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- PDB-1lsu: KTN Bsu222 Crystal Structure in Complex with NADH -

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Basic information

Entry
Database: PDB / ID: 1lsu
TitleKTN Bsu222 Crystal Structure in Complex with NADH
ComponentsConserved hypothetical protein yuaA
KeywordsTRANSPORT PROTEIN / KTN domain / NAD / RCK domain / Potassium Transport / Potassium Channel / KtrA / Rossmann Fold
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, 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 / NAD(P)-binding domain superfamily / Rossmann fold ...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 / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Ktr system potassium uptake protein A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MIR / Resolution: 2.85 Å
AuthorsRoosild, T.P. / Miller, S. / Booth, I.R. / Choe, S.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: A mechanism of regulating transmembrane potassium flux through a ligand-mediated conformational switch.
Authors: Roosild, T.P. / Miller, S. / Booth, I.R. / Choe, S.
History
DepositionMay 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE Authors state the sequence present in the B. subtilis lab strain from which they cloned ...SEQUENCE Authors state the sequence present in the B. subtilis lab strain from which they cloned may be a strain type polymorphism, or an error in the database itself.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved hypothetical protein yuaA
B: Conserved hypothetical protein yuaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7824
Polymers32,4512
Non-polymers1,3312
Water0
1
A: Conserved hypothetical protein yuaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8912
Polymers16,2261
Non-polymers6651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Conserved hypothetical protein yuaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8912
Polymers16,2261
Non-polymers6651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.600, 126.600, 98.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
DetailsThe KTN biological unit consists of two helix-swapped monomers. The asymmetric unit contains one biological unit formed by chains A & B

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Components

#1: Protein Conserved hypothetical protein yuaA


Mass: 16225.580 Da / Num. of mol.: 2 / Fragment: KTN Domain, Residues 1-143 / Mutation: C22V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: KtrA / Plasmid: pHis8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: O32080
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Ammonium Sulfate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16-8 mg/mlprotein1drop
210 mMTris-HCl1droppH8.0
31 mMdithiothreitol1drop
41 mMNAD(H)1drop
51.2 Mammonium sulfate1reservoir
6100 mMMES1reservoirpH6.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-211.071, 0.9794, 0.9252
SYNCHROTRONSSRL BL9-220.9198, 0.8611, 0.9196
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 4, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DOUBLE CRYSTALMADMx-ray1
2DOUBLE CRYSTALMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.0711
20.97941
30.92521
40.91981
50.86111
60.91961
ReflectionResolution: 2.85→30 Å / Num. all: 9667 / Num. obs: 9635 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 71.1 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.4
Reflection shellResolution: 2.85→2.95 Å / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 3.5 / Num. unique all: 947 / % possible all: 100
Reflection
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
Rmerge(I) obs: 0.343

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD, MIR / Resolution: 2.85→30 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1669970.48 / Data cutoff high rms absF: 1669970.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.329 503 5.2 %RANDOM
Rwork0.279 ---
all-9596 --
obs-9590 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.8566 Å2 / ksol: 0.354957 e/Å3
Displacement parametersBiso mean: 70.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.31 Å20 Å20 Å2
2--5.31 Å20 Å2
3----10.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2096 0 88 0 2184
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.541.5
X-RAY DIFFRACTIONc_mcangle_it2.752
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.352.5
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.467 90 5.8 %
Rwork0.43 1475 -
obs--98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3NAD_XPLOR_PAR.TXT
X-RAY DIFFRACTION4WATER_REP.PARAM
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.329 / Rfactor Rwork: 0.279
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0109
X-RAY DIFFRACTIONc_angle_deg1.594
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92
LS refinement shell
*PLUS
Rfactor Rfree: 0.467 / Rfactor Rwork: 0.43

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