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- PDB-5oml: Crystal structure of Trypanosoma Brucei PEX14 N-terminal domain i... -

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Basic information

Entry
Database: PDB / ID: 5oml
TitleCrystal structure of Trypanosoma Brucei PEX14 N-terminal domain in complex with small molecules to investigate the water envelope
ComponentsPeroxin 14
KeywordsSIGNALING PROTEIN / Peroxisomal Translocation / PPI inhibition / Protein-Inhibitor Complex
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
Chem-9YB / BETA-MERCAPTOETHANOL / Peroxisomal membrane protein PEX14
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRatkova, E.L. / Dawidowski, M. / Napolitano, V. / Dubin, G. / Fino, R. / Popowicz, G. / Sattler, M. / Tetko, I.V.
CitationJournal: To Be Published
Title: Crystal structure of Trypanosoma Brucei PEX14 N-terminal domain in complex with small molecules to investigate the water envelope
Authors: Ratkova, E.L. / Dawidowski, M. / Napolitano, V. / Dubin, G. / Fino, R. / Popowicz, G. / Sattler, M. / Tetko, I.V.
History
DepositionAug 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxin 14
B: Peroxin 14
C: Peroxin 14
D: Peroxin 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,92717
Polymers31,0204
Non-polymers2,90713
Water7,026390
1
A: Peroxin 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5545
Polymers7,7551
Non-polymers7994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peroxin 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4584
Polymers7,7551
Non-polymers7033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Peroxin 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5545
Polymers7,7551
Non-polymers7994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Peroxin 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3623
Polymers7,7551
Non-polymers6072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.863, 116.368, 38.962
Angle α, β, γ (deg.)90.000, 101.460, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLEULEUAA3 - 654 - 66
21THRTHRLEULEUBB3 - 654 - 66
12THRTHRLEULEUAA3 - 654 - 66
22THRTHRLEULEUCC3 - 654 - 66
13HISHISLEULEUAA4 - 655 - 66
23HISHISLEULEUDD4 - 655 - 66
14METMETSERSERBB0 - 661 - 67
24METMETSERSERCC0 - 661 - 67
15HISHISLEULEUBB4 - 655 - 66
25HISHISLEULEUDD4 - 655 - 66
16HISHISLEULEUCC4 - 655 - 66
26HISHISLEULEUDD4 - 655 - 66

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Peroxin 14


Mass: 7754.945 Da / Num. of mol.: 4
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
#2: Chemical
ChemComp-9YB / (3~{R})-3-[[1-(2-hydroxyethyl)-5-[(4-methoxynaphthalen-1-yl)methyl]-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-3-yl]carbonylamino]-3-phenyl-propanoic acid


Mass: 528.599 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H32N4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.22M Li2SO4 0.1M Tris-HCl pH8.5 29% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 48921 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 2.501 % / Biso Wilson estimate: 29.403 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.067 / Χ2: 1.239 / Net I/σ(I): 9.04
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.542.480.7281.3364290.5480.92688.9
1.54-1.582.5220.541.8769700.6960.68797
1.58-1.632.4860.4272.4367820.7730.54496.7
1.63-1.682.420.352.9564110.8370.44697.1
1.68-1.732.4940.2893.5764070.8720.36897.4
1.73-1.792.5840.2234.6362600.9270.28298.2
1.79-1.862.550.1725.8159060.9510.21897.8
1.86-1.942.450.1347.2256710.9650.1796.7
1.94-2.022.420.1019.0353280.9810.12895.5
2.02-2.122.5470.07711.551260.9860.09895
2.12-2.242.5540.06513.5548790.9880.08294.8
2.24-2.372.5240.05914.9545720.9880.07594.6
2.37-2.542.4330.05415.3443420.990.06895.6
2.54-2.742.5130.04716.8240430.9940.05995.4
2.74-32.5910.04518.0937050.9950.05794.3
3-3.352.4940.04218.7132660.9940.05394.4
3.35-3.872.3430.04218.8329390.9930.05394.4
3.87-4.742.610.0420.4324980.9940.0595.6
4.74-6.712.4730.03719.5219600.9950.04696.4
6.71-202.5940.03920.5310850.9940.04897.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AON

5aon


Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.67 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.076
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2021 2440 5 %RANDOM
Rwork0.1762 ---
obs0.1776 46462 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 90.4 Å2 / Biso mean: 24.751 Å2 / Biso min: 12.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0.78 Å2
2--1.35 Å20 Å2
3----0.68 Å2
Refinement stepCycle: final / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 197 392 2665
Biso mean--25.73 34.79 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.022473
X-RAY DIFFRACTIONr_bond_other_d0.0170.022447
X-RAY DIFFRACTIONr_angle_refined_deg2.4242.0623345
X-RAY DIFFRACTIONr_angle_other_deg2.5333.025677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6345305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46522.70896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66415484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3511523
X-RAY DIFFRACTIONr_chiral_restr0.1260.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022646
X-RAY DIFFRACTIONr_gen_planes_other0.010.02553
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A78740.11
12B78740.11
21A76900.12
22C76900.12
31A75600.11
32D75600.11
41B81720.14
42C81720.14
51B75340.13
52D75340.13
61C77940.12
62D77940.12
LS refinement shellResolution: 1.499→1.538 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 141 -
Rwork0.345 3078 -
all-3219 -
obs--89.22 %

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