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- PDB-6z5f: CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-... -

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Basic information

Entry
Database: PDB / ID: 6z5f
TitleCRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH 3-KETODECANOYL-COA AND OXIDISED NICOTINAMIDE ADENINE DINUCLEOTIDE
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: 2.25 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 26, 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 / Other / Category: pdbx_database_status / pdbx_related_exp_data_set
Item: _pdbx_database_status.process_site / _pdbx_database_status.status_code_sf
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)166,37311
Polymers161,8632
Non-polymers4,5109
Water2,936163
1
AAA: Peroxisomal bifunctional enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7477
Polymers80,9311
Non-polymers2,8156
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Peroxisomal bifunctional enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6274
Polymers80,9311
Non-polymers1,6953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.155, 125.977, 223.527
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, 172 molecules

#2: Chemical ChemComp-ZOZ / 3-KETO-DECANOYL-COA


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 163 / 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: 100mM MES, pH 6; 15%w/v PEG 4000; 150.91mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 28, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.25→62.63 Å / Num. obs: 88285 / % possible obs: 100 % / Redundancy: 6.45 % / Biso Wilson estimate: 51.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.042 / Net I/σ(I): 8.4
Reflection shellResolution: 2.25→2.29 Å / Rmerge(I) obs: 1.388 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4441 / CC1/2: 0.671 / Rpim(I) all: 0.587

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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: 2.25→62.63 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / Cross valid method: FREE R-VALUE / ESU R: 0.265 / ESU R Free: 0.209
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2464 4428 5.021 %
Rwork0.2093 83761 -
all0.211 --
obs-88189 99.931 %
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--1.711 Å2-0 Å20 Å2
2--2.337 Å2-0 Å2
3----0.626 Å2
Refinement stepCycle: LAST / Resolution: 2.25→62.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11006 0 290 163 11459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01211612
X-RAY DIFFRACTIONr_angle_refined_deg1.2051.64215768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29351442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6221.08537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.171151939
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.461580
X-RAY DIFFRACTIONr_chiral_restr0.10.21487
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028751
X-RAY DIFFRACTIONr_nbd_refined0.2190.25154
X-RAY DIFFRACTIONr_nbtor_refined0.310.27749
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2389
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2030.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2510.26
X-RAY DIFFRACTIONr_mcbond_it1.2263.6185738
X-RAY DIFFRACTIONr_mcangle_it2.0855.4237169
X-RAY DIFFRACTIONr_scbond_it1.7944.1745874
X-RAY DIFFRACTIONr_scangle_it2.9476.2078592
X-RAY DIFFRACTIONr_lrange_it7.52550.96817001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.3080.4462850.4086088X-RAY DIFFRACTION99.7808
2.308-2.3720.3543200.3275967X-RAY DIFFRACTION100
2.372-2.440.2882930.2885843X-RAY DIFFRACTION99.9837
2.44-2.5150.3122750.2755673X-RAY DIFFRACTION100
2.515-2.5980.2973010.2775459X-RAY DIFFRACTION100
2.598-2.6890.3062780.2555286X-RAY DIFFRACTION100
2.689-2.7910.3052850.2525120X-RAY DIFFRACTION100
2.791-2.9050.2462730.2264923X-RAY DIFFRACTION100
2.905-3.0340.282520.2254731X-RAY DIFFRACTION100
3.034-3.1820.2782570.2234508X-RAY DIFFRACTION100
3.182-3.3540.2542350.2124332X-RAY DIFFRACTION99.9781
3.354-3.5570.2452220.2074090X-RAY DIFFRACTION100
3.557-3.8030.2482170.2013874X-RAY DIFFRACTION100
3.803-4.1070.1961950.1873611X-RAY DIFFRACTION99.9737
4.107-4.4990.2121570.1713341X-RAY DIFFRACTION99.9714
4.499-5.030.1861720.1543039X-RAY DIFFRACTION100
5.03-5.8080.2541470.1962679X-RAY DIFFRACTION99.9646
5.808-7.1120.241300.2142294X-RAY DIFFRACTION99.8764
7.112-10.0520.189790.1451835X-RAY DIFFRACTION99.9478
10.052-62.60.251550.2131069X-RAY DIFFRACTION98.8566
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)
12.9980.79680.85681.82290.79681.9783-0.00250.257-0.205-0.1275-0.0221-0.0140.0738-0.00120.02470.02470.01190.0290.04170.02650.2381-103.5049.208-113.921
22.3723-0.90140.30064.1499-0.20735.5337-0.1282-0.4347-0.76310.58490.22470.36580.8952-0.3305-0.09660.3845-0.02930.03650.12110.15450.4981-71.32-5.253-93.284
31.6402-0.02090.48922.5373-0.68024.0817-0.0139-0.34970.19910.7147-0.0302-0.1358-0.28550.04690.04420.204-0.008-0.02840.09210.00630.2353-68.28122.841-88.829
44.00270.6164-2.01472.9493-0.63882.74990.23880.26710.78370.25830.15970.6513-0.5345-0.3093-0.39850.30330.05170.07970.21180.16660.6711-88.22513.938-17.827
53.2032-0.52491.32923.3612-0.55216.28770.19930.05180.0487-0.1939-0.08450.3939-1.0729-0.4167-0.11470.96640.01430.09150.1164-0.0440.4231-71.5433.882-47.217
61.37580.1176-0.05941.8331-0.87685.47150.1081-0.0025-0.129-0.5447-0.1675-0.08060.19080.6560.05950.3918-0.03730.03480.1920.07060.3386-55.0688.427-47.808
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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