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- PDB-2bry: Crystal structure of the native monooxygenase domain of MICAL at ... -

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Basic information

Entry
Database: PDB / ID: 2bry
TitleCrystal structure of the native monooxygenase domain of MICAL at 1.45 A resolution
ComponentsNEDD9 INTERACTING PROTEIN WITH CALPONIN HOMOLOGY AND LIM DOMAINS
KeywordsTRANSPORT / COILED COIL / CYTOSKELETON / FAD / FLAVOPROTEIN / LIM DOMAIN / METAL-BINDING / ZINC
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 / SYNCHROTRON / SAD / Resolution: 1.45 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
DepositionMay 13, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)112,4019
Polymers110,4752
Non-polymers1,9267
Water28,5181583
1
A: NEDD9 INTERACTING PROTEIN WITH CALPONIN HOMOLOGY AND LIM DOMAINS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2475
Polymers55,2371
Non-polymers1,0094
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)56,1544
Polymers55,2371
Non-polymers9173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)76.588, 89.548, 83.458
Angle α, β, γ (deg.)90.00, 114.35, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 6 / Auth seq-ID: 7 - 489 / Label seq-ID: 15 - 497

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.98571, 0.16785, 0.01391), (0.16843, 0.98229, 0.08208), (0.00011, 0.08325, -0.99653)
Vector: 93.6929, -9.65945, 35.6705)

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 1590 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1583 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsFUNCTION: POSSIBLE CYTOSKELETAL REGULATOR THAT CONNECTS NEDD9 TO INTERMEDIATE FILAMENTS
Sequence detailsRESIDUE TYR265 WAS MODDELED AS A265 IN CHAINS A AND B BECAUSE THE SIDE CHAIN WAS NOT VISIBLE IN THE ...RESIDUE TYR265 WAS MODDELED AS A265 IN CHAINS A AND B BECAUSE THE SIDE CHAIN WAS NOT VISIBLE IN THE ELECTRON DENSITY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 48 %
Crystal growDetails: 0.1 M NA ACETATE, PH 4.6 0.2 AMMONIUM SULFATE 30% PEG 2000 MONOMETHYL ETHER

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.957
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.957 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 160458 / % possible obs: 88.3 % / Observed criterion σ(I): 1.4 / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.3
Reflection shellResolution: 1.45→1.55 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.4 / % possible all: 54.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHARPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: SAD / Resolution: 1.45→76.03 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.29 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 6406 4 %RANDOM
Rwork0.18 ---
obs0.181 154050 88.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.76 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å20 Å2-0.73 Å2
2--1.81 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.45→76.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7482 0 124 1583 9189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227825
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.97610621
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6955954
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48423.506348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.357151318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6471558
X-RAY DIFFRACTIONr_chiral_restr0.0860.21180
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025862
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.24237
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.25336
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.21254
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.2159
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.296
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8431.54884
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26527638
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.79633394
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7664.52979
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3732 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.335
loose thermal3.5210
LS refinement shellResolution: 1.45→1.49 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 249
Rwork0.324 6188
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)
11.46190.17880.15430.27-0.38151.79660.0323-0.40290.00110.09250.01860.06140.02210.0091-0.051-0.1458-0.0130.0055-0.02530.0687-0.117258.60923.68560.129
22.6497-0.27870.26410.91470.13621.79540.08280.1094-0.0283-0.0987-0.0505-0.05110.01790.0846-0.0324-0.10760.00030.0137-0.23660.0655-0.139555.6423.84741.115
32.7787-0.3179-1.10521.665-0.01324.59610.21850.54490.3649-0.4074-0.12680.1129-0.4105-0.577-0.09180.01310.12620.00660.03710.1118-0.059830.67237.65134.29
44.5467-1.4435-0.02681.69160.22842.03890.15380.4732-0.3606-0.2132-0.1081-0.07420.3570.0365-0.0456-0.02130.0359-0.0004-0.1746-0.0165-0.07954.07812.62433.238
55.3174-0.4553-0.03192.1768-0.14112.2925-0.04830.4887-1.0851-0.1763-0.06830.0970.7334-0.06170.11670.12240.0127-0.042-0.1475-0.07050.136550.6425.22434.732
61.6630.42150.7760.3372-0.23751.18040.06050.29510.0864-0.02170.090.03320.0975-0.0006-0.1505-0.0270.0136-0.01330.0452-0.0085-0.024240.73328.3-22.261
70.9401-0.09510.59020.0493-0.11960.46080.0893-0.1072-0.0193-0.05210.0226-0.01440.0245-0.0843-0.1119-0.0194-0.0063-0.00310.0183-0.01090.006443.30326.526-3.369
80.5557-0.1005-0.1490.4364-0.20871.68790.0206-0.00740.03140.11160.0282-0.0155-0.10820.1728-0.04870.0127-0.02440.02240.0132-0.0372-0.01270.37435.2414.667
91.07660.1630.22790.3868-0.31250.47840.2262-0.1832-0.1397-0.05590.0238-0.01220.1291-0.1151-0.24990.0109-0.0626-0.06890.03170.04810.018342.89414.7113.666
101.49430.1507-0.52380.6413-0.15771.94420.2576-0.0712-0.3967-0.05230.0177-0.06290.3443-0.1816-0.27530.0352-0.0621-0.1563-0.06190.05070.069245.27.0891.767
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 80
2X-RAY DIFFRACTION2A81 - 236
3X-RAY DIFFRACTION3A237 - 369
4X-RAY DIFFRACTION4A370 - 443
5X-RAY DIFFRACTION5A444 - 489
6X-RAY DIFFRACTION6B7 - 80
7X-RAY DIFFRACTION7B81 - 236
8X-RAY DIFFRACTION8B237 - 369
9X-RAY DIFFRACTION9B370 - 443
10X-RAY DIFFRACTION10B444 - 489

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