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- PDB-3w15: Structure of peroxisomal targeting signal 2 (PTS2) of Saccharomyc... -

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Basic information

Entry
Database: PDB / ID: 3w15
TitleStructure of peroxisomal targeting signal 2 (PTS2) of Saccharomyces cerevisiae 3-ketoacyl-CoA thiolase in complex with Pex7p and Pex21p
Components
  • 3-ketoacyl-CoA thiolase, peroxisomal, Maltose-binding periplasmic protein
  • Peroxisomal membrane protein PEX21
  • Peroxisomal targeting signal 2 receptor
KeywordsPROTEIN TRANSPORT / beta-propeller / targeting signal recognition / cytosol / peroxisome
Function / homology
Function and homology information


peroxisome matrix targeting signal-2 binding / alpha-linolenic acid (ALA) metabolism / Beta-oxidation of very long chain fatty acids / positive regulation of binding / protein import into peroxisome matrix / acetyl-CoA C-acyltransferase / protein import into peroxisome matrix, docking / Peroxisomal protein import / acetyl-CoA C-acyltransferase activity / phenylacetate catabolic process ...peroxisome matrix targeting signal-2 binding / alpha-linolenic acid (ALA) metabolism / Beta-oxidation of very long chain fatty acids / positive regulation of binding / protein import into peroxisome matrix / acetyl-CoA C-acyltransferase / protein import into peroxisome matrix, docking / Peroxisomal protein import / acetyl-CoA C-acyltransferase activity / phenylacetate catabolic process / peroxisomal membrane / detection of maltose stimulus / maltose transport complex / fatty acid beta-oxidation / carbohydrate transport / peroxisomal matrix / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / Neutrophil degranulation / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / mitochondrial intermembrane space / peroxisome / outer membrane-bounded periplasmic space / periplasmic space / mRNA binding / DNA damage response / membrane / cytoplasm / cytosol
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #230 / : / Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Thiolase ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #230 / : / Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / YVTN repeat-like/Quinoprotein amine dehydrogenase / Bacterial extracellular solute-binding protein / 7 Propeller / Methylamine Dehydrogenase; Chain H / Bacterial extracellular solute-binding protein / Thiolase-like / Periplasmic binding protein-like II / Helix non-globular / Special / D-Maltodextrin-Binding Protein; domain 2 / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Maltose/maltodextrin-binding periplasmic protein / 3-ketoacyl-CoA thiolase, peroxisomal / Peroxisomal targeting signal 2 receptor / Peroxisomal membrane protein PEX21
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsPan, D. / Nakatsu, T. / Kato, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Crystal structure of peroxisomal targeting signal-2 bound to its receptor complex Pex7p-Pex21p
Authors: Pan, D. / Nakatsu, T. / Kato, H.
History
DepositionNov 6, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisomal targeting signal 2 receptor
B: Peroxisomal membrane protein PEX21
C: 3-ketoacyl-CoA thiolase, peroxisomal, Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,13118
Polymers95,4283
Non-polymers70415
Water10,142563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-60 kcal/mol
Surface area32300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.890, 52.750, 97.570
Angle α, β, γ (deg.)90.000, 106.590, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Peroxisomal targeting signal 2 receptor / PTS2 receptor / Peroxin-7 / Peroxisome import protein PAS7


Mass: 41525.809 Da / Num. of mol.: 1 / Mutation: del(E257-V265)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: PEX7 / Plasmid: pPICZA / Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1163 / References: UniProt: P39108
#2: Protein Peroxisomal membrane protein PEX21 / Peroxin-21


Mass: 11004.136 Da / Num. of mol.: 1 / Fragment: UNP residue 190-288
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: PEX21 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P50091
#3: Protein 3-ketoacyl-CoA thiolase, peroxisomal, Maltose-binding periplasmic protein / FOX3 / MBP / MMBP / Maltodextrin-binding protein


Mass: 42897.555 Da / Num. of mol.: 1 / Fragment: UNP residue 1-15, UNP residues 27-396
Source method: isolated from a genetically manipulated source
Details: chimera of 3-ketoacyl-CoA thiolase, peroxisomal, Maltose-binding periplasmic protein
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Escherichia coli (E. coli)
Strain: S288c, K12 / Gene: FOX3 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27796, UniProt: P0AEX9

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Non-polymers , 3 types, 578 molecules

#4: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: NO3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / 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: 2.04 Å3/Da / Density % sol: 39.67 % / Mosaicity: 0.879 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 25% PEG2000, 0.3M Magnesium nitrate, 0.1M Tris-HCl, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→32.24 Å / Num. all: 71460 / Num. obs: 71460 / % possible obs: 99.77 % / Redundancy: 7.12 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 20.2139
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) allNum. measured allNum. unique all% possible all
1.8-1.96.850.23.77707021031999.24
1.9-2.017.140.135.5569944979799.9
2.01-2.157.150.17.5466030923199.95
2.15-2.327.170.08962085866199.99
2.32-2.557.20.079.69570597930100
2.55-2.857.220.0511.68519657198100
2.85-3.297.230.069.61462086391100
3.29-4.027.210.087.5338892539699.99
4.02-5.697.150.0510.730213422699.96
5.69-32.246.80.0316.9615719231197.21

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 52.08 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å32.01 Å
Translation2.5 Å32.01 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALACCP4_3.3.15data scaling
PHASER2.1.4phasing
REFMACrefmac_5.5.0102refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→32.2 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.206 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.576 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 3618 5.1 %RANDOM
Rwork0.1891 ---
obs0.1908 71446 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.01 Å2 / Biso mean: 21.4142 Å2 / Biso min: 7.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å2-0.26 Å2
2--1.67 Å2-0 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6167 0 42 563 6772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226397
X-RAY DIFFRACTIONr_angle_refined_deg1.0631.9468692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.635811
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16725.222293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.372151037
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1951522
X-RAY DIFFRACTIONr_chiral_restr0.0760.2958
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214916
X-RAY DIFFRACTIONr_mcbond_it0.5321.54015
X-RAY DIFFRACTIONr_mcangle_it0.99726400
X-RAY DIFFRACTIONr_scbond_it1.41532382
X-RAY DIFFRACTIONr_scangle_it2.3954.52281
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8470.2822720.234880523498.433
1.847-1.8970.2552510.2134881514499.767
1.897-1.9520.2492420.1964715496799.799
1.952-2.0120.2392460.1934557481299.813
2.012-2.0770.2282220.194484471299.873
2.077-2.150.2282260.1914277450699.933
2.15-2.2310.2052110.1844161437499.954
2.231-2.3210.2232090.18640684277100
2.321-2.4240.2262100.19338184028100
2.424-2.5420.2262110.19836723883100
2.542-2.6780.251930.20235003693100
2.678-2.8390.2391690.20233063475100
2.839-3.0340.2361840.20131353319100
3.034-3.2740.2171800.1929223102100
3.274-3.5830.1931360.17526892825100
3.583-40.2091140.1642460257599.961
4-4.6070.1931160.1612166228499.912
4.607-5.6140.2211020.1771859196299.949
5.614-7.8210.251760.2011456153599.805
7.821-32.20.187480.21282293193.448

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