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- PDB-7cjr: Crystal structure of a periplasmic sensor domain of histidine kin... -

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Basic information

Entry
Database: PDB / ID: 7cjr
TitleCrystal structure of a periplasmic sensor domain of histidine kinase VbrK
ComponentsHistidine kinase
KeywordsSIGNALING PROTEIN / histidine kinase / sensor / transferase / tetratricopeptide repeat
Function / homology
Function and homology information


phosphorelay sensor kinase activity / membrane => GO:0016020
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. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases ...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 / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Whole genome shotgun sequence / Histidine kinase
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.28 Å
AuthorsGoh, B.C. / Chua, Y.K. / Qian, X. / Savko, M. / Lescar, J.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore) Singapore
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Crystal structure of the periplasmic sensor domain of histidine kinase VbrK suggests indirect sensing of beta-lactam antibiotics.
Authors: Goh, B.C. / Chua, Y.K. / Qian, X. / Lin, J. / Savko, M. / Dedon, P.C. / Lescar, J.
History
DepositionJul 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6375
Polymers27,2831
Non-polymers3544
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-7 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.550, 52.550, 157.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Histidine kinase


Mass: 27283.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: CGJ74_25135, WR32_19055 / Plasmid: pNIC-CH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta T1R
References: UniProt: A0A0L8SC43, UniProt: A0A0D1DAV4*PLUS, histidine kinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: 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

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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: 1.99 Å3/Da / Density % sol: 38.14 % / Mosaicity: 0.13 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.2M NaCl, 25% PEG 3350, 0.1M Bis-Tris pH5.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSOLEIL PROXIMA 210.98
SYNCHROTRONSOLEIL PROXIMA 222
Detector
TypeIDDetectorDate
DECTRIS EIGER X 9M1PIXELDec 9, 2018
DECTRIS EIGER X 9M2PIXELDec 9, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
221
ReflectionResolution: 2.28→43.68 Å / Num. obs: 10752 / % possible obs: 99.7 % / Redundancy: 25.1 % / Biso Wilson estimate: 74.57 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.0103 / Rrim(I) all: 0.052 / Net I/σ(I): 34.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-ID% possible allMean I/σ(I) obs
2.28-2.3424.31.867310.8570.3731.898195.8
2.782-2.881243.65891298.996

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3 (19-MAR-2020)refinement
XDSdata reduction
Aimless0.7.3data scaling
SHELXphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.28→43.68 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.37 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.393 / SU Rfree Blow DPI: 0.255 / SU Rfree Cruickshank DPI: 0.252
RfactorNum. reflection% reflectionSelection details
Rfree0.2731 535 5 %RANDOM
Rwork0.2316 ---
obs0.2339 10693 99.7 %-
Displacement parametersBiso max: 144.91 Å2 / Biso mean: 78.8 Å2 / Biso min: 52.28 Å2
Baniso -1Baniso -2Baniso -3
1--10.1785 Å20 Å20 Å2
2---10.1785 Å20 Å2
3---20.3571 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: final / Resolution: 2.28→43.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 0 52 27 1769
Biso mean--120.85 68.28 -
Num. residues----214
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d614SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes296HARMONIC5
X-RAY DIFFRACTIONt_it1763HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion227SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1367SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1793HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg2452HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion18.11
LS refinement shellResolution: 2.28→2.31 Å / Rfactor Rfree error: 0 / Total num. of bins used: 27
RfactorNum. reflection% reflection
Rfree0.2835 20 4.85 %
Rwork0.2659 392 -
all0.2666 412 -
obs--93.06 %

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