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- PDB-3efd: The crystal structure of the cytoplasmic domain of KcsA -

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Basic information

Entry
Database: PDB / ID: 3efd
TitleThe crystal structure of the cytoplasmic domain of KcsA
Components
  • FabH
  • FabL
  • KcsA
KeywordsIMMUNE SYSTEM / Helix bundle / C-terminus
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsUysal, S. / Vasquez, V. / Tereshko, V. / Esaki, K. / Fellouse, F.A. / Sidhu, S.S. / Koide, S. / Perozo, E. / Kossiakoff, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Crystal structure of full-length KcsA in its closed conformation.
Authors: Uysal, S. / Vasquez, V. / Tereshko, V. / Esaki, K. / Fellouse, F.A. / Sidhu, S.S. / Koide, S. / Perozo, E. / Kossiakoff, A.
History
DepositionSep 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: FabL
H: FabH
K: KcsA


Theoretical massNumber of molelcules
Total (without water)50,3013
Polymers50,3013
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.499, 115.499, 76.816
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Antibody FabL


Mass: 22960.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody FabH


Mass: 23708.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein/peptide KcsA


Mass: 3631.964 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG2000 and 20 mM Bis-Tris propane, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 15270 / Num. obs: 13735 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.6→2.7 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CCP4model building
REFMAC5.4.0073refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / SU B: 36.289 / SU ML: 0.361 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.381 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27575 1539 10.1 %RANDOM
Rwork0.22527 ---
obs0.2304 13735 98.01 %-
all-15270 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.799 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å20 Å20 Å2
2--2.61 Å20 Å2
3----5.22 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3494 0 0 59 3553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223577
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.954866
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1065451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00623.889144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.54215568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7181517
X-RAY DIFFRACTIONr_chiral_restr0.090.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212701
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4571.52269
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87823657
X-RAY DIFFRACTIONr_scbond_it1.31731308
X-RAY DIFFRACTIONr_scangle_it2.1584.51209
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.605→2.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 126 -
Rwork0.371 1005 -
obs--98.09 %
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)
16.7291.2799-0.1371.3341-0.22573.4618-0.8781-0.21320.4247-0.28950.3180.01180.0112-0.02920.56-0.06810.1187-0.1216-0.3765-0.0083-0.203421.832413.85030.7452
29.239-0.90690.22470.7109-1.14448.3051-0.63370.04280.16820.42280.3613-0.4127-1.19731.49260.2724-0.0461-0.2672-0.13140.50360.1150.074758.36521.73731.2179
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 108
2X-RAY DIFFRACTION1H1 - 120
3X-RAY DIFFRACTION1K129 - 158
4X-RAY DIFFRACTION2L109 - 211
5X-RAY DIFFRACTION2H121 - 225

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