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- PDB-1ikt: LIGANDED STEROL CARRIER PROTEIN TYPE 2 (SCP-2) LIKE DOMAIN OF HUM... -

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Basic information

Entry
Database: PDB / ID: 1ikt
TitleLIGANDED STEROL CARRIER PROTEIN TYPE 2 (SCP-2) LIKE DOMAIN OF HUMAN MULTIFUNCTIONAL ENZYME TYPE 2 (MFE-2)
ComponentsESTRADIOL 17 BETA-DEHYDROGENASE 4
KeywordsOXIDOREDUCTASE / alfa-beta fold / protein-Triton X-100 complex / hydrophobic tunnel / exposed peroxisomal targeting signal type 1 (PTS1)
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)-3-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)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / enoyl-CoA hydratase 2 / 3-hydroxyacyl-CoA dehydratase activity / alpha-linolenic acid (ALA) metabolism / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / Beta-oxidation of very long chain fatty acids / fatty acid beta-oxidation using acyl-CoA oxidase / fatty acid derivative biosynthetic process / alpha-linolenic acid metabolic process / very long-chain fatty acid metabolic process / unsaturated fatty acid biosynthetic process / (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / Sertoli cell development / enoyl-CoA hydratase activity / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / peroxisomal membrane / estrogen metabolic process / long-chain fatty acid biosynthetic 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
: / MFE-2 hydratase 2 N-terminal domain / : / SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / MaoC-like dehydratase domain / MaoC like domain ...: / MFE-2 hydratase 2 N-terminal domain / : / SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / MaoC-like dehydratase domain / MaoC like domain / 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 / 2-Layer Sandwich / 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: 1.75 Å
AuthorsHaapalainen, A.M. / van Aalten, D.M.F. / Glumoff, T.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of the liganded SCP-2-like domain of human peroxisomal multifunctional enzyme type 2 at 1.75 A resolution.
Authors: Haapalainen, A.M. / van Aalten, D.M. / Merilainen, G. / Jalonen, J.E. / Pirila, P. / Wierenga, R.K. / Hiltunen, J.K. / Glumoff, T.
History
DepositionMay 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / 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_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

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Assembly

Deposited unit
A: ESTRADIOL 17 BETA-DEHYDROGENASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1034
Polymers13,2641
Non-polymers8393
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.474, 50.028, 62.725
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ESTRADIOL 17 BETA-DEHYDROGENASE 4 / HUMAN MULTIFUNCTIONAL ENZYME TYPE 2 / MFE-2


Mass: 13264.468 Da / Num. of mol.: 1 / Fragment: C-terminal domain, Residues 618-736
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B4 / Plasmid: pET3D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS
References: UniProt: P51659, 17beta-estradiol 17-dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-OXN / OXTOXYNOL-10 / ALPHA-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENYL]-OMEGA-HYDROXYPOLY(OXY-1,2-ETHANEDIYL) / TRITON X-100


Mass: 646.849 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H62O11 / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium sulfate, sodium chloride, Triton X-100, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.30 Mammonium sulfate1reservoir
2100 mMcitric acid1reservoirpH5.6
3200 mM1reservoirNaCl
42.7 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9785 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 16, 2000 / Details: Premirror, Bent mirror monochromator
RadiationMonochromator: Double crystal focussing monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. all: 11659 / Num. obs: 11659 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.031 / Rsym value: 0.031 / Net I/σ(I): 27.7
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1132 / Rsym value: 0.259 / % possible all: 97.1
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 97.1 % / Num. unique obs: 1132

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1C44

1c44


Resolution: 1.75→18 Å / Isotropic thermal model: isotropic / Cross valid method: R-free / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 495 4.2 %random
Rwork0.192 ---
all-11554 --
obs-11554 --
Displacement parametersBiso mean: 30.3 Å2
Refinement stepCycle: LAST / Resolution: 1.75→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms898 0 35 126 1059
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.509
X-RAY DIFFRACTIONc_mcbond_it1.507
X-RAY DIFFRACTIONc_scbond_it2.087
LS refinement shellResolution: 1.75→1.82 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.278 60 4.7 %
Rwork0.225 1196 -
obs--95.2 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 18 Å / σ(F): 0 / % reflection Rfree: 4.2 % / Rfactor obs: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.3 Å2
LS refinement shell
*PLUS
Rfactor Rfree: 0.278 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.225

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