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- PDB-6i8v: KtrC with ATP bound -

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Basic information

Entry
Database: PDB / ID: 6i8v
TitleKtrC with ATP bound
ComponentsKtr system potassium uptake protein C
KeywordsMETAL TRANSPORT / Ion transport
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / plasma membrane
Similarity search - Function
Regulator of K+ conductance, C-terminal domain / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Plaits ...Regulator of K+ conductance, C-terminal domain / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 1,4-BUTANEDIOL / Ktr system potassium uptake protein C
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.991 Å
AuthorsRocha, R. / Morais-Cabral, J.H.
Funding support Portugal, 4items
OrganizationGrant numberCountry
FLAD Proj. 34/2017 and 34/2018 Portugal
FEDER POCI-01-0145-FEDER-029863 Portugal
Compete2020 Portugal
FCT PTDC/BIA-BQM/29863/2017 Portugal
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Characterization of the molecular properties of KtrC, a second RCK domain that regulates a Ktr channel in Bacillus subtilis.
Authors: Rocha, R. / Teixeira-Duarte, C.M. / Jorge, J.M.P. / Morais-Cabral, J.H.
History
DepositionNov 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ktr system potassium uptake protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1516
Polymers24,3831
Non-polymers7685
Water1,38777
1
A: Ktr system potassium uptake protein C
hetero molecules

A: Ktr system potassium uptake protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,30112
Polymers48,7662
Non-polymers1,53510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area6840 Å2
ΔGint-32 kcal/mol
Surface area19570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.155, 84.155, 83.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-302-

CA

21A-303-

CA

31A-401-

HOH

41A-423-

HOH

51A-468-

HOH

61A-474-

HOH

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Components

#1: Protein Ktr system potassium uptake protein C / K(+)-uptake protein KtrC / ORF4


Mass: 24383.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: ktrC, ykqB, ylxV, yzaC, BSU14510 / Production host: Escherichia coli (E. coli) / References: UniProt: P39760
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL / 1,4-Butanediol


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 1,4-butanediol, NaCl, HEPES-Na (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.99→48.53 Å / Num. obs: 21207 / % possible obs: 99.7 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 40.9
Reflection shellResolution: 1.99→2.04 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J90

4j90


Resolution: 1.991→48.528 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.8 / Phase error: 19.67
RfactorNum. reflection% reflection
Rfree0.2108 2140 5.45 %
Rwork0.1945 --
obs0.1954 21174 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.991→48.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 45 77 1789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081733
X-RAY DIFFRACTIONf_angle_d1.1582346
X-RAY DIFFRACTIONf_dihedral_angle_d16.605647
X-RAY DIFFRACTIONf_chiral_restr0.07286
X-RAY DIFFRACTIONf_plane_restr0.004292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9914-2.03770.20361440.22032352X-RAY DIFFRACTION95
2.0377-2.08860.24951490.21192480X-RAY DIFFRACTION100
2.0886-2.14510.25061520.22392477X-RAY DIFFRACTION100
2.1451-2.20820.21741600.20282482X-RAY DIFFRACTION100
2.2082-2.27950.23151470.20342465X-RAY DIFFRACTION100
2.2795-2.3610.22781630.20232444X-RAY DIFFRACTION100
2.361-2.45550.21871620.19572450X-RAY DIFFRACTION100
2.4555-2.56720.2466960.20952545X-RAY DIFFRACTION100
2.5672-2.70260.23251130.19852530X-RAY DIFFRACTION100
2.7026-2.87190.22541740.19392423X-RAY DIFFRACTION100
2.8719-3.09360.2268960.21452556X-RAY DIFFRACTION100
3.0936-3.40480.22151880.21272449X-RAY DIFFRACTION100
3.4048-3.89740.23771250.18892477X-RAY DIFFRACTION100
3.8974-4.90950.15071230.17042515X-RAY DIFFRACTION100
4.9095-48.54240.18351480.17952488X-RAY DIFFRACTION100
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)
12.4751-2.014-1.08995.10431.13115.21430.13050.12610.1373-0.1631-0.1843-0.0519-0.24130.10570.00570.177-0.01820.01180.23030.02250.1839-10.4101-21.058-12.8202
22.3721-1.33120.19074.9356-0.56446.7722-0.0559-0.1175-0.00030.25940.17230.1806-0.0418-0.1562-0.09560.1199-0.01840.03820.1615-0.00640.138-17.4348-22.61590.4914
30.35331.35880.20945.44920.55840.967-0.10440.0963-0.12320.34720.2338-0.05870.0746-0.0374-0.13180.2033-0.0247-0.01610.2507-0.00150.20154.058-39.62726.815
42.59410.1148-4.15957.2381-0.66286.6672-0.0613-0.1962-0.02130.3312-0.0107-0.72680.43540.51110.04660.32810.0771-0.09860.2930.01670.274212.0176-58.9149.1728
53.2477-0.8798-0.48623.90630.91114.34650.0724-0.16120.10320.0585-0.0037-0.3163-0.04960.195-0.07130.16150.02930.01060.15910.02850.23719.4082-53.18253.975
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 55 )
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 119 )
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 153 )
4X-RAY DIFFRACTION4chain 'A' and (resid 154 through 174 )
5X-RAY DIFFRACTION5chain 'A' and (resid 175 through 218 )

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