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- PDB-5szg: Structure of the bMERB domain of Mical-3 -

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Basic information

Entry
Database: PDB / ID: 5szg
TitleStructure of the bMERB domain of Mical-3
ComponentsProtein-methionine sulfoxide oxidase MICAL3
KeywordsENDOCYTOSIS / Mical-3 / DUF3585 / Mical / Rab effector / 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. / 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
DI(HYDROXYETHYL)ETHER / [F-actin]-monooxygenase MICAL3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsRai, A. / Oprisko, A. / Campos, J. / Fu, Y. / Friese, T. / Itzen, A. / Goody, R.S. / Gazdag, E.M. / Mueller, M.P.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSFB 642, grant A4 Germany
Max Planck Society Germany
CitationJournal: Elife / Year: 2016
Title: bMERB domains are bivalent Rab8 family effectors evolved by gene duplication.
Authors: Rai, A. / Oprisko, A. / Campos, J. / Fu, Y. / Friese, T. / Itzen, A. / Goody, R.S. / Gazdag, E.M. / Muller, M.P.
History
DepositionAug 14, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-methionine sulfoxide oxidase MICAL3
B: Protein-methionine sulfoxide oxidase MICAL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2864
Polymers37,0742
Non-polymers2122
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-10 kcal/mol
Surface area17250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.858, 78.848, 95.557
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1843 - 1983
2010B1843 - 1983

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Components

#1: Protein Protein-methionine sulfoxide oxidase MICAL3 / Molecule interacting with CasL protein 3 / MICAL-3


Mass: 18537.062 Da / Num. of mol.: 2 / Fragment: UNP residues 1841-1990
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, 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 / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3

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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: 2.63 Å3/Da / Density % sol: 53.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 7.0 50 % PEG 200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978956 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978956 Å / Relative weight: 1
ReflectionResolution: 2.7→47.8 Å / Num. obs: 20544 / % possible obs: 99.1 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.138 / Rsym value: 0.144 / Net I/σ(I): 16.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 13.6 % / Rmerge(I) obs: 1.15 / Mean I/σ(I) obs: 3.6 / CC1/2: 0.87 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→47.78 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.901 / SU B: 8.62 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.691 / ESU R Free: 0.348 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28208 556 5 %RANDOM
Rwork0.2509 ---
obs0.25245 10553 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 69.674 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2--1.93 Å2-0 Å2
3----3.23 Å2
Refinement stepCycle: 1 / Resolution: 2.7→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 14 0 2103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192119
X-RAY DIFFRACTIONr_bond_other_d0.0060.022092
X-RAY DIFFRACTIONr_angle_refined_deg1.8092.0022831
X-RAY DIFFRACTIONr_angle_other_deg1.54334748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7015260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.523.826115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.86515390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0381530
X-RAY DIFFRACTIONr_chiral_restr0.0990.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022396
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02484
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.36.6431046
X-RAY DIFFRACTIONr_mcbond_other6.36.6381045
X-RAY DIFFRACTIONr_mcangle_it8.5439.9241301
X-RAY DIFFRACTIONr_mcangle_other8.549.931302
X-RAY DIFFRACTIONr_scbond_it8.5677.7181073
X-RAY DIFFRACTIONr_scbond_other8.5647.7181073
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.86511.1651530
X-RAY DIFFRACTIONr_long_range_B_refined14.49150.6182216
X-RAY DIFFRACTIONr_long_range_B_other14.48950.6282217
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 10982 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.21 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.703→2.773 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 40 -
Rwork0.205 754 -
obs--97.54 %

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