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- PDB-2bob: Potassium channel KcsA-Fab complex in thallium with tetrabutylamm... -

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Basic information

Entry
Database: PDB / ID: 2bob
TitlePotassium channel KcsA-Fab complex in thallium with tetrabutylammonium (TBA)
Components
  • (ANTIBODY FAB FRAGMENT ...) x 2
  • POTASSIUM CHANNEL KCSA
KeywordsIMMUNE SYSTEM/TRANSPORT PROTEIN / COMPLEX (ANTIBODY-ION CHANNEL) / POTASSIUM CHANNEL / ION TRANSPORT / IONIC CHANNEL / PROTEIN- ANTIBODY FAB COMPLEX / IMMUNE SYSTEM-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


action potential / voltage-gated potassium channel activity / voltage-gated potassium channel complex / identical protein binding
Similarity search - Function
Voltage-gated potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / TETRABUTYLAMMONIUM ION / THALLIUM (I) ION / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesSTREPTOMYCES LIVIDANS (bacteria)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsLenaeus, M.J. / Vamvouka, M. / Focia, P.J. / Gross, A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Structural Basis of Tea Blockade in a Model Potassium Channel
Authors: Lenaeus, M.J. / Vamvouka, M. / Focia, P.J. / Gross, A.
History
DepositionApr 9, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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_symmetry
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTIBODY FAB FRAGMENT HEAVY CHAIN
B: ANTIBODY FAB FRAGMENT LIGHT CHAIN
C: POTASSIUM CHANNEL KCSA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5646
Polymers60,0593
Non-polymers5063
Water1,00956
1
A: ANTIBODY FAB FRAGMENT HEAVY CHAIN
B: ANTIBODY FAB FRAGMENT LIGHT CHAIN
C: POTASSIUM CHANNEL KCSA
hetero molecules

A: ANTIBODY FAB FRAGMENT HEAVY CHAIN
B: ANTIBODY FAB FRAGMENT LIGHT CHAIN
C: POTASSIUM CHANNEL KCSA
hetero molecules

A: ANTIBODY FAB FRAGMENT HEAVY CHAIN
B: ANTIBODY FAB FRAGMENT LIGHT CHAIN
C: POTASSIUM CHANNEL KCSA
hetero molecules

A: ANTIBODY FAB FRAGMENT HEAVY CHAIN
B: ANTIBODY FAB FRAGMENT LIGHT CHAIN
C: POTASSIUM CHANNEL KCSA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,25724
Polymers240,23412
Non-polymers2,02312
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_855-y+3,x,z1
crystal symmetry operation4_585y,-x+3,z1
crystal symmetry operation2_885-x+3,-y+3,z1
MethodPQS
Unit cell
Length a, b, c (Å)155.267, 155.267, 75.555
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-201-

TL

21C-202-

CO

31C-203-

TBA

41C-308-

HOH

51C-316-

HOH

DetailsFOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350THIS PDB ENTRY CONSISTS OF ONE CONSTITUENT CHAIN OFA POTASSIUM CHANNEL AND THE LIGHT AND HEAVY CHAINS OF AFAB WHICH IS BOUND TO THE CHANNEL PROTEIN. THE HOMO-TETRAMERIC CHANNEL IS COMPRISED OF FOUR SYMMETRY-RELATEDCOPIES OF THE CHANNEL PROTEIN.

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Components

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Protein , 1 types, 1 molecules C

#3: Protein POTASSIUM CHANNEL KCSA


Mass: 13211.582 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-124 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES LIVIDANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NOVABLUE / References: UniProt: P0A334

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Antibody , 2 types, 2 molecules AB

#1: Antibody ANTIBODY FAB FRAGMENT HEAVY CHAIN


Mass: 23411.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse)
#2: Antibody ANTIBODY FAB FRAGMENT LIGHT CHAIN


Mass: 23435.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse)

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Non-polymers , 4 types, 59 molecules

#4: Chemical ChemComp-TL / THALLIUM (I) ION


Mass: 204.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Tl
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#6: Chemical ChemComp-TBA / TETRABUTYLAMMONIUM ION


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


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN C, LEU 90 CYS
Has protein modificationY

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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: 3.79 Å3/Da / Density % sol: 67.55 %
Crystal growpH: 5.4
Details: PEG 400, MAGNESIUM ACETATE, SODIUM ACETATE, pH 5.40

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.97664
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97664 Å / Relative weight: 1
ReflectionResolution: 2.75→25 Å / Num. obs: 21783 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 3.47 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.9
Reflection shellResolution: 2.75→2.93 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.11 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K4C

1k4c


Resolution: 2.76→25 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.879 / SU B: 11.34 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.561 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: MOLECULAR REPLACEMENT AND INITIAL REFINEMENT WERE PERFORMED IN CNS. A COBALT ION WAS MODELED NEAR HIS C 124 CONSISTENT WITH ANOMALOUS DATA.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1193 5.2 %RANDOM
Rwork0.22 ---
obs0.222 21784 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.21 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å20 Å2
2--1 Å20 Å2
3----2 Å2
Refinement stepCycle: LAST / Resolution: 2.76→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4074 0 19 56 4149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214211
X-RAY DIFFRACTIONr_bond_other_d0.0010.023762
X-RAY DIFFRACTIONr_angle_refined_deg1.211.9345742
X-RAY DIFFRACTIONr_angle_other_deg0.7838763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3975531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44723.478161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.53915647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0391522
X-RAY DIFFRACTIONr_chiral_restr0.0680.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024669
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02850
X-RAY DIFFRACTIONr_nbd_refined0.1970.2824
X-RAY DIFFRACTIONr_nbd_other0.190.23749
X-RAY DIFFRACTIONr_nbtor_refined0.180.22038
X-RAY DIFFRACTIONr_nbtor_other0.0850.22409
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2141
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.232
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1580.2112
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2411.53383
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.25424304
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.17631864
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.2944.51438
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.76→2.83 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.385 87
Rwork0.34 1548

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