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- PDB-4msw: Y78 ester mutant of KcsA in high K+ -

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Basic information

Entry
Database: PDB / ID: 4msw
TitleY78 ester mutant of KcsA in high K+
Components
  • (ANTIBODY FAB FRAGMENT ...) x 2
  • pH-gated potassium channel KcsA
KeywordsTRANSPORT PROTEIN / Membrane protein / Channel / Ester / Unnatural amino acid
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
DIACYL GLYCEROL / : / 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: 2.06 Å
AuthorsMatulef, K. / Valiyaveetil, F.I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Using protein backbone mutagenesis to dissect the link between ion occupancy and C-type inactivation in K+ channels.
Authors: Matulef, K. / Komarov, A.G. / Costantino, C.A. / Valiyaveetil, F.I.
History
DepositionSep 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Nov 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: ANTIBODY FAB FRAGMENT HEAVY CHAIN
B: ANTIBODY FAB FRAGMENT LIGHT CHAIN
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,69610
Polymers57,8373
Non-polymers8607
Water4,666259
1
A: ANTIBODY FAB FRAGMENT HEAVY CHAIN
B: ANTIBODY FAB FRAGMENT LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)46,8472
Polymers46,8472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-23 kcal/mol
Surface area19350 Å2
MethodPISA
2
C: pH-gated potassium channel KcsA
hetero molecules

C: pH-gated potassium channel KcsA
hetero molecules

C: pH-gated potassium channel KcsA
hetero molecules

C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,39732
Polymers43,9594
Non-polymers3,43828
Water724
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
Buried area10750 Å2
ΔGint-99 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.530, 154.530, 75.780
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-1127-

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: 10989.735 Da / Num. of mol.: 1 / Fragment: UNP residues 22-124
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 FAB FRAGMENT HEAVY CHAIN


Mass: 23411.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell: Hybridoma / Production host: Komagataella pastoris (fungus)
#2: Antibody ANTIBODY FAB FRAGMENT LIGHT CHAIN


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

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Non-polymers , 3 types, 266 molecules

#4: Chemical ChemComp-DGA / DIACYL GLYCEROL


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


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


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHERE IS AN ESTER LINKAGE BETWEEN RESIDUES 77 AND 78 OF CHAIN C RATHER THAN A PEPTIDE BACKBONE LINKAGE.

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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: 3.91 Å3/Da / Density % sol: 68.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: PEG400, Magnesium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 291K
PH range: 5.75-6.0

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.06→42 Å / Num. obs: 54941 / % possible obs: 99.8 % / Redundancy: 7.2 % / Biso Wilson estimate: 32.53 Å2 / Rmerge(I) obs: 0.077 / Χ2: 1.029 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.06-2.14.70.56626651.057197.2
2.1-2.135.30.47726611.04199.3
2.13-2.176.10.47227640.996199.9
2.17-2.226.60.4527291.0191100
2.22-2.2770.49727431.0741100
2.27-2.327.30.38427490.981100
2.32-2.387.50.34827281.0641100
2.38-2.447.60.31627461.081100
2.44-2.517.60.25427601.0331100
2.51-2.67.60.2227271.041100
2.6-2.697.60.17827641.021100
2.69-2.87.60.14327221.0011100
2.8-2.927.60.11627611.0261100
2.92-3.087.60.09327441.0561100
3.08-3.277.60.08127560.9721100
3.27-3.527.60.06527851.0191100
3.52-3.887.60.05427521.0121100
3.88-4.447.60.04727680.9641100
4.44-5.597.60.04927801.042199.9
5.59-427.40.03928371.089199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→36.423 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8294 / SU ML: 0.22 / σ(F): 0 / Phase error: 24.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 5253 10.02 %
Rwork0.1961 --
obs0.1994 52404 95.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.66 Å2 / Biso mean: 37.6849 Å2 / Biso min: 10.18 Å2
Refinement stepCycle: LAST / Resolution: 2.06→36.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4057 0 37 259 4353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074162
X-RAY DIFFRACTIONf_angle_d1.055678
X-RAY DIFFRACTIONf_chiral_restr0.069649
X-RAY DIFFRACTIONf_plane_restr0.004719
X-RAY DIFFRACTIONf_dihedral_angle_d12.4351455
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.06-2.08610.33751710.3031281145282
2.0861-2.11060.29491580.25671383154183
2.1106-2.13640.29151500.24951416156687
2.1364-2.16340.29731620.23161494165689
2.1634-2.19190.31181520.24171483163590
2.1919-2.22190.23631430.22931536167992
2.2219-2.25360.28781690.22611499166890
2.2536-2.28730.27731570.21661489164691
2.2873-2.3230.24771700.20481543171393
2.323-2.36110.22671590.20671580173995
2.3611-2.40180.24591800.20471522170295
2.4018-2.44540.25371710.21021560173194
2.4454-2.49250.26291800.19111567174796
2.4925-2.54330.24771760.21011598177497
2.5433-2.59860.25071920.19851554174696
2.5986-2.6590.23281740.20371597177197
2.659-2.72550.25651860.20191604179097
2.7255-2.79920.2381840.20971597178198
2.7992-2.88150.23921860.20761630181698
2.8815-2.97450.27551770.21761653183099
2.9745-3.08070.23311850.21071600178599
3.0807-3.2040.26361690.1991673184299
3.204-3.34980.21711850.198716311816100
3.3498-3.52620.21741820.189716691851100
3.5262-3.74690.20812070.188916241831100
3.7469-4.03590.20051590.182816761835100
4.0359-4.44140.19752070.171316411848100
4.4414-5.08260.2021740.164416871861100
5.0826-6.39790.21421980.185416691867100
6.3979-36.42870.20881900.19251695188599

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