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- PDB-6hrv: Crystal structure of the zebrafish peroxisomal SCP2-thiolase (type-1) -

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Basic information

Entry
Database: PDB / ID: 6hrv
TitleCrystal structure of the zebrafish peroxisomal SCP2-thiolase (type-1)
Components(SCP2-thiolase (type-1)) x 2
KeywordsTRANSFERASE / Fatty acid metabolism / bile acid biosynthesis / peroxisomal beta-oxidation / thiolytic cleavage
Function / homology
Function and homology information


Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / alpha-linolenic acid (ALA) metabolism / Beta-oxidation of pristanoyl-CoA / acetyl-CoA C-myristoyltransferase / acetyl-CoA C-myristoyltransferase activity / propanoyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / lipid transport / lipid metabolic process ...Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / alpha-linolenic acid (ALA) metabolism / Beta-oxidation of pristanoyl-CoA / acetyl-CoA C-myristoyltransferase / acetyl-CoA C-myristoyltransferase activity / propanoyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / lipid transport / lipid metabolic process / peroxisome / lipid binding
Similarity search - Function
: / Thiolase C-terminal domain-like / SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain superfamily / Thiolase, conserved site / Thiolases signature 2. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, C-terminal domain ...: / Thiolase C-terminal domain-like / SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain superfamily / Thiolase, conserved site / Thiolases signature 2. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase-like
Similarity search - Domain/homology
ACETATE ION / Sterol carrier protein 2
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
DepositionSep 28, 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 1.2Feb 13, 2019Group: Data collection / Database references
Category: citation_author / database_PDB_rev ...citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation_author.identifier_ORCID
Revision 1.3Jan 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)91,7774
Polymers91,6262
Non-polymers1512
Water4,360242
1
A: SCP2-thiolase (type-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9563
Polymers45,8051
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-2 kcal/mol
Surface area15380 Å2
MethodPISA
2
B: SCP2-thiolase (type-1)

B: SCP2-thiolase (type-1)


Theoretical massNumber of molelcules
Total (without water)91,6422
Polymers91,6422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5110 Å2
ΔGint-15 kcal/mol
Surface area25130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.160, 81.940, 96.810
Angle α, β, γ (deg.)90.00, 125.81, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-617-

HOH

21A-704-

HOH

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Components

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


Mass: 45805.102 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: 45821.102 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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 295 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 100 mM HEPES, pH 6.4, 18% PEG3350, 250 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.95→29.64 Å / Num. obs: 60799 / % possible obs: 98.4 % / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Biso Wilson estimate: 34.8 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.03 / Rsym value: 0.05 / Net I/σ(I): 15.7
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.94 / Num. unique obs: 8507 / CC1/2: 0.87 / Rpim(I) all: 0.22 / Rsym value: 0.42 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSJuly 4, 2012data reduction
XSCALENovember 3, 2014data scaling
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZBG

3zbg


Resolution: 1.95→29.64 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.693 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.134 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20702 3040 5 %RANDOM
Rwork0.16943 ---
obs0.17131 57744 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.182 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20.97 Å2
2--0.22 Å20 Å2
3----0.88 Å2
Refinement stepCycle: 1 / Resolution: 1.95→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5860 0 10 242 6112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195980
X-RAY DIFFRACTIONr_bond_other_d0.0020.025503
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9618069
X-RAY DIFFRACTIONr_angle_other_deg0.95312793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0885767
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81524.618262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.749151009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6751531
X-RAY DIFFRACTIONr_chiral_restr0.080.2877
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216749
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021178
X-RAY DIFFRACTIONr_nbd_refined0.2090.2
X-RAY DIFFRACTIONr_nbd_other0.1540.2
X-RAY DIFFRACTIONr_nbtor_refined0.1710.25862
X-RAY DIFFRACTIONr_nbtor_other0.0760.25730
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2558
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0480.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1060.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.150.2115
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.230
X-RAY DIFFRACTIONr_mcbond_it2.0313.2513084
X-RAY DIFFRACTIONr_mcbond_other2.0323.253082
X-RAY DIFFRACTIONr_mcangle_it2.8014.8593845
X-RAY DIFFRACTIONr_mcangle_other2.84.863846
X-RAY DIFFRACTIONr_scbond_it2.8223.622896
X-RAY DIFFRACTIONr_scbond_other2.8223.6212897
X-RAY DIFFRACTIONr_scangle_it4.3015.2774224
X-RAY DIFFRACTIONr_scangle_other4.35.2774225
X-RAY DIFFRACTIONr_long_range_B_refined5.21238.6926588
X-RAY DIFFRACTIONr_long_range_B_other5.21238.6956589
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 225 -
Rwork0.24 4266 -
obs--99.73 %

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