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- PDB-6zib: CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-... -

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Basic information

Entry
Database: PDB / ID: 6zib
TitleCRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH ACETOACETYL-COA AND NADH
ComponentsPeroxisomal bifunctional enzyme
KeywordsOXIDOREDUCTASE / PEOXISOMES / BETA OXIDATION / HYDRATASE / DEHYDROGENASE
Function / homology
Function and homology information


Beta-oxidation of very long chain fatty acids / intramolecular oxidoreductase activity, transposing C=C bonds / Peroxisomal protein import / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / long-chain-3-hydroxyacyl-CoA dehydrogenase activity / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity ...Beta-oxidation of very long chain fatty acids / intramolecular oxidoreductase activity, transposing C=C bonds / Peroxisomal protein import / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / long-chain-3-hydroxyacyl-CoA dehydrogenase activity / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity / fatty acid beta-oxidation / NAD+ binding / peroxisome / enzyme binding / cytosol
Similarity search - Function
3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase ...3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / ClpP/crotonase-like domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETOACETYL-COENZYME A / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Peroxisomal bifunctional enzyme
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWierenga, R.K. / Sridhar, S. / Kiema, T.R.
Funding support Finland, 1items
OrganizationGrant numberCountry
European Union (EU)731005 Finland
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH ACETOACETYL-COA AND NADH
Authors: Wierenga, R.K. / Sridhar, S. / Kiema, T.R.
History
DepositionJun 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Peroxisomal bifunctional enzyme
BBB: Peroxisomal bifunctional enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,0898
Polymers161,8632
Non-polymers3,2266
Water1,20767
1
AAA: Peroxisomal bifunctional enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5444
Polymers80,9311
Non-polymers1,6133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Peroxisomal bifunctional enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5444
Polymers80,9311
Non-polymers1,6133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.937, 127.390, 228.173
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB)

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Components

#1: Protein Peroxisomal bifunctional enzyme / PBFE / Multifunctional enzyme 1 / MFE1 / Multifunctional protein 1 / MFP1


Mass: 80931.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PEROXISOMES / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ehhadh, Mfe1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P07896, enoyl-CoA hydratase, Delta3-Delta2-enoyl-CoA isomerase, 3-hydroxyacyl-CoA dehydrogenase
#2: Chemical ChemComp-CAA / ACETOACETYL-COENZYME A / Acetoacetyl-CoA


Mass: 851.607 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H40N7O18P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.93 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: MES, pH 6; 16%w/v PEG 4000; 150mM ammonium sulfate. Co-crystallized with 2mM CoA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972957 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 31, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972957 Å / Relative weight: 1
ReflectionResolution: 2.7→48.88 Å / Num. obs: 51199 / % possible obs: 95.5 % / Redundancy: 7.77 % / Biso Wilson estimate: 52.6 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.06 / Net I/σ(I): 11.7
Reflection shellResolution: 2.7→2.78 Å / Rmerge(I) obs: 1.092 / Mean I/σ(I) obs: 2 / Num. unique obs: 4422 / CC1/2: 0.691 / Rpim(I) all: 0.406

