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- PDB-1vct: Crystal structure of putative potassium channel related protein f... -

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Basic information

Entry
Database: PDB / ID: 1vct
TitleCrystal structure of putative potassium channel related protein from Pyrococcus horikoshii
Componentshypothetical protein PH0236
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / helix rich / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / metal ion binding
Similarity search - Function
PhoU domain / PhoU domain / Phosphate transport system protein phou homolog 2; domain 2 / PhoU-like domain superfamily / Regulator of K+ conductance, C-terminal domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...PhoU domain / PhoU domain / Phosphate transport system protein phou homolog 2; domain 2 / PhoU-like domain superfamily / Regulator of K+ conductance, C-terminal domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RCK C-terminal domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.85 Å
AuthorsInagaki, E. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of putative potassium channel related protein from Pyrococcus horikoshii
Authors: Inagaki, E. / Tahirov, T.H.
History
DepositionMar 12, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: hypothetical protein PH0236
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1926
Polymers23,0131
Non-polymers1795
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: hypothetical protein PH0236
hetero molecules

A: hypothetical protein PH0236
hetero molecules

A: hypothetical protein PH0236
hetero molecules

A: hypothetical protein PH0236
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,76624
Polymers92,0504
Non-polymers71620
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area14710 Å2
ΔGint-248 kcal/mol
Surface area32290 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.748, 70.748, 98.024
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-574-

HOH

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Components

#1: Protein hypothetical protein PH0236 / putative potassium channel related protein


Mass: 23012.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O57975
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 4.7
Details: sodium chloride, acetate, pH 4.7, Micro batch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Sep 21, 2003 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→35 Å / Num. all: 21771 / Num. obs: 21771 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 4.2 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.045
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.306 / Num. unique all: 2129 / % possible all: 99

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.85→33.27 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2001675.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1041 4.9 %RANDOM
Rwork0.211 ---
all0.213 21771 --
obs0.211 21398 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.7457 Å2 / ksol: 0.371326 e/Å3
Displacement parametersBiso mean: 32.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.37 Å20 Å20 Å2
2--3.37 Å20 Å2
3----6.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.85→33.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 8 182 1693
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.8
X-RAY DIFFRACTIONc_improper_angle_d0.61
X-RAY DIFFRACTIONc_mcbond_it3.121.5
X-RAY DIFFRACTIONc_mcangle_it3.972
X-RAY DIFFRACTIONc_scbond_it4.832
X-RAY DIFFRACTIONc_scangle_it6.782.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.348 178 5.2 %
Rwork0.291 3232 -
obs-2129 95.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4EG.PARAMEG.TOP

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