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- PDB-6mab: 1.7A resolution structure of RsbU from Chlamydia trachomatis (per... -

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Basic information

Entry
Database: PDB / ID: 6mab
Title1.7A resolution structure of RsbU from Chlamydia trachomatis (periplasmic domain)
ComponentsSigma regulatory family protein-PP2C phosphatase
KeywordsSIGNALING PROTEIN / RsbU / periplasmic sensor domain / Chlamydia trachomatis / TCA cycle intermediates
Function / homology
Function and homology information


signal transduction / membrane
Similarity search - Function
: / Stage II sporulation protein E (SpoIIE) / Sigma factor PP2C-like phosphatases / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Sigma regulatory family protein-PP2C phosphatase
Similarity search - Component
Biological speciesChlamydia trachomatis serovar L2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsDmitriev, A. / Lovell, S. / Battaile, K.P. / Soules, K. / Hefty, P.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM110761 United States
CitationJournal: Mol.Microbiol. / Year: 2020
Title: Structural and ligand binding analyses of the periplasmic sensor domain of RsbU in Chlamydia trachomatis support a role in TCA cycle regulation.
Authors: Soules, K.R. / Dmitriev, A. / LaBrie, S.D. / Dimond, Z.E. / May, B.H. / Johnson, D.K. / Zhang, Y. / Battaile, K.P. / Lovell, S. / Hefty, P.S.
History
DepositionAug 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.5Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sigma regulatory family protein-PP2C phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7922
Polymers30,7321
Non-polymers601
Water3,657203
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint2 kcal/mol
Surface area13210 Å2
2
A: Sigma regulatory family protein-PP2C phosphatase
hetero molecules

A: Sigma regulatory family protein-PP2C phosphatase
hetero molecules

A: Sigma regulatory family protein-PP2C phosphatase
hetero molecules

A: Sigma regulatory family protein-PP2C phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,1698
Polymers122,9284
Non-polymers2404
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area6480 Å2
ΔGint-33 kcal/mol
Surface area47170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.712, 96.712, 65.385
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Sigma regulatory family protein-PP2C phosphatase


Mass: 30732.064 Da / Num. of mol.: 1 / Fragment: Q45-R313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis serovar L2 (bacteria)
Strain: 434/Bu / ATCC VR-902B / Gene: rbsU, CTL0851 / Plasmid: pTBSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3MDU0
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.4950.55Prism
2Prism
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, sitting drop7.520% (w/v) PEG 4000, 10% (v/v) 2-propanol, 0.1 M Hepes
2982vapor diffusion, sitting drop8.51 M ammonium phosphate dibasic, 0.1 M Tris

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11002
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 17-ID11
SYNCHROTRONAPS 17-ID21
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELOct 20, 2013
DECTRIS PILATUS 6M2PIXELFeb 25, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21
ReflectionResolution: 1.7→48.36 Å / Num. obs: 33233 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 23.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Net I/σ(I): 17.9 / Num. measured all: 225529
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.7-1.736.31.1117580.6771100
9-48.366.70.0322430.999199.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.31data scaling
PHENIXphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.7→36.073 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.03 / Phase error: 20.9
RfactorNum. reflection% reflection
Rfree0.1973 1677 5.04 %
Rwork0.1636 --
obs0.1653 64844 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.46 Å2 / Biso mean: 33.4802 Å2 / Biso min: 13.68 Å2
Refinement stepCycle: final / Resolution: 1.7→36.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2077 0 4 203 2284
Biso mean--60.9 39.21 -
Num. residues----269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082147
X-RAY DIFFRACTIONf_angle_d0.9142929
X-RAY DIFFRACTIONf_chiral_restr0.055351
X-RAY DIFFRACTIONf_plane_restr0.005372
X-RAY DIFFRACTIONf_dihedral_angle_d10.5031299
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7001-1.72550.3561580.3022635279399
1.7255-1.75240.30521560.28642671282799
1.7524-1.78120.3261200.26552672279299
1.7812-1.81190.28531320.2462666279899
1.8119-1.84480.27631380.235427252863100
1.8448-1.88030.31061320.22752644277699
1.8803-1.91870.26931260.224826902816100
1.9187-1.96040.26961720.198327092881100
1.9604-2.0060.21241340.17322696283099
2.006-2.05610.22611450.172127142859100
2.0561-2.11170.18791120.163426762788100
2.1117-2.17390.16771780.16652621279999
2.1739-2.2440.1851480.149227042852100
2.244-2.32420.19251520.161526322784100
2.3242-2.41730.14841180.157226802798100
2.4173-2.52720.22171240.161227602884100
2.5272-2.66040.21521770.147626092786100
2.6604-2.82710.17961160.157226912807100
2.8271-3.04520.18291670.16232693286099
3.0452-3.35150.20981340.15562654278899
3.3515-3.8360.19091540.14632679283399
3.836-4.83110.13311100.123826992809100
4.8311-36.08120.18661630.16612658282199
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)
10.76251.32290.45622.00670.67130.1792-0.32250.07-0.2589-1.2280.4062-0.5278-0.07940.1838-0.07960.3969-0.07370.11150.2379-0.00990.265926.4063-10.8413-6.6963
23.16070.8716-0.69263.347-0.47613.32620.1386-0.19870.38070.568-0.02390.0264-0.46070.2529-0.06120.283-0.01720.04560.1757-0.02230.200339.394224.57317.0738
33.20921.33950.03472.35640.05451.9722-0.0217-0.1627-0.02890.02630.0553-0.0495-0.07630.1817-0.02840.1620.01940.02310.15650.02440.136435.648315.05854.6288
41.6972-0.17470.99864.3249-0.68395.0265-0.0162-0.0158-0.06960.0008-0.00620.01050.17030.07780.00930.15790.01420.03020.16330.03620.152228.4797-2.144411.2819
51.15750.58620.16892.4913-0.86781.99770.04290.0804-0.08570.46230.0997-0.3226-0.03010.0781-0.16430.15410.0266-0.0130.19410.04470.187432.6015-4.006714.9416
62.65581.5011.09475.78540.25723.02110.06270.01650.0855-0.22470.0221-0.50780.03360.0809-0.07070.12780.00420.04970.1275-0.00790.204428.0624-8.59454.6631
75.84095.90011.02267.75161.50061.3261-0.28340.2559-0.2978-0.43460.2497-0.14980.0075-0.04980.04170.2311-0.01310.02350.18390.01980.206120.1847-12.3910.7057
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION2chain 'A' and (resid 42 through 109 )A42 - 109
2X-RAY DIFFRACTION3chain 'A' and (resid 110 through 157 )A110 - 157
3X-RAY DIFFRACTION4chain 'A' and (resid 158 through 200 )A158 - 200
4X-RAY DIFFRACTION5chain 'A' and (resid 201 through 228 )A201 - 228
5X-RAY DIFFRACTION6chain 'A' and (resid 229 through 250 )A229 - 250
6X-RAY DIFFRACTION7chain 'A' and (resid 251 through 268 )A251 - 268

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