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

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Basic information

Entry
Database: PDB / ID: 6zic
TitleCRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH 3S-HYDROXYBUTANOYL-COA AND NADH
ComponentsPeroxisomal bifunctional enzyme
KeywordsOXIDOREDUCTASE / PEROXISOMES / 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
3-HYDROXYBUTANOYL-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: 2.2 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 3S-HYDROXYBUTANOYL-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)165,73815
Polymers161,8632
Non-polymers3,87513
Water4,594255
1
AAA: Peroxisomal bifunctional enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,09910
Polymers80,9311
Non-polymers2,1689
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Peroxisomal bifunctional enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6395
Polymers80,9311
Non-polymers1,7074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.637, 127.086, 227.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AAABBB

#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

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Non-polymers , 5 types, 268 molecules

#2: Chemical ChemComp-3HC / 3-HYDROXYBUTANOYL-COENZYME A / 3-HYDROXYBUTYRYL-COENZYME A


Mass: 853.623 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H42N7O18P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 125mM MES, pH 6; 18%w/v PEG 4000; 175mM ammonium. 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: 2.2→65.122 Å / Num. obs: 96924 / % possible obs: 99.6 % / Redundancy: 7.58 % / Biso Wilson estimate: 38.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.036 / Net I/σ(I): 11.7
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 1.022 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4732 / CC1/2: 0.715 / Rpim(I) all: 0.386 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OMO

5omo


Resolution: 2.2→65.121 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.236 / WRfactor Rwork: 0.2 / Average fsc free: 0.9146 / Average fsc work: 0.9293 / Cross valid method: FREE R-VALUE / ESU R: 0.227 / ESU R Free: 0.186
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2338 4925 5.086 %
Rwork0.2003 91900 -
all0.202 --
obs-96825 99.476 %
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: 55.296 Å2
Baniso -1Baniso -2Baniso -3
1--1.626 Å2-0 Å2-0 Å2
2--0.752 Å2-0 Å2
3---0.874 Å2
Refinement stepCycle: LAST / Resolution: 2.2→65.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11036 0 248 255 11539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01211620
X-RAY DIFFRACTIONr_angle_refined_deg1.541.6415765
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30751447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.24320.978542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.262151947
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0671584
X-RAY DIFFRACTIONr_chiral_restr0.1180.21485
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028772
X-RAY DIFFRACTIONr_nbd_refined0.2190.25190
X-RAY DIFFRACTIONr_nbtor_refined0.3120.27852
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2490
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2520.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2540.213
X-RAY DIFFRACTIONr_mcbond_it0.691.3125779
X-RAY DIFFRACTIONr_mcangle_it1.2131.9637229
X-RAY DIFFRACTIONr_scbond_it1.2641.6735841
X-RAY DIFFRACTIONr_scangle_it2.0282.4638536
X-RAY DIFFRACTIONr_lrange_it7.3119.30317179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.2893370.2666731X-RAY DIFFRACTION99.7741
2.257-2.3190.2993740.2476536X-RAY DIFFRACTION99.8266
2.319-2.3860.2873440.2376379X-RAY DIFFRACTION99.6
2.386-2.4590.2833380.246110X-RAY DIFFRACTION98.7896
2.459-2.540.2753060.2336022X-RAY DIFFRACTION99.2005
2.54-2.6290.2812830.2295892X-RAY DIFFRACTION100
2.629-2.7280.2492790.2115661X-RAY DIFFRACTION99.8655
2.728-2.840.2763270.2145392X-RAY DIFFRACTION100
2.84-2.9660.2572860.2125197X-RAY DIFFRACTION99.2578
2.966-3.1110.2462690.2164934X-RAY DIFFRACTION98.8975
3.111-3.2790.2182450.2044780X-RAY DIFFRACTION99.8014
3.279-3.4770.2522370.2094511X-RAY DIFFRACTION99.8738
3.477-3.7170.2182600.1974197X-RAY DIFFRACTION99.8879
3.717-4.0150.2252130.1813918X-RAY DIFFRACTION98.6625
4.015-4.3970.1992020.1643697X-RAY DIFFRACTION100
4.397-4.9160.1581760.1443317X-RAY DIFFRACTION99.459
4.916-5.6740.2161590.1752937X-RAY DIFFRACTION99.4859
5.674-6.9450.2911150.2222545X-RAY DIFFRACTION98.848
6.945-9.8040.1641140.1651979X-RAY DIFFRACTION98.9598
9.804-65.120.253610.2391165X-RAY DIFFRACTION97.4563
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)
12.58420.6124-0.40421.7386-1.04741.8363-0.02790.17120.1836-0.04540.0321-0.00470.0141-0.0161-0.00410.58350.0209-0.01970.01730.0060.0216-25.853-9.031-3.125
220.6596-18.58981.555217.447-1.32020.27250.55490.74780.5983-0.5659-0.6328-0.5337-0.23340.1480.07790.6014-0.0815-0.01920.12360.05680.0306-49.893-13.9153.075
34.6213-0.03580.43743.09120.00396.4906-0.0112-0.741.04380.64920.1291-0.1716-0.98480.2072-0.1180.9025-0.04750.03690.143-0.20220.3036-59.6446.18818.064
41.4026-0.3952-0.39411.52420.46573.3531-0.1147-0.2976-0.16120.42520.10280.04060.21950.01090.0120.63080.03580.01190.06540.03490.0189-62.605-22.6123.084
54.18760.76341.5923.55140.45632.49640.16330.4075-0.96070.21590.1312-0.58930.37020.0957-0.29460.641-0.0095-0.02960.0947-0.1530.3224-41.202-13.34995.521
63.17146.24872.420417.29498.76395.3586-0.0472-0.2526-0.38870.39580.063-0.35910.79620.1483-0.01580.7547-0.0543-0.02640.2720.03770.2224-63.213-17.10885.556
74.4512-2.4693-2.19474.89311.38056.14520.13060.3983-0.68470.0645-0.50560.10911.05190.11810.3751.0943-0.0103-0.10930.1116-0.08270.2664-59.218-34.37365.035
80.9822-0.4125-0.30831.98241.10084.78170.22170.179-0.0032-0.4654-0.46150.1798-0.2214-0.86990.23990.76390.0569-0.10310.3069-0.13760.1012-75.316-8.46664.888
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA-4 - 259
2X-RAY DIFFRACTION2ALLAAA260 - 280
3X-RAY DIFFRACTION3ALLAAA281 - 475
4X-RAY DIFFRACTION4ALLAAA476 - 720
5X-RAY DIFFRACTION5ALLBBB0 - 259
6X-RAY DIFFRACTION6ALLBBB260 - 280
7X-RAY DIFFRACTION7ALLBBB281 - 475
8X-RAY DIFFRACTION8ALLBBB476 - 717

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