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- PDB-5vkh: Closed conformation of KcsA Y82A-F103A mutant -

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Basic information

Entry
Database: PDB / ID: 5vkh
TitleClosed conformation of KcsA Y82A-F103A mutant
Components
  • Antibody Heavy Chain
  • Antibody Light Chain
  • pH-gated potassium channel KcsA
KeywordsIMMUNE SYSTEM/TRANSPORT PROTEIN / KcsA / closed / Y82A-F103A / potassium channel / IMMUNE SYSTEM-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


voltage-gated potassium channel activity / 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
Chem-1EM / NONAN-1-OL / : / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsCuello, L.G. / Perozo, E. / Cortes, D.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM087519 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1RO1GM097159-01A1 United States
Welch FoundationBI-1757 United States
CitationJournal: Elife / Year: 2017
Title: The gating cycle of a K+ channel at atomic resolution.
Authors: Cuello, L.G. / Cortes, D.M. / Perozo, E.
History
DepositionApr 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antibody Heavy Chain
B: Antibody Light Chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,47911
Polymers57,6583
Non-polymers8228
Water5,459303
1
A: Antibody Heavy Chain
B: Antibody Light Chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Antibody Heavy Chain
B: Antibody Light Chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Antibody Heavy Chain
B: Antibody Light Chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Antibody Heavy Chain
B: Antibody Light Chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,91644
Polymers230,63012
Non-polymers3,28632
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 area36390 Å2
ΔGint-214 kcal/mol
Surface area86600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.737, 155.737, 76.225
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-1002-

K

21C-1003-

K

31C-1004-

K

41C-1005-

K

51C-1006-

K

61C-1007-

K

71C-1120-

HOH

81C-1135-

HOH

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Components

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Protein , 1 types, 1 molecules C

#3: Protein pH-gated potassium channel KcsA / Streptomyces lividans K+ channel / SKC1


Mass: 10810.544 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: kcsA, skc1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A334

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Antibody , 2 types, 2 molecules AB

#1: Antibody Antibody 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 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, 311 molecules

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


Mass: 144.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O
#5: Chemical ChemComp-1EM / (1S)-2-HYDROXY-1-[(NONANOYLOXY)METHYL]ETHYL MYRISTATE


Mass: 442.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H50O5
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.01 Å3/Da / Density % sol: 69.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG400 , 50 mM magnesium acetate, 50 mM sodium acetate
PH range: 5.4-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→42.91 Å / Num. obs: 42773 / % possible obs: 98.43 % / Redundancy: 4.7 % / Net I/σ(I): 5.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→42.907 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.74
RfactorNum. reflection% reflection
Rfree0.2031 1532 3.58 %
Rwork0.1742 --
obs0.1752 42766 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→42.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4036 0 47 303 4386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014177
X-RAY DIFFRACTIONf_angle_d1.0545694
X-RAY DIFFRACTIONf_dihedral_angle_d4.7572460
X-RAY DIFFRACTIONf_chiral_restr0.058649
X-RAY DIFFRACTIONf_plane_restr0.006718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.32260.23641330.21763462X-RAY DIFFRACTION91
2.3226-2.40560.24331370.20643695X-RAY DIFFRACTION98
2.4056-2.50190.25341370.18753726X-RAY DIFFRACTION99
2.5019-2.61580.22511410.18133762X-RAY DIFFRACTION99
2.6158-2.75370.20151390.17563754X-RAY DIFFRACTION99
2.7537-2.92620.23821360.17763772X-RAY DIFFRACTION99
2.9262-3.1520.19831430.17413807X-RAY DIFFRACTION100
3.152-3.46910.18971380.1763769X-RAY DIFFRACTION99
3.4691-3.97080.18591420.16333789X-RAY DIFFRACTION100
3.9708-5.00160.20311430.15123811X-RAY DIFFRACTION100
5.0016-42.91470.18041430.18213887X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 135.9144 Å / Origin y: 128.0215 Å / Origin z: -8.8606 Å
111213212223313233
T0.274 Å2-0.0945 Å2-0.028 Å2-0.2813 Å20.0198 Å2--0.2611 Å2
L0.9404 °20.6091 °2-1.134 °2-0.8306 °2-0.8752 °2--1.8589 °2
S-0.0385 Å °-0.0999 Å °-0.1835 Å °0.0365 Å °-0.0178 Å °0.0208 Å °0.2744 Å °-0.1784 Å °0.0568 Å °
Refinement TLS groupSelection details: all

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