLU(chain B and (resid 5 through 33 or (resid 34...BB5 - 1545 - 154
24GLYGLYGLUGLU(chain B and (resid 5 through 33 or (resid 34...BB5 - 1545 - 154
25GLYGLYGLUGLU(chain B and (resid 5 through 33 or (resid 34...BB5 - 1545 - 154
26GLYGLYGLUGLU(chain B and (resid 5 through 33 or (resid 34...BB5 - 1545 - 154
27GLYGLYGLUGLU(chain B and (resid 5 through 33 or (resid 34...BB5 - 1545 - 154

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Components

#1: Protein Low molecular weight phosphotyrosine protein phosphatase / Phosphotyrosine protein phosphatase


Mass: 18829.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: etp / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0H5WT43, UniProt: Q9KTI6*PLUS, protein-tyrosine-phosphatase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES (pH 7.5) 1.25 M tri-sodium citrate 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→63.81 Å / Num. obs: 16904 / % possible obs: 99.9 % / Redundancy: 8.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.2
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.724 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1449 / CC1/2: 0.56

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LRQ

4lrq


Resolution: 2.201→63.809 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.72
RfactorNum. reflection% reflection
Rfree0.2571 1633 10 %
Rwork0.1879 --
obs0.1948 16331 96.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.69 Å2 / Biso mean: 63.823 Å2 / Biso min: 26.4 Å2
Refinement stepCycle: final / Resolution: 2.201→63.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2373 0 12 35 2420
Biso mean--72.75 50.73 -
Num. residues----299
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A906X-RAY DIFFRACTION1.516TORSIONAL
12B906X-RAY DIFFRACTION1.516TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.201-2.26530.37431200.275112889
2.2653-2.33840.27941340.2567113190
2.3384-2.4220.32371200.2238119494
2.422-2.51890.31581360.2235119295
2.5189-2.63360.29161240.2268124096
2.6336-2.77240.28291460.2198123997
2.7724-2.94610.27531400.2115121498
2.9461-3.17360.29291470.2127124199
3.1736-3.4930.26171590.19341264100
3.493-3.99830.21381400.17321275100
3.9983-5.03720.21821360.15371266100
5.0372-63.8090.26191310.17141314100
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)
13.82350.77510.25954.0604-0.52397.97780.4571-0.1938-0.13620.30440.36840.5848-0.0812-1.0161-0.65450.32240.06260.09170.49090.03150.31534.48450.71391.353
23.09841.645-0.77345.4564-2.29083.97650.29410.2260.30150.18830.1660.445-0.3631-0.579-0.32270.35110.12550.10240.57870.04770.31513.32356.53685.546
33.3257-0.4545-0.64215.19570.67812.0275-0.6674-0.1402-0.4201-0.3554-0.3287-0.0268-0.63170.35220.78870.4099-0.10780.18210.5702-0.21250.659615.93850.65956.291
44.65051.3907-1.27233.0365-0.62445.42270.2196-0.4091-0.1334-0.46750.0221-1.07540.4510.3641-0.18530.45710.18520.13810.592-0.14540.753113.94436.5153.318
54.2114-0.02540.43474.5154-0.39561.7232-0.03140.6221-0.4118-1.16640.1679-0.2935-0.1381-0.12380.06170.6859-0.01050.21430.5049-0.16130.535910.47942.89446.376
65.0606-1.4319-0.26176.8217-0.58714.37850.0144-0.6807-0.67120.00620.36180.47630.34890.291-0.33240.3774-00.07520.4379-0.00470.5828.19538.37656.554
72.2462-1.7796-0.12532.7746-0.12923.75860.0226-0.0907-0.3913-0.60010.0451-1.36570.31831.1366-0.0030.52210.17460.25820.9796-0.25821.069923.94736.62352.617
84.44270.42380.63936.10610.40312.21170.1463-0.0854-0.22990.2018-0.0918-0.70050.77130.7547-0.08520.29240.03770.03760.3874-0.01240.340815.16651.93585.568
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 6:43 )A6 - 43
2X-RAY DIFFRACTION2( CHAIN A AND RESID 44:125 )A44 - 125
3X-RAY DIFFRACTION3( CHAIN A AND RESID 126:153 )A126 - 153
4X-RAY DIFFRACTION4( CHAIN B AND RESID 5:17 )B5 - 17
5X-RAY DIFFRACTION5( CHAIN B AND RESID 18:43 )B18 - 43
6X-RAY DIFFRACTION6( CHAIN B AND RESID 44:82 )B44 - 82
7X-RAY DIFFRACTION7( CHAIN B AND RESID 83:125 )B83 - 125
8X-RAY DIFFRACTION8( CHAIN B AND RESID 126:154 )B126 - 154

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