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- PDB-1pn2: Crystal structure analysis of the selenomethionine labelled 2-eno... -

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Basic information

Entry
Database: PDB / ID: 1pn2
TitleCrystal structure analysis of the selenomethionine labelled 2-enoyl-CoA hydratase 2 domain of Candida tropicalis multifunctional enzyme type 2
ComponentsPeroxisomal hydratase-dehydrogenase-epimerase
KeywordsLYASE / HOT-DOG FOLD / HYDRATASE 2 MOTIF
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
MaoC-like dehydratase domain / MaoC like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / short chain dehydrogenase / PKS_KR / HotDog domain superfamily / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR ...MaoC-like dehydratase domain / MaoC like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / short chain dehydrogenase / PKS_KR / HotDog domain superfamily / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Peroxisomal hydratase-dehydrogenase-epimerase
Similarity search - Component
Biological speciesCandida tropicalis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsKoski, M.K. / Haapalainen, A.M. / Hiltunen, J.K. / Glumoff, T.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: A Two-domain Structure of One Subunit Explains Unique Features of Eukaryotic Hydratase 2.
Authors: Koski, M.K. / Haapalainen, A.M. / Hiltunen, J.K. / Glumoff, T.
History
DepositionJun 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxisomal hydratase-dehydrogenase-epimerase
B: Peroxisomal hydratase-dehydrogenase-epimerase
C: Peroxisomal hydratase-dehydrogenase-epimerase
D: Peroxisomal hydratase-dehydrogenase-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,6889
Polymers126,3774
Non-polymers3105
Water14,232790
1
A: Peroxisomal hydratase-dehydrogenase-epimerase
B: Peroxisomal hydratase-dehydrogenase-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2513
Polymers63,1892
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Peroxisomal hydratase-dehydrogenase-epimerase
D: Peroxisomal hydratase-dehydrogenase-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4376
Polymers63,1892
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint8 kcal/mol
Surface area23840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.800, 60.648, 131.117
Angle α, β, γ (deg.)90.000, 94.571, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-1012-

HOH

DetailsThe asymmetric unit is complete and the biological unit is a dimer.

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Components

#1: Protein
Peroxisomal hydratase-dehydrogenase-epimerase / HDE / Multifunctional beta-oxidation protein / MFP


Mass: 31594.322 Da / Num. of mol.: 4 / Fragment: 2-enoyl-coenzyme A hydratase 2 domain / Mutation: E627(MSE)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida tropicalis (yeast) / Gene: FOX2 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P22414, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 790 / 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: 2.8 Å3/Da / Density % sol: 56.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, HEPES , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.979852, 0.980322, 0.961123
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 30, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9798521
20.9803221
30.9611231
ReflectionResolution: 1.95→30 Å / Num. all: 102519 / Num. obs: 97595 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 17.3
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 1.73 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 3.05 / Num. unique all: 8811 / % possible all: 85.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
XDSdata reduction
SOLVEphasing
REFMAC5.1refinement
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.95→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 9760 -RANDOM
Rwork0.179 ---
obs0.182 97595 95.2 %-
all-102519 --
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8564 0 20 790 9374
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.015
X-RAY DIFFRACTIONr_angle_refined_deg1.451

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