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- PDB-7kb7: THE STRUCTURE OF A SENSOR DOMAIN OF A HISTIDINE KINASE (VxrA) FRO... -

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Basic information

Entry
Database: PDB / ID: 7kb7
TitleTHE STRUCTURE OF A SENSOR DOMAIN OF A HISTIDINE KINASE (VxrA) FROM VIBRIO CHOLERAE O1 BIOVAR ELTOR STR. N16961, N239-T240 deletion mutant
ComponentsSensor histidine kinase
KeywordsSIGNALING PROTEIN / VxrA / Two-component system / Histidine kinase / sensor domain / Structural Genomics / Center for Membrane Proteins of Infectious Diseases / MPID
Function / homology
Function and homology information


phosphorelay sensor kinase activity / histidine kinase / plasma membrane
Similarity search - Function
: / Protein of unknown function DUF3404 / Domain of unknown function (DUF3404) / : / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. ...: / Protein of unknown function DUF3404 / Domain of unknown function (DUF3404) / : / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Sensor histidine kinase VxrA
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTan, K. / Wu, R. / Jedrzejczak, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) / Center for Membrane Proteins of Infectious Diseases (MPID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: J.Bacteriol. / Year: 2021
Title: Sensor Domain of Histidine Kinase VxrA of Vibrio cholerae - A Hairpin-swapped Dimer and its Conformational Change.
Authors: Tan, K. / Teschler, J.K. / Wu, R. / Jedrzejczak, R.P. / Zhou, M. / Shuvalova, L.A. / Endres, M.J. / Welk, L.F. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Yildiz, F.H. / Joachimiak, A.
History
DepositionOct 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author / database_2
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.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,38311
Polymers24,6641
Non-polymers71910
Water48627
1
A: Sensor histidine kinase
hetero molecules

A: Sensor histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,76522
Polymers49,3282
Non-polymers1,43820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6950 Å2
ΔGint-133 kcal/mol
Surface area23570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.856, 87.856, 107.679
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Sensor histidine kinase


Mass: 24663.773 Da / Num. of mol.: 1 / Mutation: N239-T240 deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_A0565 / Plasmid: pMCSG57 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -MAGIC / References: UniProt: Q9KM24
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 4.21 Å3/Da / Density % sol: 70.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris:HCl, 1 M Magnesium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.2→46 Å / Num. obs: 22071 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 55.88 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.042 / Net I/σ(I): 29.2
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 6 % / Rmerge(I) obs: 0.86 / Num. unique obs: 1076 / Rpim(I) all: 0.381 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHENIX1.18.2_3874refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R7Q

4r7q


Resolution: 2.2→45.91 Å / SU ML: 0.224 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.2618
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 1133 5.16 %random
Rwork0.2019 20845 --
obs0.2032 21978 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.65 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1719 0 41 27 1787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311862
X-RAY DIFFRACTIONf_angle_d0.6012533
X-RAY DIFFRACTIONf_chiral_restr0.0404268
X-RAY DIFFRACTIONf_plane_restr0.0039328
X-RAY DIFFRACTIONf_dihedral_angle_d22.693676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.30.31861290.26852551X-RAY DIFFRACTION99.93
2.3-2.420.2821450.26512552X-RAY DIFFRACTION99.96
2.42-2.570.26711350.23622585X-RAY DIFFRACTION99.93
2.57-2.770.26941400.25182566X-RAY DIFFRACTION99.93
2.77-3.050.28381600.23842556X-RAY DIFFRACTION99.82
3.05-3.490.23611430.21432619X-RAY DIFFRACTION99.86
3.49-4.40.21431280.1772653X-RAY DIFFRACTION99.75
4.4-45.910.19481530.18422763X-RAY DIFFRACTION99.08
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)
13.79898105382-4.327664657220.4791001034568.41658367027-1.505208704583.21734996888-0.2264391187-0.2790962587940.3142590111341.323994690010.286665531503-0.389787834872-0.359472835577-0.0526412737003-0.04290601709940.684816416253-0.0279790635246-0.04041349078350.466148003061-0.1429452981780.501325502553-15.9142864275-14.536858800919.6925517344
25.59703266617-0.655051270177-2.227151003015.151420838771.111811787227.783182549370.05881708546240.4389231597420.00498668017455-0.3255373682090.131912412628-0.8105080510620.2849979488070.902908513664-0.1734045860030.4522266522090.0356891413191-0.02458823460840.5829998559820.01606967613320.4386768740783.16044872784-44.56381865395.33312211316
31.74012363484-3.381786435961.598007529727.83969150674-3.533363979773.39362150905-0.2151697867550.224946968462-0.8983566769710.1877880665230.381614892216-1.570238349061.127165738251.244865559840.1041341054110.5886824740150.105803631326-0.005030081217110.705678442566-0.04789790558520.7092164916257.30709082443-52.138362973611.5612933568
44.41932307419-0.927426437105-1.571681744554.238563670730.2296681897836.85003245553-0.341541386225-0.152748413196-0.5254724300570.1345817100840.2514633660530.01143347322680.903324282880.3973611432670.009432165986620.5105967900550.0609406310194-0.003284464618310.3104841680370.04647198913270.364447345052-3.02452832972-49.096160283817.1766343899
53.16978234265-3.36587628053-0.1833281459317.031088021391.225446103751.67921997131-0.117151586058-0.04142365076760.1829328905760.2304199494550.0588550114770.209451268483-0.237511414637-0.1347830213820.06941692395760.590308754729-0.0123481916414-0.001464370501790.3613617710170.02053356307260.440946999045-14.3468236185-28.490792099714.2160401102
62.03542440031-1.563387331580.5378878453843.25291948381-0.9412493421225.039511902790.102698842363-0.118776312849-0.3527398038430.6069413539050.102189501820.4919151794270.0611786210218-0.139459528947-0.1967690595670.7018811539440.00380908786170.01332574907480.336175321342-0.02074619706580.554547726178-23.1150809692-15.053342560715.9944477346
71.406293604790.542600192026-1.26765408272.898914645420.82953577967.96129536257-0.04377862749460.07471456066320.05429715632980.1364753584640.322094847718-0.8373403791430.379102537360.927379651963-0.1370969493840.5274085596950.1099831175230.02795883167310.600639449739-0.1260249354790.728042378935-11.283245552-15.497086054-1.90626847815
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 36 through 68 )36 - 681 - 33
22chain 'A' and (resid 69 through 108 )69 - 10834 - 74
33chain 'A' and (resid 109 through 123 )109 - 12375 - 89
44chain 'A' and (resid 124 through 163 )124 - 16390 - 131
55chain 'A' and (resid 164 through 211 )164 - 211132 - 183
66chain 'A' and (resid 212 through 228 )212 - 228184 - 200
77chain 'A' and (resid 229 through 253 )229 - 253201 - 225

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