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- PDB-9i5r: Interactions between Pex3 and Pex19 peptide in yeast -

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Basic information

Entry
Database: PDB / ID: 9i5r
TitleInteractions between Pex3 and Pex19 peptide in yeast
Components
  • Peroxin19 Pex19p
  • Peroxisomal biogenesis factor 3
KeywordsPROTEIN TRANSPORT / PEROXISOME
Function / homology
Function and homology information


peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / peroxisomal membrane / protein-macromolecule adaptor activity
Similarity search - Function
Peroxin-3 / Peroxin-3 / Pex19 protein / Pex19, C-terminal domain superfamily / Pex19 protein family
Similarity search - Domain/homology
Peroxisomal biogenesis factor 3 / Peroxin19 Pex19p
Similarity search - Component
Biological speciesOgataea angusta (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
Authorsde Lange, E. / Chojnowski, G. / Burgi, J. / Vlijm, R. / Wilmanns, M. / van der Klei, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs J. / Year: 2025
Title: Competition between binding partners of yeast Pex3 affects peroxisome biology.
Authors: de Lange, E.M.F. / Chojnowski, G. / Burgi, J. / Vlijm, R. / Wilmanns, M. / van der Klei, I.J.
History
DepositionJan 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxisomal biogenesis factor 3
B: Peroxin19 Pex19p


Theoretical massNumber of molelcules
Total (without water)50,7572
Polymers50,7572
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-8 kcal/mol
Surface area16920 Å2
Unit cell
Length a, b, c (Å)68.579, 137.224, 111.534
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Peroxisomal biogenesis factor 3 / Peroxin-3 / Peroxisomal membrane protein PER9


Mass: 48050.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ogataea angusta (fungus) / Gene: PEX3, PER9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01497
#2: Protein/peptide Peroxin19 Pex19p


Mass: 2705.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ogataea angusta (fungus) / Gene: PEX19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96WN7
Has protein modificationN

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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: 52.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: ammonium phosphate 0.2M + PEG 3350 20%, ph 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 13, 2023
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2.62→111.53 Å / Num. obs: 16218 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.045 / Rrim(I) all: 0.111 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.08-111.539.50.0314490.9990.0140.034
2.62-2.7412.24.75919610.3942.0485.184

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→68.612 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 33.424 / SU ML: 0.29 / Cross valid method: FREE R-VALUE / ESU R: 0.434 / ESU R Free: 0.278
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2477 844 5.211 %
Rwork0.2094 15353 -
all0.211 --
obs-16197 99.932 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 110.698 Å2
Baniso -1Baniso -2Baniso -3
1-5.35 Å20 Å2-0 Å2
2---0.837 Å20 Å2
3----4.513 Å2
Refinement stepCycle: LAST / Resolution: 2.62→68.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 0 0 2713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122745
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162676
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.8253713
X-RAY DIFFRACTIONr_angle_other_deg0.5411.776151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8185327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.585510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55310527
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.38810142
X-RAY DIFFRACTIONr_chiral_restr0.0730.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023173
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02611
X-RAY DIFFRACTIONr_nbd_refined0.2330.2658
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.22328
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21398
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21645
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.239
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1010.216
X-RAY DIFFRACTIONr_nbd_other0.2370.2101
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1110.22
X-RAY DIFFRACTIONr_mcbond_it9.2138.8951326
X-RAY DIFFRACTIONr_mcbond_other9.218.8941326
X-RAY DIFFRACTIONr_mcangle_it12.69715.9711647
X-RAY DIFFRACTIONr_mcangle_other12.69415.9741648
X-RAY DIFFRACTIONr_scbond_it12.3510.0641419
X-RAY DIFFRACTIONr_scbond_other12.34810.061418
X-RAY DIFFRACTIONr_scangle_it17.90817.9842066
X-RAY DIFFRACTIONr_scangle_other17.90417.9862067
X-RAY DIFFRACTIONr_lrange_it22.219107.18911857
X-RAY DIFFRACTIONr_lrange_other22.218107.1911858
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.62-2.6880.352600.38511160.38411790.9070.86899.74550.381
2.688-2.7620.375660.37210880.37211540.8880.8841000.363
2.762-2.8410.351680.34410590.34411270.8920.9031000.329
2.841-2.9290.357600.3310050.33210650.8990.9161000.315
2.929-3.0250.324470.27310120.27610590.9260.9481000.252
3.025-3.1310.373460.2599700.26310160.920.9531000.235
3.131-3.2480.297650.2459170.2499830.9510.96199.89830.223
3.248-3.3810.262610.1898990.1949600.9570.9771000.168
3.381-3.5310.282470.1848660.1889150.940.97999.78140.162
3.531-3.7030.197470.1748200.1768680.9710.98399.88480.157
3.703-3.9020.198420.177910.1718330.9690.9821000.159
3.902-4.1380.245360.1887560.1917920.9640.9771000.176
4.138-4.4230.222390.1827170.1847560.9620.9791000.17
4.423-4.7750.192260.1696760.177020.9760.9831000.162
4.775-5.2290.234360.1656110.1686480.9640.98499.84570.163
5.229-5.8420.201270.225550.2195830.9780.97499.82850.213
5.842-6.7370.356210.2555050.265260.9410.961000.245
6.737-8.2310.256180.2254380.2264560.9550.971000.229
8.231-11.5580.218230.1553380.1593610.9740.9881000.171
11.558-68.6120.22990.2952140.2922250.9750.95599.11110.366
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)
10.59390.19510.03290.7472-0.02981.1315-0.0137-0.0004-0.14840.00340.032-0.0363-0.00640.1176-0.01830.0046-0.0087-0.00440.2176-0.07640.0989-23.2707-13.885114.765
29.141-8.452-6.827611.95177.13040.03480.06750.06840.48830.239-0.46740.5754-0.1505-0.27380.3041-0.0276-0.0640.1686-0.04720.1317-36.4539-38.4502-3.1358
Refinement TLS groupSelection: ALL

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