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- PDB-4txk: Construct of MICAL-1 containing the monooxygenase and calponin ho... -

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Basic information

Entry
Database: PDB / ID: 4txk
TitleConstruct of MICAL-1 containing the monooxygenase and calponin homology domains
ComponentsProtein-methionine sulfoxide oxidase MICAL1
KeywordsOXIDOREDUCTASE / monooyxgenase / calponin homology / 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 / 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 / intercellular bridge / monooxygenase activity ...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 / 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 / intercellular bridge / monooxygenase activity / FAD binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of protein phosphorylation / actin filament / small GTPase binding / SH3 domain binding / actin binding / midbody / endosome membrane / negative regulation of apoptotic process / protein kinase binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
DUF3585 / bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / : / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / LIM zinc-binding domain signature. / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type ...DUF3585 / bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / : / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / LIM zinc-binding domain signature. / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / [F-actin]-monooxygenase MICAL1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.878 Å
AuthorsAlqassim, S.S. / Amzel, L.M. / Bianchet, M.A.
CitationJournal: To Be Published
Title: Structural insights into modulation of MICAL activity by its Calponin Homology (CH) domain
Authors: Alqassim, S.S. / Amzel, L.M. / Bianchet, M.A.
History
DepositionJul 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Data collection
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-methionine sulfoxide oxidase MICAL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4903
Polymers67,5981
Non-polymers8922
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.233, 50.174, 96.966
Angle α, β, γ (deg.)90.00, 101.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein-methionine sulfoxide oxidase MICAL1 / Molecule interacting with CasL protein 1 / mMical1 / NEDD9-interacting protein with calponin ...Molecule interacting with CasL protein 1 / mMical1 / NEDD9-interacting protein with calponin homology and LIM domains


Mass: 67598.156 Da / Num. of mol.: 1 / Fragment: UNP resdiues 2-615
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mical1, Mical, Nical / Production host: Escherichia coli (E. coli)
References: UniProt: Q8VDP3, 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
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.6 Å3/Da / Density % sol: 52.64 % / Mosaicity: 0.986 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 2000 MME, HEPES buffer / PH range: 7.0 - 7.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.82→26.82 Å / Num. obs: 14602 / % possible obs: 96.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.184 / Χ2: 1.046 / Net I/av σ(I): 6.602 / Net I/σ(I): 4.2 / Num. measured all: 52018
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.82-2.872.30.644820.72865.1
2.87-2.922.70.6546600.73687.9
2.92-2.983.10.6537350.76296.8
2.98-3.043.40.5697210.75696.1
3.04-3.13.60.467160.75495.9
3.1-3.183.70.3637320.78799.9
3.18-3.263.70.287640.79497.6
3.26-3.343.80.2487290.88397.7
3.34-3.443.70.2037540.911100
3.44-3.553.80.1797211.07196.5
3.55-3.683.80.1877421.588100
3.68-3.833.70.1477530.88197.5
3.83-43.70.197611.15299.6
4-4.213.70.157231.31598.1
4.21-4.483.70.1477611.83798.7
4.48-4.823.70.1457591.23699.9
4.82-5.313.70.1357590.97799.1
5.31-6.073.70.1577640.95499.5
6.07-7.653.70.1277780.9699.6
7.65-503.50.0577881.35797.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
MOLREPphasing
Cootmodel building
PDB_EXTRACT3.14data extraction
HKL-2000data scaling
RefinementResolution: 2.878→26.806 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2721 685 4.69 %RANDOM
Rwork0.2025 ---
obs0.206 14590 95.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.878→26.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4510 0 60 38 4608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014678
X-RAY DIFFRACTIONf_angle_d1.2896350
X-RAY DIFFRACTIONf_dihedral_angle_d18.0291685
X-RAY DIFFRACTIONf_chiral_restr0.046700
X-RAY DIFFRACTIONf_plane_restr0.005811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8778-3.09970.38951040.32062347X-RAY DIFFRACTION80
3.0997-3.41110.32051430.2662817X-RAY DIFFRACTION98
3.4111-3.90330.30161470.18822881X-RAY DIFFRACTION99
3.9033-4.91280.24361410.18262860X-RAY DIFFRACTION99
4.9128-26.8070.20711500.15493000X-RAY DIFFRACTION100
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)
11.30850.3123-0.3081.8735-0.26680.6408-0.0093-0.01630.0576-0.0391-0.0491-0.3727-0.21720.17740.06870.2304-0.01770.00280.2740.01920.183414.510810.647825.2469
20.86140.00020.72890.66170.27281.90560.1472-0.1794-0.05560.1367-0.14620.28390.04-0.3055-0.05810.2555-0.02650.09220.28980.00570.2573-10.9577-1.39311.1359
30.8373-0.3670.27431.0719-0.65071.05480.0699-0.1807-0.1031-0.17310.08440.01210.0267-0.0027-0.15310.232-0.0679-0.00490.20870.00340.2378-0.5221-0.224129.5551
41.74540.977-0.48974.9029-2.4985.8565-0.4916-0.5812-0.5712-0.2820.1045-0.8770.42670.71430.21380.28590.12530.01660.4118-0.02880.36218.1208-32.980958.7051
50.597-0.1044-0.27421.7193-0.61443.81060.1095-0.0373-0.1879-0.07460.02380.0489-0.66660.5343-0.1810.32310.02070.1350.33370.01270.28922.2722-25.445462.0021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 7:214)
2X-RAY DIFFRACTION2(chain A and resid 215:327)
3X-RAY DIFFRACTION3(chain A and resid 328:487)
4X-RAY DIFFRACTION4(chain A and resid 509:567)
5X-RAY DIFFRACTION5(chain A and resid 568:613)

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