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- PDB-3pjz: Crystal Structure of the Potassium Transporter TrkH from Vibrio p... -

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Basic information

Entry
Database: PDB / ID: 3pjz
TitleCrystal Structure of the Potassium Transporter TrkH from Vibrio parahaemolyticus
ComponentsPotassium uptake protein TrkH
KeywordsTRANSPORT PROTEIN / structural genomics / PSI-2 / Protein Structure Initiative / New York Consortium on Membrane Protein Structure / NYCOMPS / potassium transport / membrane
Function / homology
Function and homology information


potassium:chloride symporter activity / potassium ion binding / potassium channel activity / potassium ion transmembrane transport / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
TrkH potassium transport family / Cation transporter / Cation transport protein
Similarity search - Domain/homology
: / Trk system potassium uptake protein TrkH
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.506 Å
AuthorsCao, Y. / Jin, X. / Huang, H. / Levin, E.J. / Zhou, M. / New York Consortium on Membrane Protein Structure (NYCOMPS)
CitationJournal: Nature / Year: 2011
Title: Crystal structure of a potassium ion transporter, TrkH.
Authors: Cao, Y. / Jin, X. / Huang, H. / Derebe, M.G. / Levin, E.J. / Kabaleeswaran, V. / Pan, Y. / Punta, M. / Love, J. / Weng, J. / Quick, M. / Ye, S. / Kloss, B. / Bruni, R. / Martinez-Hackert, E. ...Authors: Cao, Y. / Jin, X. / Huang, H. / Derebe, M.G. / Levin, E.J. / Kabaleeswaran, V. / Pan, Y. / Punta, M. / Love, J. / Weng, J. / Quick, M. / Ye, S. / Kloss, B. / Bruni, R. / Martinez-Hackert, E. / Hendrickson, W.A. / Rost, B. / Javitch, J.A. / Rajashankar, K.R. / Jiang, Y. / Zhou, M.
History
DepositionNov 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium uptake protein TrkH
B: Potassium uptake protein TrkH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,3034
Polymers108,2252
Non-polymers782
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-35 kcal/mol
Surface area36770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.489, 97.406, 195.653
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 1:157 or resseq 174:484 )A1 - 157
121chain A and (resseq 1:157 or resseq 174:484 )A174 - 484
211chain B and (resseq 1:157 or resseq 174:484 )B1 - 157
221chain B and (resseq 1:157 or resseq 174:484 )B174 - 484

NCS oper: (Code: given
Matrix: (-0.943618, -0.329577, -0.031037), (-0.325107, 0.904972, 0.274465), (-0.062369, 0.26908, -0.961096)
Vector: -21.8923, 10.7965, -102.427002)

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Components

#1: Protein Potassium uptake protein TrkH


Mass: 54112.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: VP0032 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q87TN7
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K

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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: 4.03 Å3/Da / Density % sol: 69.46 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 5.3
Details: 35% PEG400, 200 mM calcium acetate, 100 mM sodium acetate, pH 5.3, microbatch, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A10.9791
SYNCHROTRONAPS 24-ID-C20.97949
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDAug 16, 2008
ADSC QUANTUM 3152CCDFeb 18, 2008
Radiation
IDMonochromatorProtocolScattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.979491
ReflectionResolution: 3.5→50 Å / Num. obs: 20487 / % possible obs: 89.5 % / Biso Wilson estimate: 63.53 Å2 / Rmerge(I) obs: 0.119 / Χ2: 1.079 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
3.5-3.630.24915950.94171.1
3.63-3.770.24718190.92581.4
3.77-3.940.22919740.9788
3.94-4.150.18420261.15888.9
4.15-4.410.17820411.0990
4.41-4.750.16320391.39191
4.75-5.230.14920891.33691.7
5.23-5.980.14922130.88495.7
5.98-7.530.11823270.90899.6
7.53-500.09123641.07595.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
DMphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.506→14.995 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7694 / SU ML: 0.54 / σ(F): 1.34 / Phase error: 29.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2986 996 5.22 %RANDOM
Rwork0.2492 ---
obs0.2518 19088 85.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 13.801 Å2 / ksol: 0.229 e/Å3
Displacement parametersBiso max: 195.3 Å2 / Biso mean: 60.4207 Å2 / Biso min: 13.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.3761 Å20 Å20 Å2
2--0.7009 Å2-0 Å2
3----1.077 Å2
Refinement stepCycle: LAST / Resolution: 3.506→14.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7240 0 2 0 7242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0197466
X-RAY DIFFRACTIONf_angle_d1.20810150
X-RAY DIFFRACTIONf_chiral_restr0.0791194
X-RAY DIFFRACTIONf_plane_restr0.0051238
X-RAY DIFFRACTIONf_dihedral_angle_d16.7942502
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3621X-RAY DIFFRACTIONPOSITIONAL0.037
12B3621X-RAY DIFFRACTIONPOSITIONAL0.037
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.506-3.68820.4019780.3031338141646
3.6882-3.91540.36181440.30292560270486
3.9154-4.21150.32221460.27142643278989
4.2115-4.6240.3071430.23442704284790
4.624-5.26760.26221640.21192754291892
5.2676-6.54350.34511670.29012953312097
6.5435-14.99520.2341540.21433140329499

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