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- PDB-3n24: The crystal structure of a two-component sensor domain (3rd form)... -

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Basic information

Entry
Database: PDB / ID: 3n24
TitleThe crystal structure of a two-component sensor domain (3rd form) from Pseudomonas aeruginosa PA01
ComponentsSensor protein
KeywordsTRANSFERASE / two-component sensor domain / 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) / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.056 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 (3rd form) from Pseudomonas aeruginosa PA01
Authors: Tan, K. / Chhor, G. / Buck, K. / Joachimiak, A.
History
DepositionMay 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
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

Downloads & links

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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
Water3,693205
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 area4050 Å2
ΔGint-44 kcal/mol
Surface area10360 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 area4200 Å2
ΔGint-46 kcal/mol
Surface area11230 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 area4400 Å2
ΔGint-50 kcal/mol
Surface area10920 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 area4320 Å2
ΔGint-47 kcal/mol
Surface area11240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.003, 61.093, 71.600
Angle α, β, γ (deg.)85.60, 70.47, 89.50
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Sensor protein /


Mass: 14557.721 Da / Num. of mol.: 8 / Fragment: sequence database residues 41-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: PA5484 / 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.: 205 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2M sodium, 0.1M phosphate citrate, 20% PEG8000, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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 315 / Detector: CCD / Date: Nov 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: 2.05→37 Å / Num. all: 46030 / Num. obs: 46030 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.4
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 1.54 / Num. unique all: 2138 / % possible all: 90

