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- PDB-6zfw: X-ray structure of the soluble N-terminal domain of T. cruzi PEX-14 -

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Basic information

Entry
Database: PDB / ID: 6zfw
TitleX-ray structure of the soluble N-terminal domain of T. cruzi PEX-14
ComponentsPeroxin-14
KeywordsPROTEIN TRANSPORT / Chagas disease / Trypanosoma Cruzi / Glycosomal import / Peroxisomes
Function / homology
Function and homology information


protein import into peroxisome matrix, docking / peroxisomal membrane
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
Similarity search - Domain/homology
ACETATE ION / BETA-MERCAPTOETHANOL / Peroxisomal membrane protein PEX14 / Peroxin-14
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsSoftley, C.A. / Ostertag, M.O. / Sattler, M. / Popowicz, G.P.
Funding support Germany, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission675555 Germany
CitationJournal: Chem.Commun.(Camb.) / Year: 2020
Title: Deep learning model predicts water interaction sites on the surface of proteins using limited-resolution data.
Authors: Zaucha, J. / Softley, C.A. / Sattler, M. / Frishman, D. / Popowicz, G.M.
History
DepositionJun 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,03213
Polymers39,3705
Non-polymers6628
Water5,855325
1
A: Peroxin-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0443
Polymers7,8741
Non-polymers1702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxin-14


Theoretical massNumber of molelcules
Total (without water)7,8741
Polymers7,8741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peroxin-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1364
Polymers7,8741
Non-polymers2623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Peroxin-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9522
Polymers7,8741
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Peroxin-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0253
Polymers7,8741
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.688, 117.382, 51.301
Angle α, β, γ (deg.)90.000, 109.235, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTRPTRP(chain 'A' and (resid -1 through 2 or resid 4...AA-1 - 13 - 5
12SERSERALAALA(chain 'A' and (resid -1 through 2 or resid 4...AA13 - 1417 - 18
13PHEPHEPHEPHE(chain 'A' and (resid -1 through 2 or resid 4...AA1721
14ASPASPASPASP(chain 'A' and (resid -1 through 2 or resid 4...AA2024
15THRTHRALAALA(chain 'A' and (resid -1 through 2 or resid 4...AA26 - 2830 - 32
16ILEILELEULEU(chain 'A' and (resid -1 through 2 or resid 4...AA32 - 4036 - 44
17GLUGLUGLUGLU(chain 'A' and (resid -1 through 2 or resid 4...AA43 - 4447 - 48
18GLUGLUPHEPHE(chain 'A' and (resid -1 through 2 or resid 4...AA47 - 4951 - 53
19ALAALAGLUGLU(chain 'A' and (resid -1 through 2 or resid 4...AA52 - 6056 - 64
110LYSLYSLYSLYS(chain 'A' and (resid -1 through 2 or resid 4...AA6367
211METMETTRPTRP(chain 'B' and (resid -1 through 2 or resid 4...BB-1 - 13 - 5
212SERSERALAALA(chain 'B' and (resid -1 through 2 or resid 4...BB13 - 1417 - 18
213PHEPHEPHEPHE(chain 'B' and (resid -1 through 2 or resid 4...BB1721
214ASPASPASPASP(chain 'B' and (resid -1 through 2 or resid 4...BB2024
215THRTHRALAALA(chain 'B' and (resid -1 through 2 or resid 4...BB26 - 2830 - 32
216ILEILELEULEU(chain 'B' and (resid -1 through 2 or resid 4...BB32 - 4036 - 44
217GLUGLUGLUGLU(chain 'B' and (resid -1 through 2 or resid 4...BB43 - 4447 - 48
218GLUGLUPHEPHE(chain 'B' and (resid -1 through 2 or resid 4...BB47 - 4951 - 53
219ALAALAGLUGLU(chain 'B' and (resid -1 through 2 or resid 4...BB52 - 6056 - 64
220LYSLYSLYSLYS(chain 'B' and (resid -1 through 2 or resid 4...BB6367
321METMETTRPTRP(chain 'C' and (resid -1 through 2 or resid 4...CC-1 - 13 - 5
322SERSERALAALA(chain 'C' and (resid -1 through 2 or resid 4...CC13 - 1417 - 18
323PHEPHEPHEPHE(chain 'C' and (resid -1 through 2 or resid 4...CC1721
324ASPASPASPASP(chain 'C' and (resid -1 through 2 or resid 4...CC2024
325THRTHRALAALA(chain 'C' and (resid -1 through 2 or resid 4...CC26 - 2830 - 32
326ILEILELEULEU(chain 'C' and (resid -1 through 2 or resid 4...CC32 - 4036 - 44
327GLUGLUGLUGLU(chain 'C' and (resid -1 through 2 or resid 4...CC43 - 4447 - 48
328GLUGLUPHEPHE(chain 'C' and (resid -1 through 2 or resid 4...CC47 - 4951 - 53
329ALAALAGLUGLU(chain 'C' and (resid -1 through 2 or resid 4...CC52 - 6056 - 64
330LYSLYSLYSLYS(chain 'C' and (resid -1 through 2 or resid 4...CC6367
431METMETTRPTRP(chain 'D' and (resid -1 through 2 or resid 4...DD-1 - 13 - 5
432SERSERALAALA(chain 'D' and (resid -1 through 2 or resid 4...DD13 - 1417 - 18
433PHEPHEPHEPHE(chain 'D' and (resid -1 through 2 or resid 4...DD1721
434ASPASPASPASP(chain 'D' and (resid -1 through 2 or resid 4...DD2024
435THRTHRALAALA(chain 'D' and (resid -1 through 2 or resid 4...DD26 - 2830 - 32
436ILEILELEULEU(chain 'D' and (resid -1 through 2 or resid 4...DD32 - 4036 - 44
437GLUGLUGLUGLU(chain 'D' and (resid -1 through 2 or resid 4...DD43 - 4447 - 48
438GLUGLUPHEPHE(chain 'D' and (resid -1 through 2 or resid 4...DD47 - 4951 - 53
439ALAALAGLUGLU(chain 'D' and (resid -1 through 2 or resid 4...DD52 - 6056 - 64
440LYSLYSLYSLYS(chain 'D' and (resid -1 through 2 or resid 4...DD6367
541METMETTRPTRP(chain 'E' and (resid -1 through 2 or resid 4...EE-1 - 13 - 5
542SERSERALAALA(chain 'E' and (resid -1 through 2 or resid 4...EE13 - 1417 - 18
543PHEPHEPHEPHE(chain 'E' and (resid -1 through 2 or resid 4...EE1721
544ASPASPASPASP(chain 'E' and (resid -1 through 2 or resid 4...EE2024
545THRTHRALAALA(chain 'E' and (resid -1 through 2 or resid 4...EE26 - 2830 - 32
546ILEILELEULEU(chain 'E' and (resid -1 through 2 or resid 4...EE32 - 4036 - 44
547GLUGLUGLUGLU(chain 'E' and (resid -1 through 2 or resid 4...EE43 - 4447 - 48
548GLUGLUPHEPHE(chain 'E' and (resid -1 through 2 or resid 4...EE47 - 4951 - 53
549ALAALAGLUGLU(chain 'E' and (resid -1 through 2 or resid 4...EE52 - 6056 - 64
550LYSLYSLYSLYS(chain 'E' and (resid -1 through 2 or resid 4...EE6367

