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- PDB-2hvk: crystal structure of the KcsA-Fab-TBA complex in high K+ -

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Basic information

Entry
Database: PDB / ID: 2hvk
Titlecrystal structure of the KcsA-Fab-TBA complex in high K+
Components
  • (Antibody Fab ...) x 2
  • Voltage-gated potassium channel
KeywordsMEMBRANE PROTEIN / potassium channel / tetrabutylammonium / K+ / KcsA
Function / homology
Function and homology information


monoatomic ion transmembrane transport / identical protein binding / plasma membrane
Similarity search - Function
Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
NONAN-1-OL / : / (2S)-3-HYDROXY-2-(NONANOYLOXY)PROPYL LAURATE / TETRABUTYLAMMONIUM ION / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhou, Y.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystallographic Study of the Tetrabutylammonium Block to the KcsA K(+) Channel.
Authors: Yohannan, S. / Hu, Y. / Zhou, Y.
History
DepositionJul 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antibody Fab heavy chain
B: Antibody Fab light chain
C: Voltage-gated potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,09412
Polymers60,0593
Non-polymers1,0369
Water3,207178
1
A: Antibody Fab heavy chain
B: Antibody Fab light chain
C: Voltage-gated potassium channel
hetero molecules

A: Antibody Fab heavy chain
B: Antibody Fab light chain
C: Voltage-gated potassium channel
hetero molecules

A: Antibody Fab heavy chain
B: Antibody Fab light chain
C: Voltage-gated potassium channel
hetero molecules

A: Antibody Fab heavy chain
B: Antibody Fab light chain
C: Voltage-gated potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,37848
Polymers240,23412
Non-polymers4,14436
Water21612
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
Buried area38690 Å2
ΔGint-217 kcal/mol
Surface area85990 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)155.874, 155.874, 76.159
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11C-3001-

K

21C-3002-

K

31C-3003-

K

41C-3004-

K

51C-3005-

K

61C-3006-

K

71C-4001-

TBA

DetailsChain A and B assemble to form the biological unit of Fab. / Chain A and B assemble to form the biological unit Fab. / The biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: -X,-Y,Z -Y,X,Z Y,-X,Z 1/2+X,1/2+Y,1/2+Z 1/2-X,1/2-Y,1/2+Z 1/2-Y,1/2+X,1/2+Z 1/2+Y,1/2-X,1/2+Z

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Components

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Protein , 1 types, 1 molecules C

#3: Protein Voltage-gated potassium channel /


Mass: 13211.582 Da / Num. of mol.: 1 / Mutation: P2A, L90C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: kcsA, skc1 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1Blue / References: UniProt: P0A334

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Antibody , 2 types, 2 molecules AB

#1: Antibody Antibody Fab heavy chain


Mass: 23411.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma cell line / Source: (natural) Mus musculus (house mouse)
#2: Antibody Antibody Fab light chain


Mass: 23435.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma cell line / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 5 types, 187 molecules

#4: Chemical ChemComp-F09 / NONAN-1-OL / 1-Nonanol


Mass: 144.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-L2C / (2S)-3-HYDROXY-2-(NONANOYLOXY)PROPYL LAURATE


Mass: 414.619 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O5
#7: Chemical ChemComp-TBA / TETRABUTYLAMMONIUM ION / Tetrabutylammonium


Mass: 242.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H36N
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 3.85 Å3/Da / Density % sol: 68.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 18-25% PEG 400, 50mM Mg(Ac)2, 50mM NaAc (pH5) or Na Cacodylate (pH6) or Hepes (PH 7), pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 7, 2006 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 71937 / Num. obs: 71466 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.058 / Χ2: 1.113 / Net I/σ(I): 16.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.413 / Num. unique all: 6654 / Χ2: 0.927 / % possible all: 92.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K4C

1k4c


Resolution: 1.9→27 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 3610 5 %random
Rwork0.228 ---
all0.228 71937 --
obs0.228 71348 99.2 %-
Solvent computationBsol: 41.126 Å2
Displacement parametersBiso mean: 37.515 Å2
Baniso -1Baniso -2Baniso -3
1--4.738 Å20 Å20 Å2
2---4.738 Å20 Å2
3---9.476 Å2
Refinement stepCycle: LAST / Resolution: 1.9→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4034 0 62 178 4274
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.3
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3single_atoms.param
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION5lipid.par

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