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- PDB-2c4c: Crystal structure of the NADPH-treated monooxygenase domain of MICAL -

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Basic information

Entry
Database: PDB / ID: 2c4c
TitleCrystal structure of the NADPH-treated monooxygenase domain of MICAL
ComponentsNEDD9-INTERACTING PROTEIN WITH CALPONIN HOMOLOGY AND LIM DOMAINS
KeywordsTRANSPORT / CYTOSKELETON / FAD / FLAVOPROTEIN / LIM DOMAIN / METAL-BINDING / SIGNALING PROTEIN
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 protein phosphorylation / actin filament / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / small GTPase binding / SH3 domain binding / actin binding / midbody / endosome membrane / negative regulation of apoptotic process / protein kinase binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
DUF3585 / bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / 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 ...DUF3585 / bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / 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 / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / [F-actin]-monooxygenase MICAL1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSiebold, C. / Berrow, N. / Walter, T.S. / Harlos, K. / Owens, R.J. / Terman, J.R. / Stuart, D.I. / Kolodkin, A.L. / Pasterkamp, R.J. / Jones, E.Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: High-Resolution Structure of the Catalytic Region of Mical (Molecule Interacting with Casl), a Multidomain Flavoenzyme-Signaling Molecule.
Authors: Siebold, C. / Berrow, N. / Walter, T.S. / Harlos, K. / Owens, R.J. / Stuart, D.I. / Terman, J.R. / Kolodkin, A.L. / Pasterkamp, R.J. / Jones, E.Y.
History
DepositionOct 18, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEDD9-INTERACTING PROTEIN WITH CALPONIN HOMOLOGY AND LIM DOMAINS
B: NEDD9-INTERACTING PROTEIN WITH CALPONIN HOMOLOGY AND LIM DOMAINS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,1176
Polymers110,4752
Non-polymers1,6424
Water72140
1
A: NEDD9-INTERACTING PROTEIN WITH CALPONIN HOMOLOGY AND LIM DOMAINS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0583
Polymers55,2371
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: NEDD9-INTERACTING PROTEIN WITH CALPONIN HOMOLOGY AND LIM DOMAINS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0583
Polymers55,2371
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)75.709, 89.915, 83.573
Angle α, β, γ (deg.)90.00, 113.82, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9898, 0.13988, 0.02689), (0.14164, 0.98655, 0.08161), (-0.01511, 0.08458, -0.9963)
Vector: 92.5197, -8.03004, 36.14296)

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Components

#1: Protein NEDD9-INTERACTING PROTEIN WITH CALPONIN HOMOLOGY AND LIM DOMAINS / MICAL / MOLECULE INTERACTING WITH CASL PROTEIN 1


Mass: 55237.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8VDP3
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 48 %
Crystal growpH: 5 / Details: pH 5.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 25263 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 10.5
Reflection shellResolution: 2.9→2.99 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2.5 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.892 / SU B: 51.871 / SU ML: 0.485 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.517 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1159 5.1 %RANDOM
Rwork0.243 ---
obs0.246 21557 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 80.51 Å2
Baniso -1Baniso -2Baniso -3
1--5 Å20 Å2-7.37 Å2
2--4.38 Å20 Å2
3----5.33 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7442 0 108 40 7590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0227755
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0151.97910526
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.25949
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.14923.468346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.119151284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6121558
X-RAY DIFFRACTIONr_chiral_restr0.0710.21151
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025882
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.23586
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.25236
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2256
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1851.54837
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.33327537
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.29733353
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.5274.52989
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.338 77
Rwork0.34 1560
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.5628-0.45972.35642.37611.01437.5840.2166-0.4235-0.11320.12090.06790.00890.4945-0.2666-0.2846-0.2382-0.179-0.0223-0.64290.1242-0.356755.75523.63547.298
26.08450.06031.63284.66830.132212.555-0.0081-0.15390.7568-0.3837-0.48690.7996-0.6942-1.64650.4950.01690.2514-0.18760.1519-0.00630.131830.41338.50334.417
37.5980.64690.3212.67691.07019.05290.79670.6158-1.1495-0.1869-0.23720.20891.5283-0.5077-0.55960.1892-0.1857-0.28-0.5848-0.0353-0.087751.4299.46533.987
45.21280.40642.04322.14-0.39775.33690.1320.4408-0.0138-0.22390.2408-0.050.41540.2967-0.3728-0.2240.0339-0.0062-0.6217-0.0548-0.354941.90927-9.784
55.5215-0.04351.48664.0639-1.352413.40750.00770.66110.23040.19440.0037-0.6411-0.52252.5332-0.0113-0.0786-0.1231-0.05170.3089-0.1602-0.014869.20636.3984.467
66.3841-0.44711.11193.7036-0.46064.80990.8172-0.5477-0.95870.15490.1303-0.10991.07640.1777-0.94740.0757-0.0261-0.2815-0.57150.0482-0.148543.8811.4342.243
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 236
2X-RAY DIFFRACTION2A237 - 369
3X-RAY DIFFRACTION3A370 - 487
4X-RAY DIFFRACTION4B7 - 236
5X-RAY DIFFRACTION5B237 - 369
6X-RAY DIFFRACTION6B370 - 487

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