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Components

#1: Protein
Peroxin-14 /


Mass: 7874.096 Da / Num. of mol.: 5
Mutation: W at terminus for purification purposes, GAMA from tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C3747_80g13 / Plasmid: pETM11 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A2V2WKZ5, UniProt: Q4D1H5*PLUS
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


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


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.58 Å3/Da / Density % sol: 52.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Na acetate, 0.1 M Tris.HCl pH 8.5, 30%(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.82656 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 1.58→48.44 Å / Num. obs: 101657 / % possible obs: 94.2 % / Redundancy: 1.73 % / Biso Wilson estimate: 22.6 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.5
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.35 / Num. unique obs: 10617 / CC1/2: 0.612 / Rrim(I) all: 0.688 / % possible all: 92.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L87

5l87


Resolution: 1.58→48.44 Å / SU ML: 0.1891 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.7883
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2065 2656 4.97 %
Rwork0.1712 50785 -
obs0.173 53441 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.54 Å2
Refinement stepCycle: LAST / Resolution: 1.58→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2719 0 40 325 3084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01192986
X-RAY DIFFRACTIONf_angle_d1.20234027
X-RAY DIFFRACTIONf_chiral_restr0.0704450
X-RAY DIFFRACTIONf_plane_restr0.0077515
X-RAY DIFFRACTIONf_dihedral_angle_d5.9507429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.610.31851410.28562695X-RAY DIFFRACTION98.54
1.61-1.640.31881420.26432656X-RAY DIFFRACTION98.45
1.64-1.670.28151330.25182686X-RAY DIFFRACTION98.5
1.67-1.710.28191440.23252686X-RAY DIFFRACTION98.26
1.71-1.750.27181240.23522601X-RAY DIFFRACTION97.22
1.75-1.790.29021080.23032624X-RAY DIFFRACTION94.47
1.79-1.840.24031360.21622673X-RAY DIFFRACTION99.05
1.84-1.90.2471490.20792699X-RAY DIFFRACTION99.03
1.9-1.960.25551450.19192667X-RAY DIFFRACTION99.01
1.96-2.030.2271390.19012674X-RAY DIFFRACTION98.88
2.03-2.110.20241330.17822712X-RAY DIFFRACTION98.44
2.11-2.20.20561370.17682648X-RAY DIFFRACTION97.58
2.2-2.320.23091550.17052662X-RAY DIFFRACTION98.91
2.32-2.470.22221470.17582708X-RAY DIFFRACTION98.93
2.47-2.660.20391430.17612670X-RAY DIFFRACTION98.67
2.66-2.920.18851280.16432690X-RAY DIFFRACTION97.61
2.92-3.350.19871390.15982679X-RAY DIFFRACTION98.63
3.35-4.210.1861470.13872666X-RAY DIFFRACTION97.4
4.22-48.440.16921660.152689X-RAY DIFFRACTION98.04

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