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- PDB-1qrq: STRUCTURE OF A VOLTAGE-DEPENDENT K+ CHANNEL BETA SUBUNIT -

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Basic information

Entry
Database: PDB / ID: 1qrq
TitleSTRUCTURE OF A VOLTAGE-DEPENDENT K+ CHANNEL BETA SUBUNIT
ComponentsPROTEIN (KV BETA2 PROTEIN)
KeywordsMETAL TRANSPORT / TIM BARREL / ALDO-KETO REDUCTASE / POTASSIUM CHANNEL SUBUNIT / VOLTAGE-DEPENDENT POTASSIUM CHANNEL
Function / homology
Function and homology information


pinceau fiber / regulation of action potential / Voltage gated Potassium channels / potassium channel complex / NADPH oxidation / axon initial segment / regulation of protein localization to cell surface / aldo-keto reductase (NADPH) activity / juxtaparanode region of axon / regulation of potassium ion transmembrane transport ...pinceau fiber / regulation of action potential / Voltage gated Potassium channels / potassium channel complex / NADPH oxidation / axon initial segment / regulation of protein localization to cell surface / aldo-keto reductase (NADPH) activity / juxtaparanode region of axon / regulation of potassium ion transmembrane transport / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / myoblast differentiation / Neutrophil degranulation / neuromuscular process / voltage-gated potassium channel activity / potassium channel regulator activity / hematopoietic progenitor cell differentiation / voltage-gated potassium channel complex / axon terminus / extrinsic component of cytoplasmic side of plasma membrane / postsynaptic density membrane / cytoplasmic side of plasma membrane / transmembrane transporter binding / postsynaptic density / cytoskeleton / neuron projection / axon / glutamatergic synapse / protein-containing complex binding / membrane / cytosol
Similarity search - Function
Potassium channel, voltage-dependent, beta subunit, KCNAB2 / Potassium channel, voltage-dependent, beta subunit, KCNAB / Potassium channel, voltage-dependent, beta subunit, KCNAB-related / NADP-dependent oxidoreductase domain / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Voltage-gated potassium channel subunit beta-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsGulbis, J.M. / Mann, S. / MacKinnon, R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Structure of a voltage-dependent K+ channel beta subunit.
Authors: Gulbis, J.M. / Mann, S. / MacKinnon, R.
History
DepositionJun 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (KV BETA2 PROTEIN)
B: PROTEIN (KV BETA2 PROTEIN)
C: PROTEIN (KV BETA2 PROTEIN)
D: PROTEIN (KV BETA2 PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,3978
Polymers145,4164
Non-polymers2,9824
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12470 Å2
ΔGint-14 kcal/mol
Surface area45850 Å2
MethodPISA
2
A: PROTEIN (KV BETA2 PROTEIN)
B: PROTEIN (KV BETA2 PROTEIN)
C: PROTEIN (KV BETA2 PROTEIN)
D: PROTEIN (KV BETA2 PROTEIN)
hetero molecules

A: PROTEIN (KV BETA2 PROTEIN)
B: PROTEIN (KV BETA2 PROTEIN)
C: PROTEIN (KV BETA2 PROTEIN)
D: PROTEIN (KV BETA2 PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,79516
Polymers290,8318
Non-polymers5,9638
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area29700 Å2
ΔGint-60 kcal/mol
Surface area86930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.746, 114.346, 93.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
PROTEIN (KV BETA2 PROTEIN)


Mass: 36353.914 Da / Num. of mol.: 4 / Fragment: BETA SUBUNIT CORE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: unidentified baculovirus / References: UniProt: P62483
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
127 mg/mlprotein1drop
24.5 mMn-octyl-beta-D-glucopyranoside1drop
3100 mMHEPES1reservoirpH7.5
426 %(w/v)mPEG20001reservoir
5400 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 19, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 40961 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 19.4 % / Biso Wilson estimate: 75.2 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 15.8
Reflection shellResolution: 2.8→2.88 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.394 / % possible all: 98.1
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 40 Å / Observed criterion σ(I): -3 / Redundancy: 19.4 % / Num. measured all: 814316 / Biso Wilson estimate: 75.2 Å2
Reflection shell
*PLUS
% possible obs: 98.1 % / Redundancy: 4.5 %

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
SCALEPACKdata scaling
RefinementResolution: 2.8→40 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: MINIMISATION AND SIMULATED ANNEALING PROCEDURES USING A MAXIMUM-LIKELIHOOD TARGET
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2050 -THIN CONCENTRIC SHELLS
Rwork0.236 ---
obs0.236 40911 97.7 %-
Refinement stepCycle: LAST / Resolution: 2.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10004 0 192 152 10348
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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