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- PDB-6s5d: Square conformation of KtrA R16A mutant ring with bound ATP -

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Basic information

Entry
Database: PDB / ID: 6s5d
TitleSquare conformation of KtrA R16A mutant ring with bound ATP
ComponentsKtr system potassium uptake protein A
KeywordsTRANSPORT PROTEIN / RCK domain / potassium homeostasis / cation channel / magnesium / square conformation octameric ring / atp
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / plasma membrane
Similarity search - Function
Regulator of K+ conductance, C-terminal domain / : / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Regulator of K+ conductance, N-terminal / RCK N-terminal domain profile. / NAD(P)-binding Rossmann-like Domain ...Regulator of K+ conductance, C-terminal domain / : / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Regulator of K+ conductance, N-terminal / RCK N-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 / Ktr system potassium uptake protein A
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.393 Å
AuthorsTeixeira-Duarte, C.M. / Fonseca, F. / Morais-Cabral, J.H.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BIA-BQM/29863/2017 Portugal
Fundacao para a Ciencia e a TecnologiaPOCI-01-0145-FEDER-007274 Portugal
CitationJournal: Elife / Year: 2019
Title: Activation of a nucleotide-dependent RCK domain requires binding of a cation cofactor to a conserved site.
Authors: Teixeira-Duarte, C.M. / Fonseca, F. / Morais Cabral, J.H.
History
DepositionJul 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_asym_id / _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_asym_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_asym_id / _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_asym_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_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,7005
Polymers49,6612
Non-polymers1,0393
Water362
1
A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
hetero molecules

A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
hetero molecules

A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
hetero molecules

A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,80020
Polymers198,6458
Non-polymers4,15512
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-y+2,x,z1
crystal symmetry operation4_575y,-x+2,z1
Unit cell
Length a, b, c (Å)121.572, 121.572, 83.726
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 Ktr system potassium uptake protein A / K(+)-uptake protein KtrA


Mass: 24830.645 Da / Num. of mol.: 2 / Mutation: R16A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: ktrA, yuaA, BSU31090 / Production host: Escherichia coli (E. coli) / References: UniProt: O32080
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.11 Å3/Da / Density % sol: 60.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7.5
Details: 100mM HEPES-NaOH pH 7.5, 2% PEG 6000, 1% 2-Methyl-2,4-pentanediol (MPD)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.39→45.6 Å / Num. obs: 8535 / % possible obs: 99.8 % / Redundancy: 8.9 % / CC1/2: 1 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.017 / Rrim(I) all: 0.05 / Net I/σ(I): 17.1
Reflection shellResolution: 3.39→3.66 Å / Redundancy: 8.5 % / Rmerge(I) obs: 1.829 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1724 / CC1/2: 0.573 / Rpim(I) all: 0.655 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4j90

4j90


Resolution: 3.393→45.598 Å / SU ML: 0.82 / Cross valid method: FREE R-VALUE / σ(F): 1.3 / Phase error: 41.08
RfactorNum. reflection% reflection
Rfree0.279 1632 9.9 %
Rwork0.2383 --
obs0.2423 8535 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.393→45.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3394 0 63 2 3459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033512
X-RAY DIFFRACTIONf_angle_d0.7454761
X-RAY DIFFRACTIONf_dihedral_angle_d13.9351309
X-RAY DIFFRACTIONf_chiral_restr0.029551
X-RAY DIFFRACTIONf_plane_restr0.002598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3931-3.49290.47791170.41931151X-RAY DIFFRACTION93
3.4929-3.60560.4411290.39351239X-RAY DIFFRACTION100
3.6056-3.73440.38431680.36921219X-RAY DIFFRACTION100
3.7344-3.88390.45421340.35781275X-RAY DIFFRACTION100
3.8839-4.06050.38861250.35961232X-RAY DIFFRACTION100
4.0605-4.27440.40171430.30271254X-RAY DIFFRACTION100
4.2744-4.5420.32481150.26321256X-RAY DIFFRACTION100
4.542-4.89230.28591560.26631264X-RAY DIFFRACTION100
4.8923-5.3840.26371330.24931218X-RAY DIFFRACTION100
5.384-6.16140.32151450.26811257X-RAY DIFFRACTION100
6.1614-7.75650.28591360.24131242X-RAY DIFFRACTION100
7.7565-45.60240.21591310.18161253X-RAY DIFFRACTION100

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