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- PDB-6rt2: Crystal structure of Trypanosoma Brucei PEX14 N-terminal domain i... -

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Basic information

Entry
Database: PDB / ID: 6rt2
TitleCrystal structure of Trypanosoma Brucei PEX14 N-terminal domain in complex with small molecules designed to investigate the water envelope
ComponentsPeroxin 14
KeywordsSIGNALING PROTEIN / Peroxisomal Translocation / PPI inhibition / Protein-Inhibitor Complex
Function / homology
Function and homology information


glycosome membrane / peroxisomal importomer complex / protein import into peroxisome matrix, docking / protein targeting to vacuole / glycosome / post-transcriptional regulation of gene expression / signaling receptor binding
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
BETA-MERCAPTOETHANOL / Chem-CV5 / Peroxisomal membrane protein PEX14
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsNapolitano, V. / Ratkova, E.L. / Dawidowski, M. / Dubin, G. / Fino, R. / Popowicz, G. / Sattler, M. / Tetko, I.V.
Funding support Poland, 1items
OrganizationGrant numberCountry
Accelerated Early staGe drug dIScovery675555 Poland
CitationJournal: Chem.Commun.(Camb.) / Year: 2020
Title: Water envelope has a critical impact on the design of protein-protein interaction inhibitors.
Authors: Ratkova, E.L. / Dawidowski, M. / Napolitano, V. / Dubin, G. / Fino, R. / Ostertag, M.S. / Sattler, M. / Popowicz, G. / Tetko, I.V.
History
DepositionMay 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
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 / 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

Downloads & links

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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)34,02318
Polymers31,0204
Non-polymers3,00314
Water8,845491
1
A: 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
2
B: Peroxin 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6506
Polymers7,7551
Non-polymers8955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 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
4
D: 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
Unit cell
Length a, b, c (Å)35.780, 115.520, 38.870
Angle α, β, γ (deg.)90.000, 101.390, 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
11HISHISLEULEUAA4 - 655 - 66
21HISHISLEULEUBB4 - 655 - 66
12HISHISLEULEUAA4 - 655 - 66
22HISHISLEULEUCC4 - 655 - 66
13HISHISSERSERAA4 - 665 - 67
23HISHISSERSERDD4 - 665 - 67
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-CV5 / (3~{S})-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.: 6 / 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.: 491 / 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: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2M Na2SO4, 0.1 M Bis-Tris propane pH 7.5, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1 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 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. obs: 145521 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 2.512 % / Biso Wilson estimate: 23.445 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.028 / Rrim(I) all: 0.035 / Χ2: 1.152 / Net I/σ(I): 14.55 / Num. measured all: 365510 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.3-1.352.4060.4681.813818516140158740.8240.57798.4
1.35-1.42.4230.3682.343313513840136740.8820.45398.8
1.4-1.52.4580.2423.585459422495222120.9410.29998.7
1.5-1.62.470.146.334164817211168600.9750.17498
1.6-1.852.5190.07511.76874728435272940.9920.09496
1.85-1.92.7210.05118.4110692404339300.9960.06297.2
1.9-22.6620.04321.2717746687766660.9970.05396.9
2-2.52.5960.0329.494957120121190930.9980.03794.9
2.5-32.3640.02434.4819368893281930.9980.03191.7
3-42.6450.0240.8917727709367020.9990.02694.5
4-52.8290.01943.886874249224300.9990.02397.5
5-62.8310.01842.893075112610860.9990.02296.4
6-102.8060.01843.243311120211800.9990.02298.2
10-202.560.02141.278373443270.9980.02695.1

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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: 1.3→20 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.723 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.051
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1889 3575 4.7 %RANDOM
Rwork0.1614 ---
obs0.1627 71864 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 84.17 Å2 / Biso mean: 21.234 Å2 / Biso min: 9.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å2-0.71 Å2
2--1.06 Å20 Å2
3----0.38 Å2
Refinement stepCycle: final / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 202 492 2770
Biso mean--20.54 31.51 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0370.022599
X-RAY DIFFRACTIONr_bond_other_d0.0220.022595
X-RAY DIFFRACTIONr_angle_refined_deg3.1252.0653540
X-RAY DIFFRACTIONr_angle_other_deg3.1183.0186038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9775334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81922.294109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12715523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6321531
X-RAY DIFFRACTIONr_chiral_restr0.180.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.022828
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02595
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A78280.13
12B78280.13
21A78480.15
22C78480.15
31A78640.16
32D78640.16
41B83660.14
42C83660.14
51B77480.16
52D77480.16
61C78860.13
62D78860.13
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 263 -
Rwork0.274 5329 -
all-5592 -
obs--99.89 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.28650.09420.02960.56640.39430.81120.0961-0.1078-0.0119-0.0798-0.08250.04790.0587-0.0214-0.01360.06910.0071-0.0120.0374-0.00420.012335.685-3.866618.0947
21.19820.4029-0.46261.10020.23671.2665-0.1045-0.10690.0432-0.1206-0.00760.105-0.0276-0.04040.11220.01830.0134-0.01830.0469-0.02640.047431.167421.064922.5722
30.7121-0.30690.57891.32010.17671.0740.03530.0127-0.05850.09740.0296-0.0340.0451-0.0093-0.06490.018-0.0083-0.00620.0483-0.01720.047550.236224.387837.0779
40.52-0.39870.22281.2921-0.11692.0091-0.0044-0.00340.00130.0074-0.054-0.0369-0.30360.05570.05840.0908-0.0232-0.00620.0350.01080.017843.8702-6.879339.7386
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 66
2X-RAY DIFFRACTION2B0 - 66
3X-RAY DIFFRACTION3C0 - 66
4X-RAY DIFFRACTION4D4 - 66

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