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- PDB-6ici: Crystal structure of human MICAL3 -

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Basic information

Entry
Database: PDB / ID: 6ici
TitleCrystal structure of human MICAL3
Components[F-actin]-monooxygenase MICAL3
KeywordsFLAVOPROTEIN / Monooxygenase / OXIDOREDUCTASE
Function / homology
Function and homology information


F-actin monooxygenase / 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 / Flemming body / intercellular bridge / exocytosis / localization / cytoskeleton organization / FAD binding / cell projection ...F-actin monooxygenase / 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 / Flemming body / intercellular bridge / exocytosis / localization / cytoskeleton organization / FAD binding / cell projection / spindle / actin binding / cell cortex / molecular adaptor activity / cell cycle / cell division / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol
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. / LIM domain / 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. / 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 / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / [F-actin]-monooxygenase MICAL3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHwang, K.Y. / Kim, J.S.
CitationJournal: Iucrj / Year: 2020
Title: Structural and kinetic insights into flavin-containing monooxygenase and calponin-homology domains in human MICAL3.
Authors: Kim, J. / Lee, H. / Roh, Y.J. / Kim, H.U. / Shin, D. / Kim, S. / Son, J. / Lee, A. / Kim, M. / Park, J. / Hwang, S.Y. / Kim, K. / Lee, Y.K. / Jung, H.S. / Hwang, K.Y. / Lee, B.C.
History
DepositionSep 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: [F-actin]-monooxygenase MICAL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,1382
Polymers83,3531
Non-polymers7861
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-6 kcal/mol
Surface area26470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.211, 93.466, 71.568
Angle α, β, γ (deg.)90.000, 92.366, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein [F-actin]-monooxygenase MICAL3 / Molecule interacting with CasL protein 3 / MICAL-3


Mass: 83352.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICAL3, KIAA0819, KIAA1364 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7RTP6, F-actin monooxygenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bicine-NaOH pH 9.2, 7% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→47.2 Å / Num. obs: 38165 / % possible obs: 99.7 % / Redundancy: 4.85 % / Biso Wilson estimate: 36.06 Å2 / Rsym value: 0.143 / Net I/σ(I): 16.89
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.72 / Num. unique obs: 5163 / Rsym value: 0.48 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4txi

4txi


Resolution: 2.3→47.2 Å / SU ML: 0.2347 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.4018
RfactorNum. reflection% reflection
Rfree0.2144 1221 3.2 %
Rwork0.1721 --
obs0.1735 38112 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.48 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4669 0 53 273 4995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00874828
X-RAY DIFFRACTIONf_angle_d0.96736535
X-RAY DIFFRACTIONf_chiral_restr0.0565718
X-RAY DIFFRACTIONf_plane_restr0.0058827
X-RAY DIFFRACTIONf_dihedral_angle_d18.98091765
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.390.23811380.18624074X-RAY DIFFRACTION99.86
2.39-2.50.3021360.18874097X-RAY DIFFRACTION99.88
2.5-2.630.26811330.19014075X-RAY DIFFRACTION99.79
2.63-2.80.23761320.19034090X-RAY DIFFRACTION99.86
2.8-3.010.23151340.18534112X-RAY DIFFRACTION99.91
3.01-3.320.24271310.18214072X-RAY DIFFRACTION99.88
3.32-3.80.21491370.16854138X-RAY DIFFRACTION99.81
3.8-4.780.16891380.14654092X-RAY DIFFRACTION99.83
4.78-47.20.20211420.1734141X-RAY DIFFRACTION98.87

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