PDB-8rqt: Crystal structure of Pichia pastoris Pex8

ID or keywords:

Entry

Database: PDB / ID: 8rqt

Title

Crystal structure of Pichia pastoris Pex8

Components

Peroxisomal biogenesis factor 8

Keywords

PROTEIN TRANSPORT / HEAT repeat / Peroxisomal protein import

Function / homology

peroxisomal matrix / Peroxisomal biogenesis factor 8

Function and homology information

Biological species

Komagataella pastoris (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.41 Å

Authors

Ekal, L. / Burgi, J. / Chojnowski, G. / WIlmanns, M.

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: Crystal structure of Pichia pastoris Pex8
Authors: Ekal, L. / Burgi, J. / Chojnowski, G. / WIlmanns, M.

History

Deposition	Jan 19, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 29, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8rqt.cif.gz	587 KB	Display	PDBx/mmCIF format
PDB format	pdb8rqt.ent.gz	411.3 KB	Display	PDB format
PDBx/mmJSON format	8rqt.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8rqt_validation.pdf.gz	424.6 KB	Display	wwPDB validaton report
Full document	8rqt_full_validation.pdf.gz	426.8 KB	Display
Data in XML	8rqt_validation.xml.gz	25.3 KB	Display
Data in CIF	8rqt_validation.cif.gz	33.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rq/8rqt ftp://data.pdbj.org/pub/pdb/validation_reports/rq/8rqt	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 8

81.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: SAXS

Unit cell

Length a, b, c (Å)	81.149, 87.842, 153.093
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Peroxisomal biogenesis factor 8 / Peroxin-8 / Peroxisomal protein PER3 Mass: 81081.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella pastoris (fungus) / Gene: PEX8, PER3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): LOBSTR / References: UniProt: Q01962
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.36 Å³/Da / Density % sol: 63.45 % / Description: Thick elongated needle
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.09M NPS, 0.1M pH 7.5 (Sodium HEPES + MOPS), 12% Ethylene glycol, 6% w/v PEG 8000, 4% Formamide

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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: 0.9762 Å

Detector

Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 16, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.9762 Å / Relative weight: 1

Reflection

Resolution: 2.41→47.03 Å / Num. obs: 43103 / % possible obs: 100 % / Redundancy: 13.2 % / B_iso Wilson estimate: 60.51 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.188 / R_pim(I) all: 0.077 / R_rim(I) all: 0.204 / Χ²: 1 / Net I/σ(I): 10

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	Χ²	% possible all
9.02-47.03	10.8	0.035	938	0.999	0.015	0.038	0.94	100
2.41-2.5	13.8	4.834	4486	0.415	1.943	5.212	0.96

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Processing

Software

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

Refinement

Method to determine structure:

SAD / Resolution: 2.41→47.03 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.939 / SU B: 24.936 / SU ML: 0.241 / Cross valid method: FREE R-VALUE / ESU R: 0.258 / ESU R Free: 0.223
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2581	2088	4.852 %
R_work	0.2122	40950	-
all	0.214	-	-
obs	-	43038	99.972 %

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: 76.887 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.62 Å²	0 Å²	-0 Å²
2-	-	1.762 Å²	-0 Å²
3-	-	-	-0.141 Å²

Refinement step

Cycle: LAST / Resolution: 2.41→47.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5016	0	0	66	5082

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	5126
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4895
X-RAY DIFFRACTION	r_angle_refined_deg	1.582	1.807	6967
X-RAY DIFFRACTION	r_angle_other_deg	0.572	1.743	11259
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.3	5	619
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.869	5	22
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.213	10	893
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.376	10	234
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	811
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	5892
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1194
X-RAY DIFFRACTION	r_nbd_refined	0.234	0.2	1178
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	4223
X-RAY DIFFRACTION	r_nbtor_refined	0.193	0.2	2600
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.072	0.2	2650
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.131	0.2	100
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.011	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.139	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.194	0.2	52
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.515	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	3.417	4.178	2482
X-RAY DIFFRACTION	r_mcbond_other	3.417	4.178	2482
X-RAY DIFFRACTION	r_mcangle_it	5.29	7.505	3099
X-RAY DIFFRACTION	r_mcangle_other	5.289	7.505	3100
X-RAY DIFFRACTION	r_scbond_it	3.971	4.516	2644
X-RAY DIFFRACTION	r_scbond_other	3.97	4.516	2645
X-RAY DIFFRACTION	r_scangle_it	6.213	8.177	3868
X-RAY DIFFRACTION	r_scangle_other	6.212	8.178	3869
X-RAY DIFFRACTION	r_lrange_it	8.053	39.985	5872
X-RAY DIFFRACTION	r_lrange_other	8.052	39.984	5872

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
2.41-2.473	0.391	138	0.404	3016	0.404	3155	0.657	0.627	99.9683	0.396
2.473-2.54	0.38	131	0.364	2920	0.364	3051	0.866	0.89	100	0.349
2.54-2.613	0.349	128	0.337	2845	0.338	2973	0.908	0.913	100	0.316
2.613-2.694	0.387	164	0.319	2710	0.323	2874	0.906	0.927	100	0.292
2.694-2.782	0.299	147	0.285	2664	0.285	2811	0.946	0.946	100	0.25
2.782-2.879	0.321	152	0.265	2540	0.268	2692	0.94	0.957	100	0.229
2.879-2.987	0.29	124	0.247	2523	0.249	2647	0.956	0.963	100	0.21
2.987-3.109	0.299	139	0.236	2361	0.239	2500	0.947	0.969	100	0.196
3.109-3.246	0.241	109	0.219	2343	0.22	2452	0.966	0.973	100	0.181
3.246-3.404	0.248	86	0.211	2233	0.213	2319	0.963	0.974	100	0.181
3.404-3.587	0.242	128	0.21	2085	0.213	2213	0.969	0.978	100	0.192
3.587-3.803	0.28	108	0.197	1995	0.201	2104	0.945	0.981	99.9525	0.182
3.803-4.064	0.229	73	0.179	1914	0.181	1987	0.971	0.983	100	0.165
4.064-4.387	0.189	88	0.161	1755	0.163	1843	0.978	0.985	100	0.148
4.387-4.801	0.212	95	0.153	1626	0.156	1721	0.974	0.986	100	0.143
4.801-5.361	0.255	80	0.198	1485	0.2	1565	0.969	0.981	100	0.186
5.361-6.177	0.298	73	0.248	1319	0.251	1392	0.956	0.972	100	0.23
6.177-7.533	0.265	63	0.201	1136	0.204	1199	0.969	0.978	100	0.191
7.533-10.519	0.188	40	0.136	909	0.138	949	0.974	0.989	100	0.143
10.519-47.03	0.219	22	0.221	571	0.221	596	0.971	0.971	99.4966	0.227

Refinement TLS params.

Method: refined / Origin x: 9.2669 Å / Origin y: -13.2754 Å / Origin z: -12.8955 Å

	11	12	13	21	22	23	31	32	33
T	0.0201 Å²	0.0032 Å²	-0.0228 Å²	-	0.6277 Å²	0.0192 Å²	-	-	0.1334 Å²
L	0.3989 °²	0.4107 °²	0.4898 °²	-	0.9122 °²	0.4571 °²	-	-	2.1093 °²
S	-0.0744 Å °	-0.0426 Å °	0.1031 Å °	-0.1264 Å °	-0.0504 Å °	0.0949 Å °	-0.1228 Å °	-0.1417 Å °	0.1248 Å °

Refinement TLS group

Selection: ALL

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