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- PDB-6c6m: IgCam3 of human MLCK1 -

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Basic information

Entry
Database: PDB / ID: 6c6m
TitleIgCam3 of human MLCK1
ComponentsMyosin light chain kinase, smooth muscleMyosin light-chain kinase
KeywordsCELL ADHESION / IgCAM MLCK1 IBD
Function / homology
Function and homology information


aorta smooth muscle tissue morphogenesis / tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / cellular hypotonic response / bleb assembly / positive regulation of calcium ion transport / positive regulation of wound healing / RHO GTPases activate PAKs / cleavage furrow ...aorta smooth muscle tissue morphogenesis / tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / cellular hypotonic response / bleb assembly / positive regulation of calcium ion transport / positive regulation of wound healing / RHO GTPases activate PAKs / cleavage furrow / smooth muscle contraction / Smooth Muscle Contraction / stress fiber / actin cytoskeleton / lamellipodium / actin binding / calmodulin binding / positive regulation of cell migration / protein phosphorylation / ATP binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Myosin Light Chain Kinase 1, Kinase domain / Unstructured linker between I-set domains 2 and 3 on MYLCK / 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 ...Myosin Light Chain Kinase 1, Kinase domain / Unstructured linker between I-set domains 2 and 3 on MYLCK / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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 / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Myosin light chain kinase, smooth muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsZuccola, H.J. / Turner, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK61931 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK068271 United States
CitationJournal: Nat. Med. / Year: 2019
Title: Intracellular MLCK1 diversion reverses barrier loss to restore mucosal homeostasis.
Authors: Graham, W.V. / He, W. / Marchiando, A.M. / Zha, J. / Singh, G. / Li, H.S. / Biswas, A. / Ong, M.L.D.M. / Jiang, Z.H. / Choi, W. / Zuccola, H. / Wang, Y. / Griffith, J. / Wu, J. / Rosenberg, ...Authors: Graham, W.V. / He, W. / Marchiando, A.M. / Zha, J. / Singh, G. / Li, H.S. / Biswas, A. / Ong, M.L.D.M. / Jiang, Z.H. / Choi, W. / Zuccola, H. / Wang, Y. / Griffith, J. / Wu, J. / Rosenberg, H.J. / Wang, Y. / Snapper, S.B. / Ostrov, D. / Meredith, S.C. / Miller, L.W. / Turner, J.R.
History
DepositionJan 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myosin light chain kinase, smooth muscle
B: Myosin light chain kinase, smooth muscle
C: Myosin light chain kinase, smooth muscle


Theoretical massNumber of molelcules
Total (without water)34,8993
Polymers34,8993
Non-polymers00
Water1,02757
1
A: Myosin light chain kinase, smooth muscle


Theoretical massNumber of molelcules
Total (without water)11,6331
Polymers11,6331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Myosin light chain kinase, smooth muscle


Theoretical massNumber of molelcules
Total (without water)11,6331
Polymers11,6331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Myosin light chain kinase, smooth muscle


Theoretical massNumber of molelcules
Total (without water)11,6331
Polymers11,6331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.693, 74.693, 131.481
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Myosin light chain kinase, smooth muscle / Myosin light-chain kinase / smMLCK / Kinase-related protein / KRP / Telokin


Mass: 11632.965 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYLK, MLCK, MLCK1, MYLK1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15746, myosin-light-chain kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.22 Å3/Da / Density % sol: 61.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 200mM ammonium dihydrogen phosphate, 20% PEG3350

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→46 Å / Num. obs: 14445 / % possible obs: 98.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 64.42 Å2 / Net I/σ(I): 13.2
Reflection shellResolution: 2.5→2.7 Å

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
autoPROCdata scaling
BUSTERphasing
RefinementResolution: 2.5→46 Å / Cor.coef. Fo:Fc: 0.858 / Cor.coef. Fo:Fc free: 0.812 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.36 / SU Rfree Blow DPI: 0.264
RfactorNum. reflection% reflectionSelection details
Rfree0.272 784 5.44 %RANDOM
Rwork0.226 ---
obs0.228 14404 99.7 %-
Displacement parametersBiso mean: 81.4 Å2
Baniso -1Baniso -2Baniso -3
1--20.3142 Å20 Å20 Å2
2---20.3142 Å20 Å2
3---40.6285 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: 1 / Resolution: 2.5→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2247 0 0 57 2304
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114463HARMONIC1
X-RAY DIFFRACTIONt_angle_deg1.438036HARMONIC1
X-RAY DIFFRACTIONt_dihedral_angle_d956SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes710HARMONIC5
X-RAY DIFFRACTIONt_it4463HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.28
X-RAY DIFFRACTIONt_other_torsion20.07
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion287SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4406SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.7 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3008 167 5.67 %
Rwork0.2522 2780 -
all0.2551 2947 -
obs--99.29 %
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)
13.533-0.7054-0.42882.1690.88173.9285-0.23490.06730.1351-0.11170.10960.2140.0770.34820.12530.06730.02170.1191-0.07620.0537-0.1869-30.062813.91450.2962
22.6659-0.39280.4910.93641.06314.12890.1066-0.2310.01270.01-0.10610.16170.2038-0.0735-0.0005-0.02050.13730.02550.06440.0055-0.1691-40.413811.282821.8575
32.09750.2474-0.26392.58820.49545.11810.1216-0.06880.04380.1268-0.12750.1267-0.29850.06160.0059-0.0729-0.0037-0.0332-0.0371-0.0294-0.1469-2.90489.88052.5011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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