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- PDB-3uto: Twitchin kinase region from C.elegans (Fn31-NL-kin-CRD-Ig26) -

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Basic information

Entry
Database: PDB / ID: 3uto
TitleTwitchin kinase region from C.elegans (Fn31-NL-kin-CRD-Ig26)
ComponentsTwitchin
KeywordsTRANSFERASE / kinase / muscle sarcomere
Function / homology
Function and homology information


positive regulation of sarcomere organization / positive regulation of locomotion / positive regulation of striated muscle contraction / A band / negative regulation of cell division / behavioral response to nicotine / M band / sarcomere organization / adult locomotory behavior / calmodulin binding ...positive regulation of sarcomere organization / positive regulation of locomotion / positive regulation of striated muscle contraction / A band / negative regulation of cell division / behavioral response to nicotine / M band / sarcomere organization / adult locomotory behavior / calmodulin binding / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / ATP binding / metal ion binding
Similarity search - Function
: / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...: / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / DI(HYDROXYETHYL)ETHER / Twitchin
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCastelmur, E. / Barbieri, S. / Mayans, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Identification of an N-terminal inhibitory extension as the primary mechanosensory regulator of twitchin kinase.
Authors: von Castelmur, E. / Strumpfer, J. / Franke, B. / Bogomolovas, J. / Barbieri, S. / Qadota, H. / Konarev, P.V. / Svergun, D.I. / Labeit, S. / Benian, G.M. / Schulten, K. / Mayans, O.
History
DepositionNov 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Twitchin
B: Twitchin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,2046
Polymers130,4902
Non-polymers7144
Water7,638424
1
A: Twitchin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6334
Polymers65,2451
Non-polymers3873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Twitchin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5722
Polymers65,2451
Non-polymers3261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.700, 158.210, 60.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Twitchin / Uncoordinated protein 22


Mass: 65245.203 Da / Num. of mol.: 2
Fragment: twitchin kinase region (Fn3-NL-kin-CRD-Ig), UNP residues 6108-6675
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: unc-22, ZK617.1 / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli)
References: UniProt: Q23551, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 428 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG 600, 100 mM sodium citrate pH 5.5, 50 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.4→19.87 Å / Num. obs: 45313 / % possible obs: 97.2 % / Observed criterion σ(I): 3 / Redundancy: 4.86 % / Rsym value: 0.097 / Net I/σ(I): 14.43
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 4.82 % / Num. unique all: 2670 / Rsym value: 0.58 / % possible all: 96.9

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.6.0119refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.87 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.84 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.532 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21326 1165 2.6 %RANDOM
Rwork0.17458 ---
obs0.17557 44098 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.693 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2--1.14 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9027 0 48 424 9499
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.029302
X-RAY DIFFRACTIONr_bond_other_d0.0030.026468
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.95612591
X-RAY DIFFRACTIONr_angle_other_deg0.955315716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90651122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77924.048457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.078151582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.441563
X-RAY DIFFRACTIONr_chiral_restr0.0690.21320
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110335
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021892
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 91 -
Rwork0.231 2924 -
obs--96.67 %
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)
16.47071.05021.22234.1518-0.00816.3158-0.03180.35640.2986-0.14720.0455-0.4297-0.37330.4376-0.01370.1035-0.04580.0040.06760.05210.23726.037.057-15.315
20.7588-0.00820.14880.9768-0.56291.47040.0019-0.01440.08940.00920.0027-0.0532-0.09810.0033-0.00460.0246-0.00390.01730.0221-0.01440.034110.738-15.957-3.064
31.84680.0592-0.41234.4985-1.76992.8723-0.028-0.317-0.4858-0.0021-0.0776-0.23790.35750.16870.10550.08890.04090.00460.13250.03940.20220.566-51.38.112
42.9522-0.5731-0.43774.12960.78723.9393-0.00210.0158-0.410.0428-0.03880.1270.40430.03090.04090.063-0.01390.03430.0256-0.01470.1738-15.779-74.2834.907
50.87370.1527-0.43080.8863-0.18951.2944-0.03440.0844-0.0464-0.10560.04430.04450.0458-0.1104-0.00980.0195-0.0216-0.00190.0496-0.02360.0505-7.117-48.904-8.916
64.60542.9352-2.52235.3682-1.52583.3801-0.10210.31130.0626-0.45760.1-0.2618-0.20910.29040.0020.1128-0.01560.01250.2706-0.03810.125126.524-36.32-22.636
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 96
2X-RAY DIFFRACTION2A108 - 468
3X-RAY DIFFRACTION3A473 - 564
4X-RAY DIFFRACTION4B5 - 98
5X-RAY DIFFRACTION5B105 - 468
6X-RAY DIFFRACTION6B473 - 564

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