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- PDB-2v9a: Structure of Citrate-free Periplasmic Domain of Sensor Histidine ... -

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Basic information

Entry
Database: PDB / ID: 2v9a
TitleStructure of Citrate-free Periplasmic Domain of Sensor Histidine Kinase CitA
ComponentsSENSOR KINASE CITA
KeywordsTRANSFERASE / SIGNAL TRANSDUCTION / SENSOR HISTIDINE KINASE / CITA / KINASE / MEMBRANE / SENSOR DOMAIN / TRANSMEMBRANE / INNER MEMBRANE / PHOSPHORYLATION / TWO-COMPONENT REGULATORY SYSTEM
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / ATP binding / plasma membrane
Similarity search - Function
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. / Beta-Lactamase / PAS 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. / Beta-Lactamase / PAS domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Sensor histidine kinase CitA
Similarity search - Component
Biological speciesKLEBSIELLA PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSevvana, M. / Vijayan, V. / Zweckstetter, M. / Reinelt, S. / Madden, D.R. / Sheldrick, G.M. / Bott, M. / Griesinger, C. / Becker, S.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: A Ligand-Induced Switch in the Periplasmic Domain of Sensor Histidine Kinase Cita.
Authors: Sevvana, M. / Vijayan, V. / Zweckstetter, M. / Reinelt, S. / Madden, D.R. / Herbst-Irmer, R. / Sheldrick, G.M. / Bott, M. / Griesinger, C. / Becker, S.
History
DepositionAug 23, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SENSOR KINASE CITA
B: SENSOR KINASE CITA


Theoretical massNumber of molelcules
Total (without water)28,9992
Polymers28,9992
Non-polymers00
Water4,125229
1
A: SENSOR KINASE CITA

A: SENSOR KINASE CITA

A: SENSOR KINASE CITA

A: SENSOR KINASE CITA


Theoretical massNumber of molelcules
Total (without water)57,9984
Polymers57,9984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455y-1,-x,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area5740 Å2
ΔGint-42.2 kcal/mol
Surface area25150 Å2
MethodPQS
2
B: SENSOR KINASE CITA

B: SENSOR KINASE CITA

B: SENSOR KINASE CITA

B: SENSOR KINASE CITA


Theoretical massNumber of molelcules
Total (without water)57,9984
Polymers57,9984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5480 Å2
ΔGint-34.5 kcal/mol
Surface area24510 Å2
MethodPQS
Unit cell
Length a, b, c (Å)64.163, 64.163, 144.746
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein SENSOR KINASE CITA / SENSOR HISTIDINE KINASE CITA PERIPLASMIC DOMAIN


Mass: 14499.438 Da / Num. of mol.: 2
Fragment: PERIPLASMIC LIGAND BINDING DOMAIN, RESIDUES 45-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KLEBSIELLA PNEUMONIAE (bacteria) / Plasmid: PET16B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52687, histidine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.3 % / Description: MEROHEDRAL TWINNING ALONG 110
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP, VAPOUR DIFFUSION, RESERVOIR: 20MM HEPES,PH 7.5,0.63M NAH2PO4,0.63M KH2PO4, PROTEIN SOLUTION: 15 MG/ML,MIXING RATIO 1:1,TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 8, 2006 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 19151 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 5.49 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.7
Reflection shellResolution: 2→2.1 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.19 / % possible all: 84.1

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Processing

Software
NameClassification
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J80

2j80


Resolution: 2→24.6626 Å
Details: THE STRUCTURE WAS FIRST REFINED WITH CNS, FOLLOWED BY SHELXL AND FOR BETTER CONVERGENCE WITH PHENIX.REFINE TWIN REFINEMENT PROTOCOL TWIN LAW 1 0 0 0 -1 0 0 0 -1 TWIN FRACTION 0.40
RfactorNum. reflection% reflection
Rfree0.2783 956 5 %
Rwork0.2124 --
obs-19151 97 %
Refinement stepCycle: LAST / Resolution: 2→24.6626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 0 229 1725

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