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- PDB-6z5v: CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-... -

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Basic information

Entry
Database: PDB / ID: 6z5v
TitleCRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH 3-KETODECANOYL-COA IN CROTONASE FOLD AND OXIDISED NICOTINAMIDE ADENINE DINUCLEOTIDE IN HAD FOLD
ComponentsPeroxisomal bifunctional enzyme
KeywordsOXIDOREDUCTASE / 3-KETODECANOYL-COA / BETA-OXIDATION / PEROXISOME.
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-KETO-DECANOYL-COA / Peroxisomal bifunctional enzyme
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsWierenga, R.K. / Sridhar, S. / Kiema, T.R.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Crystallographic binding studies of rat peroxisomal multifunctional enzyme type 1 with 3-ketodecanoyl-CoA: capturing active and inactive states of its hydratase and dehydrogenase catalytic sites.
Authors: Sridhar, S. / Schmitz, W. / Hiltunen, J.K. / Venkatesan, R. / Bergmann, U. / Kiema, T.R. / Wierenga, R.K.
History
DepositionMay 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 21, 2021Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Jan 24, 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)165,53711
Polymers161,8632
Non-polymers3,6759
Water3,009167
1
AAA: Peroxisomal bifunctional enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8156
Polymers80,9311
Non-polymers1,8835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Peroxisomal bifunctional enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7235
Polymers80,9311
Non-polymers1,7914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.314, 126.298, 224.900
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


Mass: 80931.352 Da / Num. of mol.: 2 / Mutation: 0
Source method: isolated from a genetically manipulated source
Details: Peroxisome / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ehhadh / 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, 176 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-ZOZ / 3-KETO-DECANOYL-COA


Mass: 935.767 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H52N7O18P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.8 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 125mM MES, pH 6; 17%w/v PEG4000; 175mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 12, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.32→29.15 Å / Num. obs: 80007 / % possible obs: 99.2 % / Redundancy: 6.66 % / Biso Wilson estimate: 53.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.022 / Net I/σ(I): 17.9
Reflection shellResolution: 2.33→2.37 Å / Rmerge(I) obs: 0.798 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3880 / CC1/2: 0.649 / Rpim(I) all: 0.359 / % possible all: 86.6

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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: 2.33→29.149 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / Cross valid method: FREE R-VALUE / ESU R: 0.298 / ESU R Free: 0.208
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2258 4072 5.095 %
Rwork0.2035 75851 -
all0.205 --
obs-79923 99.048 %
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: 70 Å2
Baniso -1Baniso -2Baniso -3
1-4.177 Å20 Å20 Å2
2---1.923 Å20 Å2
3----2.254 Å2
Refinement stepCycle: LAST / Resolution: 2.33→29.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11000 0 234 167 11401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01211528
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.6415645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.09351434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40921.109532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.064151932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4411580
X-RAY DIFFRACTIONr_chiral_restr0.0980.21475
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028696
X-RAY DIFFRACTIONr_nbd_refined0.2120.25144
X-RAY DIFFRACTIONr_nbtor_refined0.3080.27779
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2405
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2130.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3050.210
X-RAY DIFFRACTIONr_mcbond_it1.1022.8175739
X-RAY DIFFRACTIONr_mcangle_it1.914.2167172
X-RAY DIFFRACTIONr_scbond_it1.3793.225789
X-RAY DIFFRACTIONr_scangle_it2.1874.7848473
X-RAY DIFFRACTIONr_lrange_it9.10438.91716956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.3880.3372800.3214943X-RAY DIFFRACTION89.2821
2.388-2.4540.2893160.2795420X-RAY DIFFRACTION99.9826
2.454-2.5250.2792740.2635351X-RAY DIFFRACTION100
2.525-2.6020.3032580.2645156X-RAY DIFFRACTION99.9815
2.602-2.6880.282480.2495036X-RAY DIFFRACTION99.9811
2.688-2.7820.2792430.2424823X-RAY DIFFRACTION99.9803
2.782-2.8870.2672740.2414659X-RAY DIFFRACTION100
2.887-3.0050.2742570.2334487X-RAY DIFFRACTION99.9789
3.005-3.1390.2452110.2234364X-RAY DIFFRACTION99.9781
3.139-3.2920.2432370.2174134X-RAY DIFFRACTION99.9771
3.292-3.470.262080.233967X-RAY DIFFRACTION99.9043
3.47-3.680.2432020.2163721X-RAY DIFFRACTION99.7965
3.68-3.9340.2081910.2013514X-RAY DIFFRACTION99.8383
3.934-4.2490.2131770.1883299X-RAY DIFFRACTION99.8277
4.249-4.6550.1791630.173059X-RAY DIFFRACTION99.7832
4.655-5.2040.1971420.162763X-RAY DIFFRACTION99.8282
5.204-6.0080.1981420.1912460X-RAY DIFFRACTION99.8082
6.008-7.3570.2211030.2022110X-RAY DIFFRACTION99.8196
7.357-10.3990.1681000.1361647X-RAY DIFFRACTION99.6009
10.399-29.140.21460.203938X-RAY DIFFRACTION94.4338
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)
13.13441.03560.67582.39490.9782.2709-0.03770.2077-0.2804-0.0614-0.04330.07790.0658-0.05720.0810.0110.02620.04610.52530.01520.565-39.3518.952-114.963
22.3721-0.87070.56443.9012-0.1456.8769-0.1948-0.4317-0.61871.06760.37910.29031.1282-0.3599-0.18430.58790.01580.03280.50710.15220.6722-6.091-5.921-93.624
31.1686-0.16750.53392.1148-1.00444.1377-0.0279-0.23580.13110.6613-0.0119-0.1276-0.30840.09270.03990.20850.0139-0.03160.5153-0.00380.4764-2.77522.67-89.415
44.03561.5393-2.02953.7122-1.4833.16240.34360.21330.67080.32720.0530.5899-0.5983-0.1417-0.39650.1697-0.02480.04650.54650.12250.7035-24.61613.674-17.403
53.55740.6011.17984.9064-0.62176.92070.1730.0590.1599-0.5402-0.19610.3068-1.5324-0.47420.02311.23290.0510.04950.5164-0.01580.5442-7.39134.212-47.848
61.1585-0.1904-0.07461.9857-0.98455.05480.1273-0.0124-0.1322-0.6442-0.2577-0.10110.17540.8230.13030.4121-0.09050.03420.70620.15990.63939.818.713-47.861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA-4 - 259
2X-RAY DIFFRACTION2ALLAAA281 - 475
3X-RAY DIFFRACTION3ALLAAA476 - 720
4X-RAY DIFFRACTION4ALLBBB0 - 259
5X-RAY DIFFRACTION5ALLBBB281 - 475
6X-RAY DIFFRACTION6ALLBBB476 - 717

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