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- PDB-1pn4: Crystal structure of 2-enoyl-CoA hydratase 2 domain of Candida tr... -

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Basic information

Entry
Database: PDB / ID: 1pn4
TitleCrystal structure of 2-enoyl-CoA hydratase 2 domain of Candida tropicalis multifunctional enzyme type 2 complexed with (3R)-hydroxydecanoyl-CoA.
ComponentsPeroxisomal hydratase-dehydrogenase-epimerase
KeywordsLYASE / Hot-Dog fold / Hydratase 2 motif / Oxyanion hole / Enzyme-product complex
Function / homology
Function and homology information


: / (3R)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / enoyl-CoA hydratase 2 / (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) 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 Thioesterase / Thiol Ester Dehydrase; Chain A / short chain dehydrogenase / HotDog domain superfamily / PKS_KR ...: / MFE-2 hydratase 2 N-terminal domain / : / MaoC-like dehydratase domain / MaoC like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / short chain dehydrogenase / HotDog domain superfamily / PKS_KR / 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
3R-HYDROXYDECANOYL-COENZYME A / Peroxisomal hydratase-dehydrogenase-epimerase
Similarity search - Component
Biological speciesCandida tropicalis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 1.3Jul 24, 2019Group: Advisory / Data collection / Refinement description
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification ..._diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name / _software.version
Revision 1.4Oct 27, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)128,64911
Polymers125,5874
Non-polymers3,0627
Water8,377465
1
A: Peroxisomal hydratase-dehydrogenase-epimerase
B: Peroxisomal hydratase-dehydrogenase-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9178
Polymers62,7932
Non-polymers2,1246
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint31 kcal/mol
Surface area22050 Å2
MethodPISA
2
C: Peroxisomal hydratase-dehydrogenase-epimerase
D: Peroxisomal hydratase-dehydrogenase-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7313
Polymers62,7932
Non-polymers9381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint6 kcal/mol
Surface area22400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.640, 151.290, 81.620
Angle α, β, γ (deg.)90.000, 90.500, 90.000
Int Tables number4
Space group name H-MP1211
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: 31396.729 Da / Num. of mol.: 4 / Fragment: 2-enoyl-CoA hydratase 2 domain / Mutation: E627M, H813Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida tropicalis (yeast) / Gene: FOX2 / Plasmid: pET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P22414, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Chemical ChemComp-HDC / 3R-HYDROXYDECANOYL-COENZYME A / 3R-HYDROXYDECANOYL-COA


Mass: 937.783 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C31H54N7O18P3S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 2000 MME, HEPES, trans-2-decenoyl-CoA, 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: X13 / Wavelength: 0.8019 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 9, 2002
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8019 Å / Relative weight: 1
ReflectionResolution: 2.35→35 Å / Num. all: 49040 / Num. obs: 47255 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 30.14 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.1
Reflection shellResolution: 2.35→2.5 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 4.53 / Num. unique all: 7461 / % possible all: 90.1

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Processing

Software
NameVersionClassification
REFMAC5.1refinement
XDSdata reduction
CNSrefinement
DENZOdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Subunit D of PDB ENTRY 1PN2

1pn2


Resolution: 2.35→35 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2363 -random
Rwork0.171 ---
obs0.174 47255 96.4 %-
all-49040 --
Refinement stepCycle: LAST / Resolution: 2.35→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8426 0 196 465 9087
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.014
X-RAY DIFFRACTIONr_angle_refined_deg1.55

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