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- PDB-6hsj: Crystal structure of the zebrafish peroxisomal SCP2-thiolase (typ... -

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Basic information

Entry
Database: PDB / ID: 6hsj
TitleCrystal structure of the zebrafish peroxisomal SCP2-thiolase (type-1) in complex with CoA
Components(SCP2-thiolase (type- ...) x 2
KeywordsTRANSFERASE / thiolase fold / peroxisome / CoA binding
Function / homology
Function and homology information


alpha-linolenic acid (ALA) metabolism / Beta-oxidation of pristanoyl-CoA / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / propanoyl-CoA C-acyltransferase activity / propionyl-CoA C2-trimethyltridecanoyltransferase activity / acetyl-CoA C-myristoyltransferase / acetyl-CoA C-myristoyltransferase activity / propanoyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity ...alpha-linolenic acid (ALA) metabolism / Beta-oxidation of pristanoyl-CoA / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / propanoyl-CoA C-acyltransferase activity / propionyl-CoA C2-trimethyltridecanoyltransferase activity / acetyl-CoA C-myristoyltransferase / acetyl-CoA C-myristoyltransferase activity / propanoyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / intracellular cholesterol transport / phospholipid transport / peroxisome / lipid binding / mitochondrion
Similarity search - Function
SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain superfamily / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal ...SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain superfamily / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase-like
Similarity search - Domain/homology
ACETATE ION / COENZYME A / Sterol carrier protein 2
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.46 Å
AuthorsWierenga, R.K. / Kiema, T.R. / Thapa, C.J.
CitationJournal: Biochem. J. / Year: 2019
Title: The peroxisomal zebrafish SCP2-thiolase (type-1) is a weak transient dimer as revealed by crystal structures and native mass spectrometry.
Authors: Kiema, T.R. / Thapa, C.J. / Laitaoja, M. / Schmitz, W. / Maksimainen, M.M. / Fukao, T. / Rouvinen, J. / Janis, J. / Wierenga, R.K.
History
DepositionOct 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SCP2-thiolase (type-1)
B: SCP2-thiolase (type-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2967
Polymers90,2272
Non-polymers1,0705
Water9,764542
1
A: SCP2-thiolase (type-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2233
Polymers45,1051
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SCP2-thiolase (type-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0734
Polymers45,1211
Non-polymers9523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.960, 80.880, 96.470
Angle α, β, γ (deg.)90.00, 126.29, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-613-

HOH

21A-826-

HOH

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Components

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SCP2-thiolase (type- ... , 2 types, 2 molecules AB

#1: Protein SCP2-thiolase (type-1) / Sterol carrier protein 2a


Mass: 45105.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: scp2a, scp2 / Plasmid: pGS21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pGro7
References: UniProt: Q6P4V5, propanoyl-CoA C-acyltransferase
#2: Protein SCP2-thiolase (type-1) / Sterol carrier protein 2a


Mass: 45121.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: scp2a, scp2 / Plasmid: pGS21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pGro7
References: UniProt: Q6P4V5, propanoyl-CoA C-acyltransferase

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Non-polymers , 4 types, 547 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / 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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM HEPES, pH 7.0, 15 % PEG3350, 250 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9174 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9174 Å / Relative weight: 1
ReflectionResolution: 1.46→47.59 Å / Num. obs: 140415 / % possible obs: 98.2 % / Observed criterion σ(I): 2.9 / Redundancy: 7.5 % / Biso Wilson estimate: 18.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.04 / Net I/σ(I): 13.7
Reflection shellResolution: 1.46→1.56 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.85 / Num. unique obs: 25212 / CC1/2: 0.856 / Rpim(I) all: 0.19 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSNovember 3, 2014data reduction
XSCALENovember 3, 2014data scaling
REFMAC5.8.0232phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6HRV

6hrv


Resolution: 1.46→47.59 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.014 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.058 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17423 7005 5 %RANDOM
Rwork0.15648 ---
obs0.15736 133408 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.128 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0 Å20.35 Å2
2---0.25 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.46→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5872 0 68 542 6482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136151
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175662
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.6518326
X-RAY DIFFRACTIONr_angle_other_deg1.521.58413188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4215801
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56323.013302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.462151047
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6991533
X-RAY DIFFRACTIONr_chiral_restr0.0780.2788
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026971
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021241
X-RAY DIFFRACTIONr_nbd_refined0.2220.21199
X-RAY DIFFRACTIONr_nbd_other0.1780.25226
X-RAY DIFFRACTIONr_nbtor_refined0.170.23017
X-RAY DIFFRACTIONr_nbtor_other0.0830.22616
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2394
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0120.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1530.2116
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.242
X-RAY DIFFRACTIONr_mcbond_it1.1541.2683126
X-RAY DIFFRACTIONr_mcbond_other1.1531.2673123
X-RAY DIFFRACTIONr_mcangle_it1.8051.8973906
X-RAY DIFFRACTIONr_mcangle_other1.8051.8983907
X-RAY DIFFRACTIONr_scbond_it2.0671.6113025
X-RAY DIFFRACTIONr_scbond_other2.0671.6113025
X-RAY DIFFRACTIONr_scangle_it3.2362.3084404
X-RAY DIFFRACTIONr_scangle_other3.2362.3084405
X-RAY DIFFRACTIONr_long_range_B_refined4.42916.456918
X-RAY DIFFRACTIONr_long_range_B_other4.4316.4566919
LS refinement shellResolution: 1.46→1.498 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 524 -
Rwork0.335 9821 -
obs--98.31 %

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