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- PDB-7ji4: Universal stress protein (USP) domain of KdpD histidine kinase in... -

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Basic information

Entry
Database: PDB / ID: 7ji4
TitleUniversal stress protein (USP) domain of KdpD histidine kinase in complex with second messenger c-di-AMP
ComponentsKdpD
KeywordsSIGNALING PROTEIN / Universal stress protein / histidine kinase / second messenger / two component system
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020 / ATP binding / plasma membrane
Similarity search - Function
Signal transduction histidine kinase, osmosensitive K+ channel sensor, N-terminal / Sensor protein KdpD, transmembrane domain / KdpD, transmembrane domain superfamily / Osmosensitive K+ channel His kinase sensor domain / Domain of unknown function (DUF4118) / 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 / Signal transduction histidine kinase-related protein, C-terminal ...Signal transduction histidine kinase, osmosensitive K+ channel sensor, N-terminal / Sensor protein KdpD, transmembrane domain / KdpD, transmembrane domain superfamily / Osmosensitive K+ channel His kinase sensor domain / Domain of unknown function (DUF4118) / 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 / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / GAF-like domain superfamily / 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
Chem-2BA / Histidine kinase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus MRSA252 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.3 Å
AuthorsDutta, A. / Parashar, V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM119504 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural basis of KdpD histidine kinase binding to the second messenger c-di-AMP.
Authors: Dutta, A. / Batish, M. / Parashar, V.
History
DepositionJul 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KdpD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3122
Polymers17,6541
Non-polymers6581
Water43224
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7510 Å2
Unit cell
Length a, b, c (Å)54.411, 54.411, 96.526
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-506-

HOH

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Components

#1: Protein KdpD / Sensor protein / KdpD histidine kinase


Mass: 17653.535 Da / Num. of mol.: 1
Fragment: Universal stress protein (USP) domain (UNP residues 213-364)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus MRSA252 (bacteria)
Gene: kdpD_1, ERS072840_01892, SAMEA1469884_01983, SAMEA1531680_02090, SAMEA1531701_02007, SAST44_02327, SAST45_02303
Plasmid: pBB75 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A167RS01
#2: Chemical ChemComp-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
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: 2.02 Å3/Da / Density % sol: 39.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.11 M lithium sulfate, 0.1 M Tris-HCl, pH 8.5, 21% PEG3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 2, 2018
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 6957 / % possible obs: 100 % / Redundancy: 23.7 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.023 / Rrim(I) all: 0.115 / Χ2: 1.003 / Net I/σ(I): 8.3 / Num. measured all: 164630
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.3421.80.4443310.9820.0920.4540.98799.1
2.34-2.3821.40.4743400.9860.1010.4850.957100
2.38-2.4323.10.4073400.9840.0840.4151.004100
2.43-2.4824.40.3943390.9890.0790.4020.996100
2.48-2.53250.3613270.9880.0720.3681.044100
2.53-2.5924.30.2953450.9930.060.3020.961100
2.59-2.6624.30.2743240.990.0560.281.025100
2.66-2.7323.20.2423520.9910.050.2481.001100
2.73-2.81250.2143360.9950.0430.2190.993100
2.81-2.924.50.1873340.9960.0380.1911.002100
2.9-323.80.1743440.9950.0350.1780.989100
3-3.1225.40.1613450.9940.0320.1641.012100
3.12-3.2624.70.1463440.9940.0290.1491100
3.26-3.44240.1353450.9950.0280.1380.994100
3.44-3.6523.60.1273530.9960.0260.131.037100
3.65-3.9323.60.123520.9980.0250.1230.912100
3.93-4.3324.70.1093490.9960.0220.1110.989100
4.33-4.9523.50.1013670.9970.0210.1041.014100
4.95-6.2422.90.0923670.9980.0190.0941.058100
6.24-5020.80.0884230.9970.0190.0911.071100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.3 Å47.4 Å

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660-000refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.3→47.4 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.89 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.249 692 10.03 %
Rwork0.2077 6205 -
obs0.2118 6897 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.26 Å2 / Biso mean: 63.4322 Å2 / Biso min: 41.42 Å2
Refinement stepCycle: final / Resolution: 2.3→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 44 24 1025
Biso mean--56.72 65.43 -
Num. residues----125
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.480.31171340.23991202133699
2.48-2.730.3491360.240612051341100
2.73-3.120.31341350.248512181353100
3.12-3.930.25551380.224112491387100
3.93-47.40.20891490.183513311480100

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