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- PDB-6s6r: First crystal structure of parasitic PEX14 in complex with a frag... -

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Basic information

Entry
Database: PDB / ID: 6s6r
TitleFirst crystal structure of parasitic PEX14 in complex with a fragment molecule 1H-indole-7-carboxylic acid
ComponentsPeroxin 14
KeywordsSIGNALING PROTEIN / PEX14 / PPI / PEX14/PEX5 / Trypanosomes / FBDD
Function / homology
Function and homology information


glycosome membrane / protein import into peroxisome matrix, docking / protein targeting to vacuole / glycosome / post-transcriptional regulation of gene expression
Similarity search - Function
Peroxisome membrane anchor protein Pex14p, N-terminal / Peroxisomal membrane protein 14 / Pex14 N-terminal domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1~{H}-indole-7-carboxylic acid / Peroxisomal membrane protein PEX14
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58000903163 Å
AuthorsHassaan, E. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Commission Germany
CitationJournal: To Be Published
Title: First crystal structure of parasitic PEX14 in complex with a fragment molecule 1H-indole-7-carboxylic acid
Authors: Hassaan, E. / Heine, A. / Klebe, G.
History
DepositionJul 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxin 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5037
Polymers7,8831
Non-polymers6206
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-25 kcal/mol
Surface area4910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.306, 43.306, 80.942
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Peroxin 14


Mass: 7883.075 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PEX14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IEW2

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Non-polymers , 5 types, 48 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-KXQ / 1~{H}-indole-7-carboxylic acid


Mass: 161.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium sulphate, 50% PEG 8000, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.58→43.306 Å / Num. obs: 10965 / % possible obs: 98.4 % / Redundancy: 8.22 % / Biso Wilson estimate: 18.9861182796 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.074 / Net I/σ(I): 16.93
Reflection shellResolution: 1.58→1.588 Å / Num. unique obs: 10965

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHASERphasing
Cootmodel building
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58000903163→38.1843205977 Å / SU ML: 0.165444141052 / Cross valid method: FREE R-VALUE / σ(F): 1.37743608206 / Phase error: 23.5566591667
RfactorNum. reflection% reflection
Rfree0.234797926369 549 5.00912408759 %
Rwork0.187401299496 --
obs0.189694410404 10960 98.3488872936 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.7840108874 Å2
Refinement stepCycle: LAST / Resolution: 1.58000903163→38.1843205977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms534 0 37 42 613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00563253602607595
X-RAY DIFFRACTIONf_angle_d0.76842617257801
X-RAY DIFFRACTIONf_chiral_restr0.042625548323887
X-RAY DIFFRACTIONf_plane_restr0.00385084213775111
X-RAY DIFFRACTIONf_dihedral_angle_d14.2229275146361
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.58-1.7390.2764014330981320.166421004247250797.5600739372
1.739-1.99060.2256623382531350.166497961512255498.2462550237
1.9906-2.50790.2302933387461360.184629837648258698.6231884058
2.50790.2326442514911460.196058614765276498.9123045547

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