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- PDB-5omo: CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-... -

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Basic information

Entry
Database: PDB / ID: 5omo
TitleCRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH WITH 3S-HYDROXY-DECANOYL-COA AND 3-KETO-DECANOYL-COA
ComponentsPeroxisomal bifunctional enzyme
KeywordsOXIDOREDUCTASE / 3S-HYDROXY-DECANOYL-COA / 3-KETO-DECANOYL-COA / MFE1 / BETA-OXIDATION / FATTY ACID / CROTONASE / 3-HYDROXYACYL-COA- DEHYDROGENASE / HYDRATASE
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
N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 - #50 / 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. / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 ...N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 - #50 / 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. / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / ClpP/crotonase-like domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
(S)-3-HYDROXYDECANOYL-COA / 3-KETO-DECANOYL-COA / Peroxisomal bifunctional enzyme
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.49 Å
AuthorsKasaragod, P. / Kiema, T.-R. / Schmitz, W. / Hiltunen, J.K. / Wierenga, R.K.
CitationJournal: Not Published
Title: CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE 1 (RPMFE1) COMPLEXED WITH 3S-HYDROXY-DECANOYL-COA AND 3- KETO-DECANOYL-COA
Authors: Kasaragod, P. / Balcha, G. / Sridhar, S. / Schmitz, W. / Kiema, T.-R. / Hiltunen, J.K. / Wierenga, R.K.
History
DepositionAug 1, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionSep 6, 2017ID: 5AAJ
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.2Mar 20, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_abbrev
Revision 1.3Jan 17, 2024Group: 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxisomal bifunctional enzyme
B: Peroxisomal bifunctional enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,51914
Polymers161,8632
Non-polymers3,65612
Water5,080282
1
A: Peroxisomal bifunctional enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2738
Polymers80,9311
Non-polymers2,3427
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxisomal bifunctional enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2456
Polymers80,9311
Non-polymers1,3145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.960, 125.080, 223.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 0 - 716 / Label seq-ID: 20 - 736

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Peroxisomal bifunctional enzyme / PBFE


Mass: 80931.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 3S-HYDROXY-DECANOYL-COA BOUND IN THE CROTONASE DOMAIN AND 3-KETO-DECANOYL-COA BOUND IN THE 3-HYDROXYACYL-COA-DEHYDROGENASE DOMAIN
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ehhadh / Plasmid: PET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P07896, enoyl-CoA hydratase, Delta3-Delta2-enoyl-CoA isomerase, 3-hydroxyacyl-CoA dehydrogenase

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Non-polymers , 5 types, 294 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-HSC / (S)-3-HYDROXYDECANOYL-COA


Mass: 933.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H50N7O18P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZOZ / 3-KETO-DECANOYL-COA


Mass: 935.767 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H52N7O18P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.81 Å3/Da / Density % sol: 56.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6
Details: 100MM MES PH 6.0, 150MM AMMONIUM SULPHATE, 15% W/V PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93928 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93928 Å / Relative weight: 1
ReflectionResolution: 2.49→47.9 Å / Num. obs: 64401 / % possible obs: 99.2 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.029 / Net I/σ(I): 16.6
Reflection shellResolution: 2.49→2.62 Å / Redundancy: 4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 8976 / Rpim(I) all: 0.158 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
REFMAC5.8.0158phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2X58

2x58


Resolution: 2.49→47.9 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.921 / SU B: 16.867 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.436 / ESU R Free: 0.253 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22831 3208 5 %RANDOM
Rwork0.19271 ---
obs0.19446 60931 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.337 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0 Å20 Å2
2---2.45 Å20 Å2
3---2.82 Å2
Refinement stepCycle: 1 / Resolution: 2.49→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11076 0 228 282 11586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911557
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211006
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.98115665
X-RAY DIFFRACTIONr_angle_other_deg1.0392.98525563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92451441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62223.035458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.153151934
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8591579
X-RAY DIFFRACTIONr_chiral_restr0.0820.21735
X-RAY DIFFRACTIONr_chiral_restr_other1.9750.216
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112635
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022271
X-RAY DIFFRACTIONr_nbd_refined0.19145920.2
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1440.221098
X-RAY DIFFRACTIONr_nbtor_refined0.1670.211122
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.211554
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2798
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.227
X-RAY DIFFRACTIONr_nbd_other0.2390.299
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.29
X-RAY DIFFRACTIONr_mcbond_it1.2393.3945770
X-RAY DIFFRACTIONr_mcbond_other1.243.3935769
X-RAY DIFFRACTIONr_mcangle_it2.1865.0877209
X-RAY DIFFRACTIONr_mcangle_other2.1865.0887210
X-RAY DIFFRACTIONr_scbond_it1.2983.675787
X-RAY DIFFRACTIONr_scbond_other1.2973.6665785
X-RAY DIFFRACTIONr_scangle_it2.2345.4418456
X-RAY DIFFRACTIONr_scangle_other2.2345.4418456
X-RAY DIFFRACTIONr_long_range_B_refined4.67339.67712671
X-RAY DIFFRACTIONr_long_range_B_other4.67339.68112672
X-RAY DIFFRACTIONr_ncsr_local_group_10.0870.0544904
Refine LS restraints NCS

Ens-ID: 1 / Number: 44904 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.487→2.552 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 217 -
Rwork0.254 4117 -
obs--92.06 %
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)
11.25130.64810.39770.76170.79930.96780.00460.0465-0.0894-0.00640.0053-0.0308-0.0309-0.0469-0.00990.04010.00990.02650.3007-0.00250.0923-71.6428.537-114.28
20.7525-1.11040.55121.99-0.37531.0616-0.0975-0.1177-0.24390.27680.28940.38240.1489-0.0941-0.19190.1510.00030.05260.26650.11460.1628-39.428-3.905-94.074
30.3806-0.16160.23410.6597-0.54711.6206-0.0563-0.00020.04930.15590.0011-0.0648-0.1061-0.06650.05520.11120.0143-0.01430.2817-0.00580.066-35.34922.356-88.997
41.42650.5156-1.15141.7393-0.35190.94910.14050.09690.33490.18420.11090.3893-0.1021-0.0133-0.25150.0695-0.01930.02570.30850.11450.1799-56.99813.811-17.402
50.192-0.4680.1521.445-0.3361.56340.0798-0.0835-0.122-0.30790.08320.2328-0.6887-0.0143-0.1630.5582-0.06130.03870.10550.06360.1034-39.80332.159-46.084
60.23690.1364-0.00110.8379-0.62981.98430.0727-0.2011-0.0037-0.3069-0.10780.05070.09930.24860.03510.2318-0.0551-0.01460.27470.04750.0234-22.7128.723-47.747
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 259
2X-RAY DIFFRACTION2A260 - 475
3X-RAY DIFFRACTION3A476 - 720
4X-RAY DIFFRACTION4B0 - 259
5X-RAY DIFFRACTION5B260 - 475
6X-RAY DIFFRACTION6B476 - 717

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