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Processing

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

3kkb


Resolution: 2.056→36.63 Å / SU ML: 0.32 / σ(F): 0.01 / σ(I): 0 / Phase error: 30.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2816 2144 4.99 %random
Rwork0.2025 ---
obs0.2064 42970 90.35 %-
all-42970 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.744 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.253 Å2-1.68 Å20.0424 Å2
2--6.2552 Å23.4825 Å2
3----3.0022 Å2
Refinement stepCycle: LAST / Resolution: 2.056→36.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6888 0 0 205 7093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077090
X-RAY DIFFRACTIONf_angle_d1.0229578
X-RAY DIFFRACTIONf_dihedral_angle_d21.1972706
X-RAY DIFFRACTIONf_chiral_restr0.0641075
X-RAY DIFFRACTIONf_plane_restr0.0041320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0556-2.1290.33741750.25073192X-RAY DIFFRACTION71
2.129-2.21420.34231910.2353750X-RAY DIFFRACTION82
2.2142-2.3150.30341890.21133916X-RAY DIFFRACTION87
2.315-2.4370.28592160.2084058X-RAY DIFFRACTION90
2.437-2.58970.29862180.2034116X-RAY DIFFRACTION91
2.5897-2.78960.27882180.1914219X-RAY DIFFRACTION94
2.7896-3.07020.27542580.19944317X-RAY DIFFRACTION96
3.0702-3.51410.25582330.18094396X-RAY DIFFRACTION97
3.5141-4.42620.27392100.174475X-RAY DIFFRACTION98
4.4262-36.63590.27392360.23194387X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.00770.1774-0.20420.1674-0.09280.18220.0114-0.43120.001-0.096-0.0855-0.00750.1321-0.11160.00630.1337-0.0128-0.01260.1495-0.02330.2115-4.8641-1.52599.1519
2-0.0151-0.05270.0912-0.0074-0.02120.0533-0.06990.5113-0.13010.06450.01930.40760.10330.2161-0.00040.2631-0.0242-0.04060.18-0.01280.3021-4.6662-0.5808-6.6702
30.7426-0.26870.32140.1976-0.21410.5282-0.29560.10030.09790.1118-0.01-0.31480.12370.434-0.06740.15030.03640.05780.36480.09440.25358.3992.4617-7.7564
40.3417-0.0855-0.16120.03530.04240.109-0.17811.50250.18-0.38750.0449-0.06680.0023-0.2463-0.00820.2989-0.0597-0.00360.40390.03740.11820.31084.0898-15.3395
50.28830.00970.04150.0326-0.07110.2998-0.2272-0.14230.0106-0.0240.2557-0.00850.05060.1697-0.00250.15820.00360.02140.25130.00540.1795.3719-5.27645.2314
61.5720.2367-0.07690.07240.08861.772-0.0372-0.09880.0009-0.023-0.08070.05470.1105-0.063-0.44190.07860.0173-0.00320.0042-0.01660.07387.155931.62538.6274
70.6996-0.19150.18290.1756-0.16050.5163-0.0760.31050.0747-0.0834-0.1372-0.11010.15180.4836-0.00810.23210.02820.03120.21910.03490.185319.869734.615725.4612
80.0624-0.02610.02540.0513-0.0170.05160.22490.56160.1498-0.51680.0009-0.3027-0.15610.03570.00060.329-0.0383-0.07330.25630.03550.185811.73838.033918.4623
90.44530.00180.03750.0439-0.0890.2668-0.1826-0.09670.0534-0.09180.3592-0.11720.04910.29990.00350.15880.0252-0.01320.1225-0.01950.092717.489728.431338.8859
100.6760.27510.26060.08510.00870.2326-0.1181-0.19250.3948-0.02420.1586-0.4253-0.06550.3182-0.01210.16120.10580.01050.70470.10330.197638.157730.013640.5529
110.609-0.234-0.12690.81430.24550.5666-0.0906-0.5924-0.34480.3116-0.30210.02070.64850.3364-0.04240.33030.07570.04530.52610.19670.201331.663222.839246.5661
120.25170.01680.13120.0269-0.01170.1522-0.338-0.5821-0.19360.31760.41250.252-0.07040.394-0.00340.12980.03410.0540.20830.04050.18443.93726.168230.3008
131.1434-0.5416-0.10420.41880.22650.3873-0.0020.58180.15160.0307-0.1360.00350.1415-0.49630.01430.1738-0.15960.010.2462-0.05060.080137.978726.830621.2231
140.4725-0.044-0.08890.04310.0310.2633-0.41030.10310.0737-0.17820.46960.0929-0.02630.0635-0.00380.1751-0.06580.03810.1208-0.01140.132629.285627.929634.8652
151.0645-0.21120.08950.10890.0340.8461-0.0441-0.42230.12880.14130.0229-0.05380.11430.2354-0.00060.14350.03460.00330.25290.01010.171823.1141-7.02610.8689
160.09830.0710.12020.01850.03580.0879-0.03150.10360.12290.43230.2312-0.2714-0.07290.1869-00.23630.0270.00990.1846-0.03160.179432.1789-7.8159-2.9059
170.5388-0.17940.24390.28420.13280.74960.11060.13670.1211-0.0159-0.18760.14120.0347-0.0108-00.151-00.01060.1492-0.03130.128626.1986-7.66-11.6061
180.23230.0177-0.01250.0153-0.00240.058-0.1988-0.34480.0398-0.47130.384-0.10910.03840.04940.00060.1753-0.0035-0.01070.1347-0.00520.189217.1802-4.34221.9858
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A resid 43:124
2X-RAY DIFFRACTION2chain A resid 132:158
3X-RAY DIFFRACTION3chain B resid 49:96
4X-RAY DIFFRACTION4chain B resid 103:122
5X-RAY DIFFRACTION5chain B resid 131:164
6X-RAY DIFFRACTION6chain C resid 41:163
7X-RAY DIFFRACTION7chain D resid 47:98
8X-RAY DIFFRACTION8chain D resid 102:122
9X-RAY DIFFRACTION9chain D resid 131:162
10X-RAY DIFFRACTION10chain E resid 42:72
11X-RAY DIFFRACTION11chain E resid 77:120
12X-RAY DIFFRACTION12chain E resid 132:158
13X-RAY DIFFRACTION13chain F resid 42:124
14X-RAY DIFFRACTION14chain F resid 132:162
15X-RAY DIFFRACTION15chain G resid 40:124
16X-RAY DIFFRACTION16chain G resid 132:157
17X-RAY DIFFRACTION17chain H resid 42:123
18X-RAY DIFFRACTION18chain H resid 133:161

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