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- PDB-4hp4: Crystal structure of PAS domain from the fruit-fly ELK potassium ... -

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Basic information

Entry
Database: PDB / ID: 4hp4
TitleCrystal structure of PAS domain from the fruit-fly ELK potassium channel
ComponentsEag-like K[+] channel
KeywordsTRANSPORT PROTEIN / Potassium channel domain / PAS domain
Function / homology
Function and homology information


Voltage gated Potassium channels / voltage-gated monoatomic cation channel activity / voltage-gated potassium channel activity / voltage-gated potassium channel complex / potassium ion transmembrane transport / regulation of membrane potential / potassium ion transport / plasma membrane
Similarity search - Function
Potassium channel, voltage-dependent, ELK / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Cyclic nucleotide-monophosphate binding domain ...Potassium channel, voltage-dependent, ELK / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Cyclic nucleotide-monophosphate binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Beta-Lactamase / PAS repeat profile. / PAS domain / RmlC-like jelly roll fold / PAS domain superfamily / Ion transport domain / Ion transport protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Eag-like K[+] channel, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsAdaixo, R. / Morais-Cabral, J.H.
CitationJournal: Plos One / Year: 2013
Title: Structural properties of PAS domains from the KCNH potassium channels
Authors: Adaixo, R. / Harley, C.A. / Castro-Rodrigues, A.F. / Morais-Cabral, J.H.
History
DepositionOct 23, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 8, 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eag-like K[+] channel
B: Eag-like K[+] channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5235
Polymers30,2392
Non-polymers2843
Water3,783210
1
A: Eag-like K[+] channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3083
Polymers15,1191
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Eag-like K[+] channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2152
Polymers15,1191
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.306, 150.306, 150.306
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11B-396-

HOH

21B-412-

HOH

31B-413-

HOH

DetailsThe biological unit is most likely a monomer. There are 2 biological units in the asymmetric unit

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Components

#1: Protein Eag-like K[+] channel


Mass: 15119.406 Da / Num. of mol.: 2 / Fragment: PAS domain of KCNH channel, UNP residues 11-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dmel_CG5076, elk / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)
References: UniProt: A1ZB14, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 4.81 Å3/Da / Density % sol: 74.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG5000, 0.35M ammonium sulfate, 0.1M MES, pH 6.5, vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→53.149 Å / Num. all: 39431 / Num. obs: 39431 / % possible obs: 99.5 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 1.4 / Redundancy: 14.7 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 19.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2-2.1170.551.40.55199.4
2.11-2.247.30.4081.60.408199.8
2.24-2.397.70.2512.90.251199.9
2.39-2.5816.10.2762.60.2761100
2.58-2.83180.1853.70.1851100
2.83-3.1619.30.1240.12199.9
3.16-3.6521.20.07590.075199.5
3.65-4.4723.30.05710.80.057198.9
4.47-6.3223.20.0511.40.05197.7
6.32-61.36221.30.0518.40.051195.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
PHENIX1.8.1_1168refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BYW

1byw


Resolution: 2→53.141 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.16 / SU R Cruickshank DPI: 0.1197 / σ(F): 1.35 / Phase error: 16.66 / Stereochemistry target values: ML
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflection
Rfree0.1912 1999 5.08 %
Rwork0.1727 --
obs0.1736 39372 99.16 %
all-39360 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.219 Å2
Refinement stepCycle: LAST / Resolution: 2→53.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 16 210 2268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032121
X-RAY DIFFRACTIONf_angle_d0.7422872
X-RAY DIFFRACTIONf_dihedral_angle_d12.873788
X-RAY DIFFRACTIONf_chiral_restr0.046302
X-RAY DIFFRACTIONf_plane_restr0.003360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.05040.2591580.2335260599
2.0504-2.10580.24011450.2106260299
2.1058-2.16780.24631320.2055264699
2.1678-2.23780.24981620.20742619100
2.2378-2.31770.22711440.18082632100
2.3177-2.41050.20041370.17662664100
2.4105-2.52020.16531410.17062656100
2.5202-2.65310.1671540.16822649100
2.6531-2.81930.16121380.16682674100
2.8193-3.0370.17871350.16882702100
3.037-3.34260.19041250.16942699100
3.3426-3.82610.18121390.1545270799
3.8261-4.820.15341300.1412272698
4.82-53.15990.21151590.1943279295
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)
12.5441-0.8580.26437.58493.37444.88280.0712-0.06730.16280.28710.1976-0.05630.03270.0355-0.26710.27530.01350.04680.08950.07190.2310.2823-0.683538.4973
22.81970.074-0.04524.6291-0.55662.0984-0.0205-0.4114-0.03960.93260.44171.0438-0.0754-0.5387-0.38180.40930.06990.27930.31640.15260.5239-11.9542-2.771147.415
32.33222.01191.4456.3397-0.80314.3576-0.0212-1.14210.05761.27550.1634-0.09970.13830.1518-0.01370.36550.02030.14380.1150.1210.4518-0.3665-6.174346.9817
45.7531.68891.76733.2254-0.53684.83750.15220.1006-0.57760.31890.18650.47250.5192-0.2063-0.44390.3530.05770.06850.19540.10820.4657-6.7736-8.356543.1891
58.4534-0.2581-0.27164.4193-1.17473.4145-0.1437-0.83140.30171.08040.35010.23-0.5709-0.0355-0.15780.46230.05560.03740.15730.01710.2516-0.148715.072443.3967
61.3473-1.128-0.60591.76731.03592.844-0.06910.02790.24080.14180.0851-0.0145-0.3241-0.051-0.05530.2052-0.00570.01820.11090.02310.22672.613320.621328.438
75.6065-1.9983-3.7113.32120.07125.87910.0190.10730.1422-0.09010.03710.2503-0.0644-0.1773-0.01960.1428-0.0211-0.01180.08590.01080.179-2.427212.551922.3329
84.0324-0.433-2.18333.91541.04444.0052-0.3063-0.3285-0.78110.484-0.12781.19780.182-0.17810.40040.2054-0.00430.10810.18270.02790.3029-5.160212.571133.0291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 12 through 45 )
2X-RAY DIFFRACTION2chain A and (resid 46 through 104 )
3X-RAY DIFFRACTION3chain A and (resid 105 through 121 )
4X-RAY DIFFRACTION4chain A and (resid 122 through 134 )
5X-RAY DIFFRACTION5chain B and (resid 11 through 28 )
6X-RAY DIFFRACTION6chain B and (resid 29 through 74 )
7X-RAY DIFFRACTION7chain B and (resid 76 through 115 )
8X-RAY DIFFRACTION8chain B and (resid 117 through 135 )

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