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OMO

5omo


Resolution: 2.7→48.88 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.866 / WRfactor Rfree: 0.263 / WRfactor Rwork: 0.226 / Average fsc free: 0.8567 / Average fsc work: 0.8749 / Cross valid method: FREE R-VALUE / ESU R: 1.303 / ESU R Free: 0.371
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2733 2540 4.993 %
Rwork0.2316 48331 -
all0.234 --
obs-50871 94.554 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 72.958 Å2
Baniso -1Baniso -2Baniso -3
1-6.068 Å20 Å20 Å2
2---1.042 Å20 Å2
3----5.026 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11074 0 206 67 11347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01211582
X-RAY DIFFRACTIONr_angle_refined_deg1.0811.65115725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06851448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.07121.165541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.798151944
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3041581
X-RAY DIFFRACTIONr_chiral_restr0.0950.21480
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028756
X-RAY DIFFRACTIONr_nbd_refined0.2080.25213
X-RAY DIFFRACTIONr_nbtor_refined0.3070.27775
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2355
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2460.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1870.24
X-RAY DIFFRACTIONr_mcbond_it0.5821.2715774
X-RAY DIFFRACTIONr_mcangle_it1.0861.9017213
X-RAY DIFFRACTIONr_scbond_it0.6661.5875808
X-RAY DIFFRACTIONr_scangle_it1.1562.3868507
X-RAY DIFFRACTIONr_lrange_it7.17918.33917054
X-RAY DIFFRACTIONr_ncsr_local_group_10.0970.0522641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.3241920.3193573X-RAY DIFFRACTION95.5099
2.77-2.8460.3222190.3093481X-RAY DIFFRACTION97.6253
2.846-2.9280.2911730.2793463X-RAY DIFFRACTION97.2713
2.928-3.0180.3411750.2673319X-RAY DIFFRACTION96.8404
3.018-3.1170.2991590.2723232X-RAY DIFFRACTION96.4997
3.117-3.2270.31630.2533039X-RAY DIFFRACTION95.0995
3.227-3.3490.2781430.2382833X-RAY DIFFRACTION90.1545
3.349-3.4850.2841620.2492951X-RAY DIFFRACTION97.8008
3.485-3.640.3461260.2942677X-RAY DIFFRACTION92.7838
3.64-3.8180.4191430.3662537X-RAY DIFFRACTION92.3183
3.818-4.0240.2671210.2252512X-RAY DIFFRACTION95.1228
4.024-4.2680.2631100.2072353X-RAY DIFFRACTION93.4725
4.268-4.5630.1961240.1792101X-RAY DIFFRACTION89.7539
4.563-4.9280.1951060.172143X-RAY DIFFRACTION97.1071
4.928-5.3990.1791000.1771962X-RAY DIFFRACTION95.7733
5.399-6.0350.2931040.21722X-RAY DIFFRACTION93.1633
6.035-6.9680.291660.211454X-RAY DIFFRACTION87.963
6.968-8.5320.2760.1571367X-RAY DIFFRACTION96.5217
8.532-12.0580.197620.1431007X-RAY DIFFRACTION90.8241
12.058-48.880.399160.291605X-RAY DIFFRACTION87.5882
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)
12.57370.841-0.512.1662-0.92811.4358-0.06130.05730.1094-0.03210.0193-0.0559-0.01070.02290.0420.00480.0264-0.00940.337-0.01780.6815.202-9.591-2.869
22.708-0.65170.16422.9085-0.05566.5815-0.1188-0.43370.70910.80430.166-0.162-0.95320.3326-0.04720.6139-0.01820.01880.428-0.12040.8261-27.5975.57317.303
31.66260.1471-0.26162.79130.16364.2765-0.038-0.3983-0.12510.87340.02220.0640.25110.01280.01580.32720.06040.04220.39830.01970.6545-30.252-22.76923.195
43.78110.71721.17792.03650.60952.17690.12420.2638-0.45560.0498-0.0307-0.35060.4310.1053-0.09360.2-0.02420.04470.4332-0.10550.8019-9.125-13.24195.582
53.3443-1.0293-1.74623.3340.27546.6270.27920.4202-0.705-0.5215-0.4942-0.18621.32220.66970.2151.3160.1839-0.04440.6688-0.09471.0276-26.623-33.99465.998
61.2905-0.5301-0.32092.51090.47075.73710.2180.30660.0354-0.8509-0.29620.0966-0.3916-0.55180.07830.69830.0184-0.06030.5806-0.10550.7407-42.243-8.42665.468
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA-4 - 275
2X-RAY DIFFRACTION2ALLAAA276 - 478
3X-RAY DIFFRACTION3ALLAAA479 - 720
4X-RAY DIFFRACTION4ALLBBB0 - 275
5X-RAY DIFFRACTION5ALLBBB276 - 478
6X-RAY DIFFRACTION6ALLBBB479 - 717

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