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- PDB-5le0: MICAL1 Cterminal domain -

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Basic information

Entry
Database: PDB / ID: 5le0
TitleMICAL1 Cterminal domain
ComponentsProtein-methionine sulfoxide oxidase MICAL1
KeywordsOXIDOREDUCTASE / MICAL
Function / homology
Function and homology information


hippocampal mossy fiber expansion / NADPH oxidase H202-forming activity / F-actin monooxygenase / NAD(P)H oxidase (H2O2-forming) / sulfur oxidation / regulation of regulated secretory pathway / NAD(P)H oxidase H2O2-forming activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / actin filament depolymerization / intermediate filament ...hippocampal mossy fiber expansion / NADPH oxidase H202-forming activity / F-actin monooxygenase / NAD(P)H oxidase (H2O2-forming) / sulfur oxidation / regulation of regulated secretory pathway / NAD(P)H oxidase H2O2-forming activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / actin filament depolymerization / intermediate filament / intercellular bridge / actin filament bundle assembly / cytoskeleton organization / FAD binding / negative regulation of protein phosphorylation / actin filament / monooxygenase activity / small GTPase binding / SH3 domain binding / actin filament binding / actin cytoskeleton / actin binding / Factors involved in megakaryocyte development and platelet production / midbody / endosome membrane / negative regulation of apoptotic process / protein kinase binding / signal transduction / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
DUF3585 / bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / FAD-binding domain ...DUF3585 / bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / FAD-binding domain / FAD binding domain / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
[F-actin]-monooxygenase MICAL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsHammich, H. / Pylypenko, O. / Houdusse, A.
CitationJournal: Nat Commun / Year: 2017
Title: Oxidation of F-actin controls the terminal steps of cytokinesis.
Authors: Fremont, S. / Hammich, H. / Bai, J. / Wioland, H. / Klinkert, K. / Rocancourt, M. / Kikuti, C. / Stroebel, D. / Romet-Lemonne, G. / Pylypenko, O. / Houdusse, A. / Echard, A.
History
DepositionJun 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Protein-methionine sulfoxide oxidase MICAL1


Theoretical massNumber of molelcules
Total (without water)17,6671
Polymers17,6671
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.780, 52.780, 157.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Protein-methionine sulfoxide oxidase MICAL1 / Molecule interacting with CasL protein 1 / MICAL-1 / NEDD9-interacting protein with calponin ...Molecule interacting with CasL protein 1 / MICAL-1 / NEDD9-interacting protein with calponin homology and LIM domains


Mass: 17666.594 Da / Num. of mol.: 1 / Fragment: UNP residues 918-1067
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICAL1, MICAL, NICAL / Production host: Escherichia coli (E. coli)
References: UniProt: Q8TDZ2, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor

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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: 3.74 Å3/Da / Density % sol: 67.09 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: EG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97887 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97887 Å / Relative weight: 1
ReflectionResolution: 3.3→43.8 Å / Num. obs: 3734 / % possible obs: 99.6 % / Redundancy: 7 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 26.56
Reflection shellResolution: 3.3→3.418 Å / Rmerge(I) obs: 0.317 / Num. unique all: 358

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.3→43.8 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.23
RfactorNum. reflection% reflection
Rfree0.3063 185 4.96 %
Rwork0.2708 --
obs0.2725 3729 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 0 0 0 956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005958
X-RAY DIFFRACTIONf_angle_d0.5971287
X-RAY DIFFRACTIONf_dihedral_angle_d9.982605
X-RAY DIFFRACTIONf_chiral_restr0.031153
X-RAY DIFFRACTIONf_plane_restr0.003171
LS refinement shellResolution: 3.3→3.4179 Å
RfactorNum. reflection% reflection
Rfree0.4159 18 -
Rwork0.3117 338 -
obs--99 %

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