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- PDB-3oml: Structure of full-length peroxisomal multifunctional enzyme type ... -

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Basic information

Entry
Database: PDB / ID: 3oml
TitleStructure of full-length peroxisomal multifunctional enzyme type 2 from Drosophila melanogaster
ComponentsPeroxisomal Multifunctional Enzyme Type 2, CG3415
KeywordsOxidoreductase / Hydrolase / Rossmann fold / hot-dog fold / hydratase 2 motif / Peroxisomes / lyase
Function / homology
Function and homology information


Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / alpha-linolenic acid (ALA) metabolism / Beta-oxidation of pristanoyl-CoA / Beta-oxidation of very long chain fatty acids / Peroxisomal protein import / : / (3R)-hydroxyacyl-CoA dehydrogenase (NAD+) activity / enoyl-CoA hydratase 2 / 3-hydroxyacyl-CoA dehydratase activity / fatty acid beta-oxidation using acyl-CoA oxidase ...Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / alpha-linolenic acid (ALA) metabolism / Beta-oxidation of pristanoyl-CoA / Beta-oxidation of very long chain fatty acids / Peroxisomal protein import / : / (3R)-hydroxyacyl-CoA dehydrogenase (NAD+) activity / enoyl-CoA hydratase 2 / 3-hydroxyacyl-CoA dehydratase activity / fatty acid beta-oxidation using acyl-CoA oxidase / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / 3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / fatty acid beta-oxidation / peroxisome / protein homodimerization activity
Similarity search - Function
Helix Hairpins - #4290 / : / MFE-2 hydratase 2 N-terminal domain / : / MaoC-like dehydratase domain / MaoC like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / short chain dehydrogenase ...Helix Hairpins - #4290 / : / MFE-2 hydratase 2 N-terminal domain / : / MaoC-like dehydratase domain / MaoC like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / short chain dehydrogenase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / Helix Hairpins / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Roll / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Peroxisomal multifunctional enzyme type 2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHaataja, T.J.K. / Koski, M.K. / Glumoff, T. / Hiltunen, J.K.
CitationJournal: Biochem.J. / Year: 2011
Title: Peroxisomal multifunctional enzyme type 2 from the fruitfly: dehydrogenase and hydratase act as separate entities, as revealed by structure and kinetics.
Authors: Haataja, T.J. / Koski, M.K. / Hiltunen, J.K. / Glumoff, T.
History
DepositionAug 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Oct 8, 2014Group: Database references
Revision 1.4Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxisomal Multifunctional Enzyme Type 2, CG3415


Theoretical massNumber of molelcules
Total (without water)66,1741
Polymers66,1741
Non-polymers00
Water2,486138
1
A: Peroxisomal Multifunctional Enzyme Type 2, CG3415

A: Peroxisomal Multifunctional Enzyme Type 2, CG3415


Theoretical massNumber of molelcules
Total (without water)132,3482
Polymers132,3482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area11320 Å2
ΔGint-90 kcal/mol
Surface area45150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.480, 114.480, 89.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Peroxisomal Multifunctional Enzyme Type 2, CG3415 / GH14720p


Mass: 66174.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG3415, Dmel_CG3415 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q9VXJ0, 17beta-estradiol 17-dehydrogenase, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris, 1.0 M NaCl, 20 % (w/v) PEG 5000 MME, 5 mM NAD+ , VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2008
RadiationMonochromator: Si 311 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.15→28.1 Å / Num. all: 31114 / Num. obs: 31008 / % possible obs: 99.66 %
Reflection shellResolution: 2.15→2.21 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1PN4 AND 1GZ6

1pn4

1gz6


Resolution: 2.15→28.1 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.914 / SU B: 18.872 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28542 1636 5 %RANDOM
Rwork0.23431 ---
obs0.23686 31008 99.66 %-
all-31114 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.15→28.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4038 0 0 138 4176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223972
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.9655394
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9395526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.61124.78159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86615617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7561519
X-RAY DIFFRACTIONr_chiral_restr0.0830.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212998
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4471.52613
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.81224158
X-RAY DIFFRACTIONr_scbond_it1.31531359
X-RAY DIFFRACTIONr_scangle_it1.9814.51236
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 118 -
Rwork0.319 2253 -
obs--100 %
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)
14.3534-2.772-1.53064.731.55882.7944-0.8579-0.2705-1.2311.4305-0.10980.93321.2589-0.28850.96770.9429-0.20640.61360.23-0.07980.5713-59.79534.8045.412
27.2348-3.1814-1.88746.08523.63692.53960.08390.54640.9293-0.1632-0.2385-0.2801-0.2039-0.560.15460.25090.0584-0.00450.5421-0.23770.4398-69.18870.5940.473
35.5854-2.3081-0.18124.4087-0.67013.50040.0788-0.0951-0.3474-0.07770.06641.01770.0857-1.0351-0.14520.0944-0.1138-0.01130.44720.01180.2475-49.06786.0556.563
43.1896-0.3132-0.11153.23710.07374.3938-0.0129-0.34160.5977-0.01150.10040.3681-0.5626-0.5687-0.08750.12660.0315-0.01190.1836-0.0320.2046-41.02898.1174.923
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 251
2X-RAY DIFFRACTION2A252 - 312
3X-RAY DIFFRACTION3A313 - 450
4X-RAY DIFFRACTION4A459 - 592

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