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- PDB-2et6: (3R)-Hydroxyacyl-CoA Dehydrogenase Domain of Candida tropicalis P... -

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Basic information

Entry
Database: PDB / ID: 2et6
Title(3R)-Hydroxyacyl-CoA Dehydrogenase Domain of Candida tropicalis Peroxisomal Multifunctional Enzyme Type 2
Components(3R)-hydroxyacyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / MFE-2 / beta-oxidation / peroxisome / SDR
Function / homology
Function and homology information


: / (3R)-hydroxyacyl-CoA dehydrogenase (NAD+) activity / enoyl-CoA hydratase 2 / 3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity / fatty acid beta-oxidation / isomerase activity / peroxisome
Similarity search - Function
: / MFE-2 hydratase 2 N-terminal domain / : / MaoC-like dehydratase domain / MaoC like domain / HotDog domain superfamily / short chain dehydrogenase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. ...: / MFE-2 hydratase 2 N-terminal domain / : / MaoC-like dehydratase domain / MaoC like domain / HotDog domain superfamily / short chain dehydrogenase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peroxisomal hydratase-dehydrogenase-epimerase
Similarity search - Component
Biological speciesCandida tropicalis (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsYlianttila, M.S. / Hiltunen, J.K. / Glumoff, T.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of Yeast Peroxisomal Multifunctional Enzyme: Structural Basis for Substrate Specificity of (3R)-hydroxyacyl-CoA Dehydrogenase Units.
Authors: Ylianttila, M.S. / Pursiainen, N.V. / Haapalainen, A.M. / Juffer, A.H. / Poirier, Y. / Hiltunen, J.K. / Glumoff, T.
History
DepositionOct 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (3R)-hydroxyacyl-CoA dehydrogenase


Theoretical massNumber of molelcules
Total (without water)65,5571
Polymers65,5571
Non-polymers00
Water6,215345
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.895, 78.340, 95.445
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains only one biological unit that is one monomer.

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Components

#1: Protein (3R)-hydroxyacyl-CoA dehydrogenase / Peroxisomal hydratase-dehydrogenase-epimerase / HDE / Multifunctional beta-oxidation protein / MFP


Mass: 65557.094 Da / Num. of mol.: 1 / Mutation: T506S, F508M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida tropicalis (yeast) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus(DE3)-RIL
References: UniProt: P22414, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.13 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 30% PEG 4000, 0.1 M sodium acetate pH 4.2, 0.2 M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 23, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.22→20 Å / Num. all: 28316 / Num. obs: 27948 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Net I/σ(I): 12.56
Reflection shellResolution: 2.22→2.36 Å / Mean I/σ(I) obs: 4.74 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY IGZ6

Resolution: 2.22→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.876 / SU B: 8.344 / SU ML: 0.201 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.359 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25183 1355 4.9 %RANDOM
Rwork0.19515 ---
all0.19784 27928 --
obs0.19784 26573 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.514 Å2
Baniso -1Baniso -2Baniso -3
1--4.52 Å20 Å20 Å2
2---1.34 Å20 Å2
3---5.86 Å2
Refinement stepCycle: LAST / Resolution: 2.22→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4465 0 0 345 4810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224554
X-RAY DIFFRACTIONr_bond_other_d0.0030.024111
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.9476167
X-RAY DIFFRACTIONr_angle_other_deg0.78939596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8715579
X-RAY DIFFRACTIONr_chiral_restr0.0740.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025094
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02889
X-RAY DIFFRACTIONr_nbd_refined0.1960.21045
X-RAY DIFFRACTIONr_nbd_other0.2260.24938
X-RAY DIFFRACTIONr_nbtor_other0.0820.22705
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2292
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1360.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.212
X-RAY DIFFRACTIONr_mcbond_it1.4932877
X-RAY DIFFRACTIONr_mcangle_it2.09944611
X-RAY DIFFRACTIONr_scbond_it1.37431677
X-RAY DIFFRACTIONr_scangle_it1.90241556
LS refinement shellResolution: 2.22→2.341 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.299 200 -
Rwork0.252 3667 -
obs-3667 96.4 %
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)
11.5030.2059-0.33070.2167-0.01190.35840.03110.0210.02810.0301-0.0051-0.0417-0.00060.02-0.02590.47550.01320.00590.3843-0.00930.02639.17238.30616.435
21.82620.1506-0.07280.55910.03630.42010.02560.04510.06890.0001-0.00710.02580.0037-0.057-0.01850.47620.00680.01160.3814-0.00470.018618.69439.84219.265
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 313
2X-RAY DIFFRACTION2A314 - 592

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