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- PDB-4h33: Crystal structure of a voltage-gated K+ channel pore module in a ... -

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Basic information

Entry
Database: PDB / ID: 4h33
TitleCrystal structure of a voltage-gated K+ channel pore module in a closed state in lipid membranes, tetragonal crystal form
ComponentsLmo2059 protein
KeywordsMEMBRANE PROTEIN / BILAYERS / KVLM / LIPIDIC CUBIC PHASE (LCP) / PORE MODULE / ION CHANNEL
Function / homology
Function and homology information


action potential / voltage-gated potassium channel activity / voltage-gated potassium channel complex / potassium ion transmembrane transport / membrane
Similarity search - Function
Voltage-gated potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Voltage-dependent channel domain superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Lmo2059 protein
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSantos, J.S. / Asmar-Rovira, G.A. / Han, G.W. / Liu, W. / Syeda, R. / Cherezov, V. / Baker, K.A. / Stevens, R.C. / Montal, M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal Structure of a Voltage-gated K+ Channel Pore Module in a Closed State in Lipid Membranes.
Authors: Santos, J.S. / Asmar-Rovira, G.A. / Han, G.W. / Liu, W. / Syeda, R. / Cherezov, V. / Baker, K.A. / Stevens, R.C. / Montal, M.
History
DepositionSep 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Lmo2059 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1058
Polymers15,5611
Non-polymers1,5437
Water00
1
A: Lmo2059 protein
hetero molecules

A: Lmo2059 protein
hetero molecules

A: Lmo2059 protein
hetero molecules

A: Lmo2059 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,42032
Polymers62,2464
Non-polymers6,17428
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area8040 Å2
ΔGint-76 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.370, 53.370, 108.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-201-

K

21A-202-

K

31A-203-

K

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Components

#1: Protein Lmo2059 protein


Mass: 15561.433 Da / Num. of mol.: 1
Fragment: KVLM PORE MODULE, TRUNCATED C-TERMINUS (UNP RESIDUES 98-233)
Mutation: A98C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: ATCC BAA-679 / EGD-e / Gene: lmo2059 / Plasmid: pQE-70 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q8Y5K1
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H40O4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 32

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 293 K / pH: 7
Details: 26-30% (v/v) PEG-MME-550, 0.5 M to 0.6 M ammonium sulfate, and 50 mM ADA, Lipidic Cubic Phase (LCP) , pH 7.0, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 2994 / % possible obs: 94.4 % / Redundancy: 7.1 % / Biso Wilson estimate: 80.28 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 18.6
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.45 / % possible all: 75

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EFF, 2ATK, 2A79 and 1ORQ

3eff

2atk

2a79

1orq


Resolution: 3.1→16.4 Å / Cor.coef. Fo:Fc: 0.8555 / Cor.coef. Fo:Fc free: 0.7825 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.305 369 13.8 %RANDOM
Rwork0.2814 ---
obs0.2845 2674 85.11 %-
Displacement parametersBiso mean: 114.2 Å2
Baniso -1Baniso -2Baniso -3
1--6.6701 Å20 Å20 Å2
2---6.6701 Å20 Å2
3---13.3403 Å2
Refine analyzeLuzzati coordinate error obs: 1.248 Å
Refinement stepCycle: LAST / Resolution: 3.1→16.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms673 0 60 0 733
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01744HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.011006HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d332SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes8HARMONIC2
X-RAY DIFFRACTIONt_gen_planes101HARMONIC5
X-RAY DIFFRACTIONt_it744HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 3.1→3.47 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2978 58 12.98 %
Rwork0.2488 389 -
all0.2551 447 -
obs--85.11 %
Refinement TLS params.Method: refined / Origin x: 15.3567 Å / Origin y: -5.4997 Å / Origin z: 34.4487 Å
111213212223313233
T-0.6079 Å20.0224 Å2-0.116 Å2--0.5678 Å20.0132 Å2--0.6079 Å2
L5.0033 °2-0.0692 °2-1.6422 °2-2.9151 °20.4075 °2--1.6606 °2
S0.0599 Å °0.822 Å °-0.1525 Å °-0.7685 Å °-0.0491 Å °0.2122 Å °0.0875 Å °-0.4165 Å °-0.0108 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|30 - A|120 A|3001 - A|3007 }A30 - 120
2X-RAY DIFFRACTION1{ A|30 - A|120 A|3001 - A|3007 }A3001 - 3007

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