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

ID or keywords:

Entry

Database: PDB / ID: 9i5r

Title

Interactions between Pex3 and Pex19 peptide in yeast

Components

Peroxin19 Pex19p
Peroxisomal biogenesis factor 3

Keywords

PROTEIN 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

Biological species

Ogataea angusta (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.62 Å

Authors

de Lange, E. / Chojnowski, G. / Burgi, J. / Vlijm, R. / Wilmanns, M. / van der Klei, I.

Funding support

1items

Citation

Journal: To Be Published
Title: Competition of yeast Pex3 binding partners affects peroxisome biology
Authors: de Lange, E. / Chojnowski, G. / Burgi, J. / Vlijm, R. / Wilmanns, M. / van der Klei, I.

History

Deposition	Jan 28, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 19, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9i5r.cif.gz	322.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9i5r.ent.gz	225 KB	Display	PDB format
PDBx/mmJSON format	9i5r.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i5/9i5r ftp://data.pdbj.org/pub/pdb/validation_reports/i5/9i5r	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Peroxisomal biogenesis factor 3

B: Peroxin19 Pex19p

50.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	68.579, 137.224, 111.534
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	20
Space group name H-M	C222₁

#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 modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.58 Å³/Da / Density % sol: 52.42 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: ammonium phosphate 0.2M + PEG 3350 20%, ph 7.0

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

PETRA III, EMBL c/o DESY

/ Beamline: P13 (MX1) / Wavelength: 0.97624 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 13, 2023

Radiation

Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97624 Å / Relative weight: 1

Reflection

Resolution: 2.62→111.53 Å / Num. obs: 16218 / % possible obs: 100 % / Redundancy: 11.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.101 / R_pim(I) all: 0.045 / R_rim(I) all: 0.111 / Net I/σ(I): 11

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
9.08-111.53	9.5	0.031	449	0.999	0.014	0.034
2.62-2.74	12.2	4.759	1961	0.394	2.048	5.184

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.62→68.612 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection
R_free	0.2477	844	5.211 %
R_work	0.2094	15353	-
all	0.211	-	-
obs	-	16197	99.932 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 110.698 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.35 Å²	0 Å²	-0 Å²
2-	-	-0.837 Å²	0 Å²
3-	-	-	-4.513 Å²

Refinement step

Cycle: LAST / Resolution: 2.62→68.612 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2713	0	0	0	2713

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	2745
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2676
X-RAY DIFFRACTION	r_angle_refined_deg	1.631	1.825	3713
X-RAY DIFFRACTION	r_angle_other_deg	0.541	1.77	6151
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.818	5	327
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	18.585	5	10
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.553	10	527
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.388	10	142
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	443
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3173
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	611
X-RAY DIFFRACTION	r_nbd_refined	0.233	0.2	658
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.18	0.2	2328
X-RAY DIFFRACTION	r_nbtor_refined	0.186	0.2	1398
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	1645
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.116	0.2	39
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.101	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.237	0.2	101
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.111	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	9.213	8.895	1326
X-RAY DIFFRACTION	r_mcbond_other	9.21	8.894	1326
X-RAY DIFFRACTION	r_mcangle_it	12.697	15.971	1647
X-RAY DIFFRACTION	r_mcangle_other	12.694	15.974	1648
X-RAY DIFFRACTION	r_scbond_it	12.35	10.064	1419
X-RAY DIFFRACTION	r_scbond_other	12.348	10.06	1418
X-RAY DIFFRACTION	r_scangle_it	17.908	17.984	2066
X-RAY DIFFRACTION	r_scangle_other	17.904	17.986	2067
X-RAY DIFFRACTION	r_lrange_it	22.219	107.189	11857
X-RAY DIFFRACTION	r_lrange_other	22.218	107.19	11858

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.62-2.688	0.352	60	0.385	1116	0.384	1179	0.907	0.868	99.7455	0.381
2.688-2.762	0.375	66	0.372	1088	0.372	1154	0.888	0.884	100	0.363
2.762-2.841	0.351	68	0.344	1059	0.344	1127	0.892	0.903	100	0.329
2.841-2.929	0.357	60	0.33	1005	0.332	1065	0.899	0.916	100	0.315
2.929-3.025	0.324	47	0.273	1012	0.276	1059	0.926	0.948	100	0.252
3.025-3.131	0.373	46	0.259	970	0.263	1016	0.92	0.953	100	0.235
3.131-3.248	0.297	65	0.245	917	0.249	983	0.951	0.961	99.8983	0.223
3.248-3.381	0.262	61	0.189	899	0.194	960	0.957	0.977	100	0.168
3.381-3.531	0.282	47	0.184	866	0.188	915	0.94	0.979	99.7814	0.162
3.531-3.703	0.197	47	0.174	820	0.176	868	0.971	0.983	99.8848	0.157
3.703-3.902	0.198	42	0.17	791	0.171	833	0.969	0.982	100	0.159
3.902-4.138	0.245	36	0.188	756	0.191	792	0.964	0.977	100	0.176
4.138-4.423	0.222	39	0.182	717	0.184	756	0.962	0.979	100	0.17
4.423-4.775	0.192	26	0.169	676	0.17	702	0.976	0.983	100	0.162
4.775-5.229	0.234	36	0.165	611	0.168	648	0.964	0.984	99.8457	0.163
5.229-5.842	0.201	27	0.22	555	0.219	583	0.978	0.974	99.8285	0.213
5.842-6.737	0.356	21	0.255	505	0.26	526	0.941	0.96	100	0.245
6.737-8.231	0.256	18	0.225	438	0.226	456	0.955	0.97	100	0.229
8.231-11.558	0.218	23	0.155	338	0.159	361	0.974	0.988	100	0.171
11.558-68.612	0.229	9	0.295	214	0.292	225	0.975	0.955	99.1111	0.366

Refinement TLS params.

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

ID	L11 (°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)
1	0.5939	0.1951	0.0329	0.7472	-0.0298	1.1315	-0.0137	-0.0004	-0.1484	0.0034	0.032	-0.0363	-0.0064	0.1176	-0.0183	0.0046	-0.0087	-0.0044	0.2176	-0.0764	0.0989	-23.2707	-13.8851	14.765
2	9.141	-8.452	-6.8276	11.951	7	7.1304	0.0348	0.0675	0.0684	0.4883	0.239	-0.4674	0.5754	-0.1505	-0.2738	0.3041	-0.0276	-0.064	0.1686	-0.0472	0.1317	-36.4539	-38.4502	-3.1358

Refinement TLS group

Selection: ALL

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