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- PDB-1fhg: HIGH RESOLUTION REFINEMENT OF TELOKIN -

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Basic information

Entry
Database: PDB / ID: 1fhg
TitleHIGH RESOLUTION REFINEMENT OF TELOKIN
ComponentsTELOKIN
KeywordsCONTRACTILE PROTEIN / immunoglobulin fold / beta barrel
Function / homology
Function and homology information


Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins ...Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMeleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / IR / Resolution: 2 Å
AuthorsTomchick, D.R. / Minor, W. / Kiyatkin, A. / Lewinski, K. / Somlyo, A.V. / Somlyo, A.P.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: X-ray structure determination of telokin, the C-terminal domain of myosin light chain kinase, at 2.8 A resolution.
Authors: Holden, H.M. / Ito, M. / Hartshorne, D.J. / Rayment, I.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: X-Ray Structure Determination of Telokin, the C-terminal Domain of Myosin Light Chain Kinase, at 2.8 Angstroms Resolution
Authors: Holden, H.M. / Ito, M. / Hartshorne, D.J. / Rayment, I.
#2: Journal: ACTA PHYSIOL.SCAND. / Year: 1998
Title: Regulation of the Cross-bridge Cycle: the Effects of MgADP, LC17 Isoforms and Telokin.
Authors: Somlyo, A.V. / Matthew, J.D. / Wu, X. / Khromov, A.S. / Somlyo, A.P.
#3: Journal: J.Biol.Chem. / Year: 1998
Title: Acceleration of Myosin Light Chain Dephosphorylation and Relaxation of Smooth Muscle by Telokin. Synergism with Cyclic Nucleotide-activated Kinase.
Authors: Wu, X. / Haystead, T.A. / Nakamoto, R.K. / Somlyo, A.V. / Somlyo, A.P.
History
DepositionAug 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / database_2
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TELOKIN


Theoretical massNumber of molelcules
Total (without water)16,9741
Polymers16,9741
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.710, 63.710, 58.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-277-

HOH

21A-279-

HOH

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Components

#1: Protein TELOKIN


Mass: 16974.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Meleagris gallopavo (turkey) / Tissue: GIZZARD / References: UniProt: P56276
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.03 Å3/Da / Density % sol: 30 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 4
Details: PEG6000, sodium acetate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 273.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1
DetectorDetector: CCD / Date: Sep 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→20 Å / Num. all: 9904 / Num. obs: 9904 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 47.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 35.7
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.34 / Num. unique all: 967 / % possible all: 99.6

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: IR
Starting model: 1tlk

1tlk


Resolution: 2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 506 5 %RANDOM
Rwork0.21 ---
all0.233 9598 --
obs0.233 9598 99.5 %-
Solvent computationBsol: 52.72 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso mean: 42.95 Å2
Baniso -1Baniso -2Baniso -3
1--2.801 Å2-4.624 Å20 Å2
2---2.801 Å20 Å2
3---5.602 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms814 0 0 82 896
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.669
X-RAY DIFFRACTIONc_dihedral_angle_d26.771
X-RAY DIFFRACTIONc_improper_angle_d1.046
X-RAY DIFFRACTIONc_mcbond_it1.681.5
X-RAY DIFFRACTIONc_mcangle_it2.692
X-RAY DIFFRACTIONc_scbond_it2.582
X-RAY DIFFRACTIONc_scangle_it4.052.5
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.302 49 5 %
Rwork0.267 888 -
obs--99.79 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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