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- PDB-8bjp: The N288D mutant cytoplasmic PAS domain of Geobacillus thermodeni... -

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Basic information

Entry
Database: PDB / ID: 8bjp
TitleThe N288D mutant cytoplasmic PAS domain of Geobacillus thermodenitrificans histidine kinase CitA
Componentscytoplasmic PAS domain of CitA from Geobacillus thermodenitrificans
KeywordsSIGNALING PROTEIN / cytoplasmic PAS domain / CitA / histidine kinase / transmembrane signaling
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / nucleotide binding / plasma membrane
Similarity search - Function
SpoOB, alpha-helical domain / Sensor_kinase_SpoOB-type, alpha-helical domain / Single cache domain 3 / Single cache domain 3 / Signal transduction histidine kinase, sporulation regulator SpoOB / Periplasmic sensor-like domain superfamily / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. ...SpoOB, alpha-helical domain / Sensor_kinase_SpoOB-type, alpha-helical domain / Single cache domain 3 / Single cache domain 3 / Signal transduction histidine kinase, sporulation regulator SpoOB / Periplasmic sensor-like domain superfamily / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Biological speciesGeobacillus thermodenitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsBecker, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: The N288D mutant cytoplasmic PAS domain of Geobacillus thermodenitrificans histidine kinase CitA
Authors: Becker, S.
History
DepositionNov 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: cytoplasmic PAS domain of CitA from Geobacillus thermodenitrificans
BBB: cytoplasmic PAS domain of CitA from Geobacillus thermodenitrificans
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9163
Polymers24,8922
Non-polymers241
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-31 kcal/mol
Surface area10270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.166, 49.295, 92.199
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein cytoplasmic PAS domain of CitA from Geobacillus thermodenitrificans


Mass: 12445.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N288D mutant; MSE: seleno-methionine
Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria)
Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: A0A1W6VSR4
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.4M magnesium chloride, 0.1M Tris/HCl, pH 8.5, 20.5% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97957, 0.9800, 0.97188
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979571
20.981
30.971881
ReflectionResolution: 2.1→43.509 Å / Num. obs: 12630 / % possible obs: 92.1 % / Redundancy: 3.12 % / Rrim(I) all: 0.038 / Net I/σ(I): 20.96
Reflection shellResolution: 2.1→2.15 Å / Num. unique obs: 582 / Rrim(I) all: 0.267

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SADABSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→43.509 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.937 / SU ML: 0.131 / Cross valid method: FREE R-VALUE / ESU R: 0.236 / ESU R Free: 0.189
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2326 640 5.067 %
Rwork0.1951 11990 -
all0.197 --
obs-12630 92.203 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 42.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.255 Å2-0 Å2-0 Å2
2---0.347 Å20 Å2
3---0.602 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1594 0 1 33 1628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131632
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151609
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.6482225
X-RAY DIFFRACTIONr_angle_other_deg1.3241.5713655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.955221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.30222.05573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51215251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0771512
X-RAY DIFFRACTIONr_chiral_restr0.0680.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021893
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02359
X-RAY DIFFRACTIONr_nbd_refined0.2060.2286
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.21529
X-RAY DIFFRACTIONr_nbtor_refined0.150.2815
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.2818
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.231
X-RAY DIFFRACTIONr_metal_ion_refined0.0420.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0990.28
X-RAY DIFFRACTIONr_nbd_other0.2060.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2570.23
X-RAY DIFFRACTIONr_mcbond_it3.7164.308884
X-RAY DIFFRACTIONr_mcbond_other3.6764.303883
X-RAY DIFFRACTIONr_mcangle_it4.9096.4461105
X-RAY DIFFRACTIONr_mcangle_other4.916.451106
X-RAY DIFFRACTIONr_scbond_it5.3294.936748
X-RAY DIFFRACTIONr_scbond_other5.3254.938749
X-RAY DIFFRACTIONr_scangle_it7.8977.1441120
X-RAY DIFFRACTIONr_scangle_other7.8937.1441120
X-RAY DIFFRACTIONr_lrange_it9.47552.4181657
X-RAY DIFFRACTIONr_lrange_other9.45652.3881655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1520.295430.242732X-RAY DIFFRACTION77.2682
2.152-2.2110.267400.22892X-RAY DIFFRACTION96.5803
2.211-2.2750.235480.219843X-RAY DIFFRACTION96.2203
2.275-2.3440.241480.213846X-RAY DIFFRACTION96.2325
2.344-2.4210.339400.201787X-RAY DIFFRACTION95.2765
2.421-2.5060.224460.205766X-RAY DIFFRACTION92.6941
2.506-2.60.294470.217755X-RAY DIFFRACTION96.2785
2.6-2.7060.3420.209710X-RAY DIFFRACTION95.4315
2.706-2.8260.264370.22695X-RAY DIFFRACTION94.4516
2.826-2.9630.265390.194641X-RAY DIFFRACTION93.9227
2.963-3.1230.226290.205645X-RAY DIFFRACTION92.8375
3.123-3.3110.266240.206581X-RAY DIFFRACTION90.8408
3.311-3.5380.257280.205560X-RAY DIFFRACTION92.5984
3.538-3.820.195280.19511X-RAY DIFFRACTION91.6667
3.82-4.1820.263180.188482X-RAY DIFFRACTION91.2409
4.182-4.6710.22240.144426X-RAY DIFFRACTION90.5433
4.671-5.3840.121260.166378X-RAY DIFFRACTION89.3805
5.384-6.5720.39110.233327X-RAY DIFFRACTION87.5648
6.572-9.2010.168140.176254X-RAY DIFFRACTION86.7314
9.201-43.5090.23480.204159X-RAY DIFFRACTION83.0846

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