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- PDB-4lbe: Structure of KcsA with R122A mutation -

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Basic information

Entry
Database: PDB / ID: 4lbe
TitleStructure of KcsA with R122A mutation
Components
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
  • pH-gated potassium channel KcsA
KeywordsTRANSPORT PROTEIN / membrane protein / Metal Transport / pH-gated potassium channel
Function / homology
Function and homology information


delayed rectifier potassium channel activity / voltage-gated potassium channel complex / identical protein binding
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
DIACYL GLYCEROL / NONAN-1-OL / : / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesMus musculus (house mouse)
Streptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.751 Å
AuthorsNimigean, C.M. / Posson, D.J. / McCoy, J.M.
CitationJournal: J.Gen.Physiol. / Year: 2013
Title: Molecular interactions involved in proton-dependent gating in KcsA potassium channels.
Authors: Posson, D.J. / Thompson, A.N. / McCoy, J.G. / Nimigean, C.M.
History
DepositionJun 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Apr 2, 2014Group: Other
Revision 1.3Nov 15, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,7248
Polymers60,8373
Non-polymers8875
Water1,60389
1
A: Fab light chain
B: Fab heavy chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Fab light chain
B: Fab heavy chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Fab light chain
B: Fab heavy chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Fab light chain
B: Fab heavy chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,89632
Polymers243,35012
Non-polymers3,54620
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Unit cell
Length a, b, c (Å)155.938, 155.938, 75.814
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11C-1002-

K

21C-1003-

K

31C-1004-

K

41C-1120-

HOH

51C-1121-

HOH

61C-1122-

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: 13990.396 Da / Num. of mol.: 1 / Mutation: R122A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: kcsA, skc1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P0A334

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Antibody , 2 types, 2 molecules AB

#1: Antibody Fab light chain / Fragment antigen-binding


Mass: 23411.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pASK90 / Production host: mus musculus (house mouse)
#2: Antibody Fab heavy chain / Fragment antigen-binding


Mass: 23435.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: mus musculus (house mouse)

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Non-polymers , 4 types, 94 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-DGA / DIACYL GLYCEROL / Diglyceride


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 3.78 Å3/Da / Density % sol: 67.49 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 400, MgAcetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: Double silicon(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.75→100 Å / Num. obs: 23784 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.083 / Χ2: 0.894 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.75-2.856.20.65523520.742199.2
2.85-2.966.70.51723500.763199.9
2.96-3.16.90.35323770.829199.9
3.1-3.2670.24423570.8991100
3.26-3.467.20.16923780.9581100
3.46-3.737.30.11523691.0651100
3.73-4.117.40.07823780.9271100
4.11-4.77.40.05123870.9981100
4.7-5.927.30.05223940.9791100
5.92-10070.02924420.733199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.751→42.871 Å / Occupancy max: 1 / Occupancy min: 0.06 / FOM work R set: 0.8611 / SU ML: 0.29 / σ(F): 1.35 / Phase error: 21.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2018 1214 5.11 %
Rwork0.1673 22561 -
obs0.169 23775 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.1 Å2 / Biso mean: 72.718 Å2 / Biso min: 21.06 Å2
Refinement stepCycle: LAST / Resolution: 2.751→42.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4067 0 44 89 4200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124262
X-RAY DIFFRACTIONf_angle_d1.8195755
X-RAY DIFFRACTIONf_chiral_restr0.1653
X-RAY DIFFRACTIONf_plane_restr0.01723
X-RAY DIFFRACTIONf_dihedral_angle_d12.9031508
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.751-2.86110.26871380.23552453259199
2.8611-2.99130.25641370.217425132650100
2.9913-3.14890.23321510.193124672618100
3.1489-3.34620.22331380.176224802618100
3.3462-3.60440.19671360.155425022638100
3.6044-3.96690.18151410.14425042645100
3.9669-4.54040.17981330.133925062639100
4.5404-5.71820.17521170.152225412658100
5.7182-42.8760.20791230.190825952718100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.931.0846-2.45566.4651-2.10564.3132-0.44270.4521-0.489-0.4770.1956-0.35040.669-0.15630.24350.6285-0.130.06580.3844-0.01370.4878-10.8541-34.0397-48.4178
21.75410.84-1.85171.8186-1.31023.0095-0.4203-0.1261-0.2771-0.08790.1246-0.03150.8609-0.41070.15690.646-0.21830.02030.46030.07740.5816-20.5429-37.4233-34.9301
33.14360.425-2.25340.9319-0.42762.0056-0.33670.2691-0.3955-0.089-0.04460.01930.921-0.70190.13660.9695-0.43730.04270.74090.12790.6202-33.0246-43.11-27.351
42.7527-0.6604-0.68513.90630.01354.48390.098-0.08260.20990.29670.03140.4113-0.0097-0.4872-0.12040.3142-0.07340.02940.38140.03280.3659-20.5589-13.5578-39.7943
51.65120.9284-1.62261.479-0.73852.59270.2264-0.04670.09420.20940.0120.2615-0.1881-0.4566-0.16110.4118-0.10290.02910.46070.08640.4038-21.6597-17.8645-34.5275
61.9459-0.2343-0.76531.3272-0.33640.872-0.0389-0.7512-0.3040.1029-0.0453-0.32470.6369-0.1660.05371.1383-0.29810.05870.95410.24710.6227-31.4496-39.9331-12.1315
72.8641-1.79520.36375.3907-1.96081.79610.3007-0.3214-0.01590.1625-0.175-0.1968-0.1770.1909-0.12590.7004-0.18650.0390.89710.10930.5379-27.5155-30.7472-19.2776
82.1221-0.4673-0.65812.9545-1.14232.31170.0485-0.9241-0.59580.8625-0.00950.070.4366-0.16450.12291.0981-0.38220.07271.20620.36520.7395-32.5601-41.9585-7.037
92.00530.4079-0.13942.2004-0.5363.1037-0.10790.1166-0.0178-0.29520.09680.04920.6442-0.4343-0.05530.2645-0.0956-0.01050.2248-0.0650.3251-7.4394-16.1002-72.0374
100.9492-1.09190.76462.45190.01531.46240.0963-0.25320.157-0.0811-0.1961-0.28980.3862-0.06590.04410.2853-0.0326-0.00520.2908-0.01890.2793-5.9583-9.3884-63.7915
111.6119-0.73690.77393.5135-1.38715.07640.03590.62650.1556-0.693-0.12310.32430.0839-0.12360.03990.350.01960.03550.4415-0.01690.3414-3.649-5.5773-85.3204
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:83)A1 - 83
2X-RAY DIFFRACTION2chain 'A' and (resseq 84:139)A84 - 139
3X-RAY DIFFRACTION3chain 'A' and (resseq 140:219)A140 - 219
4X-RAY DIFFRACTION4chain 'B' and (resseq 1:75)B1 - 75
5X-RAY DIFFRACTION5chain 'B' and (resseq 76:113)B76 - 113
6X-RAY DIFFRACTION6chain 'B' and (resseq 114:155)B114 - 155
7X-RAY DIFFRACTION7chain 'B' and (resseq 156:174)B156 - 174
8X-RAY DIFFRACTION8chain 'B' and (resseq 175:212)B175 - 212
9X-RAY DIFFRACTION9chain 'C' and (resseq 22:61)C22 - 61
10X-RAY DIFFRACTION10chain 'C' and (resseq 62:85)C62 - 85
11X-RAY DIFFRACTION11chain 'C' and (resseq 86:124)C86 - 124

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