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- PDB-1s9c: Crystal structure analysis of the 2-enoyl-CoA hydratase 2 domain ... -

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Basic information

Entry
Database: PDB / ID: 1s9c
TitleCrystal structure analysis of the 2-enoyl-CoA hydratase 2 domain of human peroxisomal multifunctional enzyme type 2
ComponentsPeroxisomal multifunctional enzyme type 2
KeywordsLYASE / HOT-DOG FOLD / HYDRATASE 2 MOTIF / MULTIFUNCTIONAL
Function / homology
Function and homology information


3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase / 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity / very long-chain fatty-acyl-CoA metabolic process / Beta-oxidation of pristanoyl-CoA / TYSND1 cleaves peroxisomal proteins / medium-chain fatty-acyl-CoA metabolic process / (3R)-hydroxyacyl-CoA dehydrogenase (NAD+) activity / : / enoyl-CoA hydratase 2 / 3-hydroxyacyl-CoA dehydratase activity ...3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase / 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity / very long-chain fatty-acyl-CoA metabolic process / Beta-oxidation of pristanoyl-CoA / TYSND1 cleaves peroxisomal proteins / medium-chain fatty-acyl-CoA metabolic process / (3R)-hydroxyacyl-CoA dehydrogenase (NAD+) activity / : / enoyl-CoA hydratase 2 / 3-hydroxyacyl-CoA dehydratase activity / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / alpha-linolenic acid (ALA) metabolism / Beta-oxidation of very long chain fatty acids / very long-chain fatty acid metabolic process / 3-hydroxyacyl-CoA dehydrogenase activity / Sertoli cell development / estradiol 17-beta-dehydrogenase [NAD(P)] activity / enoyl-CoA hydratase activity / peroxisomal membrane / estrogen metabolic process / fatty acid beta-oxidation / peroxisomal matrix / androgen metabolic process / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / isomerase activity / Peroxisomal protein import / osteoblast differentiation / peroxisome / protein homodimerization activity / membrane / cytosol
Similarity search - Function
SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain superfamily / MaoC-like dehydratase domain / MaoC like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / short chain dehydrogenase / PKS_KR / HotDog domain superfamily ...SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain superfamily / 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 multifunctional enzyme type 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKoski, M.K. / Haapalainen, A.M. / Hiltunen, J.K. / Glumoff, T.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of 2-enoyl-CoA hydratase 2 from human peroxisomal multifunctional enzyme type 2.
Authors: Koski, M.K. / Haapalainen, A.M. / Hiltunen, J.K.
History
DepositionFeb 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: 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 / Category: database_2 / diffrn_source / struct_ref_seq_dif
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_ref_seq_dif.details
Revision 1.4Aug 23, 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

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Assembly

Deposited unit
A: Peroxisomal multifunctional enzyme type 2
B: Peroxisomal multifunctional enzyme type 2
C: Peroxisomal multifunctional enzyme type 2
D: Peroxisomal multifunctional enzyme type 2
E: Peroxisomal multifunctional enzyme type 2
F: Peroxisomal multifunctional enzyme type 2
G: Peroxisomal multifunctional enzyme type 2
H: Peroxisomal multifunctional enzyme type 2
I: Peroxisomal multifunctional enzyme type 2
J: Peroxisomal multifunctional enzyme type 2
K: Peroxisomal multifunctional enzyme type 2
L: Peroxisomal multifunctional enzyme type 2


Theoretical massNumber of molelcules
Total (without water)386,83212
Polymers386,83212
Non-polymers00
Water3,243180
1
A: Peroxisomal multifunctional enzyme type 2
B: Peroxisomal multifunctional enzyme type 2


Theoretical massNumber of molelcules
Total (without water)64,4722
Polymers64,4722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-17 kcal/mol
Surface area21300 Å2
MethodPISA
2
C: Peroxisomal multifunctional enzyme type 2
D: Peroxisomal multifunctional enzyme type 2


Theoretical massNumber of molelcules
Total (without water)64,4722
Polymers64,4722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-17 kcal/mol
Surface area22680 Å2
MethodPISA
3
E: Peroxisomal multifunctional enzyme type 2
F: Peroxisomal multifunctional enzyme type 2


Theoretical massNumber of molelcules
Total (without water)64,4722
Polymers64,4722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-19 kcal/mol
Surface area22370 Å2
MethodPISA
4
G: Peroxisomal multifunctional enzyme type 2
H: Peroxisomal multifunctional enzyme type 2


Theoretical massNumber of molelcules
Total (without water)64,4722
Polymers64,4722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-17 kcal/mol
Surface area22120 Å2
MethodPISA
5
I: Peroxisomal multifunctional enzyme type 2
J: Peroxisomal multifunctional enzyme type 2


Theoretical massNumber of molelcules
Total (without water)64,4722
Polymers64,4722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-18 kcal/mol
Surface area22540 Å2
MethodPISA
6
K: Peroxisomal multifunctional enzyme type 2
L: Peroxisomal multifunctional enzyme type 2


Theoretical massNumber of molelcules
Total (without water)64,4722
Polymers64,4722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-19 kcal/mol
Surface area21950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.295, 105.431, 206.944
Angle α, β, γ (deg.)90.00, 103.37, 90.00
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 multifunctional enzyme type 2 / MFE-2 / D-bifunctional protein / DBP / 17-beta-hydroxysteroid dehydrogenase 4 / 17-beta-HSD 4


Mass: 32235.971 Da / Num. of mol.: 12 / Fragment: 2-enoyl-coenzyme A hydratase 2 domain / Mutation: S318M, T319A, I559V, T615L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B4, EDH17B4 / Plasmid: pET3D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P51659, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.7 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 10000, HEPES, MnCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG X1110.909
SYNCHROTRONEMBL/DESY, HAMBURG X1320.8019
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEJun 28, 1999
MARRESEARCH2CCDAug 9, 2002
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9091
20.80191
ReflectionResolution: 2.99→30 Å / Num. all: 82559 / Num. obs: 77386 / % possible obs: 93.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 43.9 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 14.2
Reflection shellResolution: 2.99→3.2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4.6 / Num. unique all: 5253 / % possible all: 70.2

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Processing

Software
NameClassification
DENZOdata reduction
XDSdata reduction
CNSrefinement
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PN2

1pn2


Resolution: 3→30 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2646 3870 -RANDOM
Rwork0.2285 ---
all-82559 --
obs-77386 93.7 %-
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24344 0 0 180 24524
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0094
X-RAY DIFFRACTIONc_angle_deg1.4094

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