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- PDB-3l34: The crystal structure of a two-component sensor domain (2nd form)... -

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Basic information

Entry
Database: PDB / ID: 3l34
TitleThe crystal structure of a two-component sensor domain (2nd form) from Pseudomonas aeruginosa PA01
ComponentsSensor protein
KeywordsTRANSFERASE / two-component sensor / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / ATP-binding / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Transmembrane
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / phosphatase activity / membrane
Similarity search - Function
Histidine kinase (KinB), sensor domain / Alginate biosynthesis sensor protein KinB, sensor domain / KinB, N-terminal domain superfamily / Sensor domain of alginate biosynthesis sensor protein KinB / PAS fold-4 / PAS fold / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain ...Histidine kinase (KinB), sensor domain / Alginate biosynthesis sensor protein KinB, sensor domain / KinB, N-terminal domain superfamily / Sensor domain of alginate biosynthesis sensor protein KinB / PAS fold-4 / PAS fold / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / 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. / PAS domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTan, K. / Chhor, G. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a two-component sensor domain from Pseudomonas aeruginosa PA01
Authors: Tan, K. / Chhor, G. / Buck, K. / Joachimiak, A.
History
DepositionDec 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensor protein
B: Sensor protein
C: Sensor protein
D: Sensor protein
E: Sensor protein
F: Sensor protein
G: Sensor protein
H: Sensor protein


Theoretical massNumber of molelcules
Total (without water)116,4628
Polymers116,4628
Non-polymers00
Water10,863603
1
A: Sensor protein
B: Sensor protein


Theoretical massNumber of molelcules
Total (without water)29,1152
Polymers29,1152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-51 kcal/mol
Surface area11570 Å2
MethodPISA
2
C: Sensor protein
D: Sensor protein


Theoretical massNumber of molelcules
Total (without water)29,1152
Polymers29,1152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-52 kcal/mol
Surface area11480 Å2
MethodPISA
3
E: Sensor protein
F: Sensor protein


Theoretical massNumber of molelcules
Total (without water)29,1152
Polymers29,1152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-54 kcal/mol
Surface area11630 Å2
MethodPISA
4
G: Sensor protein
H: Sensor protein


Theoretical massNumber of molelcules
Total (without water)29,1152
Polymers29,1152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-53 kcal/mol
Surface area11760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.506, 103.081, 69.465
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211
DetailsExperimentally unknown. The chains A and B, C and D, E and F, G and H are expected to form dimers, respectively.

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Components

#1: Protein
Sensor protein /


Mass: 14557.721 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA5484, Pseudomonas aeruginosa / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q9HT87, histidine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 1.89 Å3/Da / Density % sol: 34.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M Ammonium acetate 0.1M Sodium acettae 30% PEG4000, 15% glycerol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 16, 2009 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.7→42 Å / Num. all: 93984 / Num. obs: 93984 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 26.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.735 / Mean I/σ(I) obs: 1.5 / Num. unique all: 4477 / % possible all: 94.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPCCP4phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KKB

3kkb


Resolution: 1.7→41.392 Å / SU ML: 0.21 / σ(F): 0.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 4441 5.04 %random
Rwork0.1821 ---
all0.1843 88133 --
obs0.1843 88133 92.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.659 Å2 / ksol: 0.352 e/Å3
Refinement stepCycle: LAST / Resolution: 1.7→41.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7629 0 0 603 8232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067725
X-RAY DIFFRACTIONf_angle_d0.90410464
X-RAY DIFFRACTIONf_dihedral_angle_d17.9512952
X-RAY DIFFRACTIONf_chiral_restr0.0581177
X-RAY DIFFRACTIONf_plane_restr0.0031450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6997-1.76040.33330.24716488X-RAY DIFFRACTION72
1.7604-1.83090.28073560.22967565X-RAY DIFFRACTION84
1.8309-1.91430.25034580.2027919X-RAY DIFFRACTION88
1.9143-2.01520.26054350.19318316X-RAY DIFFRACTION92
2.0152-2.14140.23184520.17958666X-RAY DIFFRACTION96
2.1414-2.30680.21174970.16648813X-RAY DIFFRACTION98
2.3068-2.53890.2374330.18578885X-RAY DIFFRACTION99
2.5389-2.90620.23675370.18298919X-RAY DIFFRACTION99
2.9062-3.66110.20834620.17489033X-RAY DIFFRACTION100
3.6611-41.40380.20374780.1719088X-RAY DIFFRACTION99
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.3747-0.0485-0.42631.18090.33012.4952-0.01040.1728-0.03160.0283-0.0540.0927-0.028-0.18680.05820.1379-0.0028-0.01620.1371-0.01460.1636-20.2389-2.644447.0678
20.8161-0.31530.04730.5955-0.2181.98620.0637-0.02540.14940.0199-0.01370.0618-0.11070.0648-0.03640.0775-0.02670.00040.0112-0.00320.0937
30.28720.20530.31320.8480.19882.11370.0291-0.0357-0.03440.0311-0.0412-0.02430.1733-0.12630.01620.1597-0.01610.00180.1042-0.00980.1383
41.38850.21851.2320.91070.04492.3276-0.1470.35730.1897-0.03-0.0232-0.0921-0.05410.19460.15650.0804-0.0218-0.00370.11120.03520.1056
50.76740.32490.45020.8945-0.0743.04210.03050.05-0.2512-0.02910.0312-0.02670.10360.1566-0.05730.14260.01350.00780.1302-0.01980.1601
60.72790.0330.52451.36590.3563.28250.0067-0.0909-0.0051-0.03590.00390.0428-0.0344-0.2238-0.00970.12590.0210.01130.11650.0010.1321
71.6426-0.4888-0.62990.59790.1452.43750.0323-0.08990.2446-0.02780.0361-0.0825-0.1760.0144-0.05540.1571-0.00870.00360.0794-0.01650.1518
82.6370.326-1.89020.8713-0.02022.7538-0.1826-0.8664-0.2577-0.0162-0.0549-0.12460.10640.53820.1980.13120.04940.00680.34350.07970.1727
Refinement TLS groupSelection details: chain H

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