PDB-2gop: The beta-propeller domain of the Trilobed protease from Pyrococcu...

ID or keywords:

Entry

Database: PDB / ID: 2gop

Title

The beta-propeller domain of the Trilobed protease from Pyrococcus furiosus reveals an open velcro topology

Components

Trilobed Protease

Keywords

HYDROLASE / beta propeller / open velcro

Function / homology

WD40-like beta propeller / WD40-like Beta Propeller Repeat / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Six-bladed beta-propeller, TolB-like / serine-type peptidase activity / Alpha/Beta hydrolase fold / : / Acylaminoacyl-peptidase-like protein

Function and homology information

Biological species

Pyrococcus furiosus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIR / Resolution: 2 Å

Authors

Bosch, J. / Tamura, T. / Tamura, N. / Baumeister, W. / Essen, L.-O.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2007
Title: The beta-propeller domain of the trilobed protease from Pyrococcus furiosus reveals an open Velcro topology.
Authors: Bosch, J. / Tamura, T. / Tamura, N. / Baumeister, W. / Essen, L.O.

History

Deposition	Apr 13, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 23, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Feb 14, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2gop.cif.gz	145.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2gop.ent.gz	116.7 KB	Display	PDB format
PDBx/mmJSON format	2gop.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2gop_validation.pdf.gz	428.3 KB	Display	wwPDB validaton report
Full document	2gop_full_validation.pdf.gz	450.6 KB	Display
Data in XML	2gop_validation.xml.gz	26.4 KB	Display
Data in CIF	2gop_validation.cif.gz	37.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/go/2gop ftp://data.pdbj.org/pub/pdb/validation_reports/go/2gop	HTTPS FTP

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Related structure data

Similar structure data	3cyv-1 1x1q-d 1ock-d 22630 4y8e-d 1jpi-1 5dc7-d 4bia-1 Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#202 - Oct 2016 Dipeptidyl Peptidase 4 similarity (2) #126 - Jun 2010 Epidermal Growth Factor similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1) #225 - Sep 2018 Phytase similarity (1) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

A: Trilobed Protease

B: Trilobed Protease

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	54.747, 88.504, 153.966
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Trilobed Protease Mass: 41108.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: GenBank: 18892268, UniProt: Q8U3Y3*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

Crystal	Density Matthews: 2.27 Å³/Da / Density % sol: 45.76 %
Crystal grow	Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: 100 mM sodium acetate pH 4.4, 20 mM MgCl2, 300 mM 1,6-hexanediol, 10 % PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	MPG/DESY, HAMBURG	BW6	1	1.00, 1.10, 1.03
SYNCHROTRON	ESRF	ID14-1	2	1.07

Detector

Type	ID	Detector	Date
MAR CCD 165 mm	1	CCD	Oct 10, 2004
ADSC QUANTUM 4	2	CCD	Dec 10, 2004

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1	1
2	1.1	1
3	1.03	1
4	1.07	1

Reflection

Resolution: 2→18.72 Å / Num. all: 39936 / Num. obs: 39936 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

Reflection shell

Resolution: 2→2.107 Å / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
ADSC		data collection
MOSFLM		data reduction
SOLVE		phasing

Refinement

Method to determine structure:

MIR / Resolution: 2→18.72 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.924 / SU B: 9.112 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25824	1235	3 %	RANDOM
R_work	0.2087	-	-	-
all	0.21014	39936	-	-
obs	0.21014	39936	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 45.852 Å²

	B_aniso -1	B_aniso -2
1-	-0.05 Å²	0 Å²
2-	-	0.05 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 2→18.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5198	0	0	242	5440

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	5366
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3807
X-RAY DIFFRACTION	r_angle_refined_deg	1.134	1.952	7235
X-RAY DIFFRACTION	r_angle_other_deg	0.825	3	9239
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.149	5	634
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.131	24.207	271
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.637	15	1018
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.486	15	34
X-RAY DIFFRACTION	r_chiral_restr	0.133	0.2	759
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	5866
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1137
X-RAY DIFFRACTION	r_nbd_refined	0.18	0.2	871
X-RAY DIFFRACTION	r_nbd_other	0.185	0.2	3805
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	2420
X-RAY DIFFRACTION	r_nbtor_other	0.081	0.2	2992
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.12	0.2	274
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.206	0.2	21
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.16	0.2	58
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.194	0.2	11
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.987	4	4117
X-RAY DIFFRACTION	r_mcbond_other	0.387	4	1271
X-RAY DIFFRACTION	r_mcangle_it	2.34	6	5057
X-RAY DIFFRACTION	r_scbond_it	2.454	6	2760
X-RAY DIFFRACTION	r_scangle_it	3.388	10	2170
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2→2.107 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.285	190	-
R_work	0.239	6797	-
obs	-	-	100 %

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	1.4835	1.715	-0.6164	2.3466	-1.2344	6.8918	0.572	-0.0742	-0.0744	0.4134	-0.4429	-0.2746	0.127	0.6825	-0.129	0.1434	-0.0945	-0.0524	0.0984	-0.0444	0.1007	42.9409	29.162	34.7559
2	4.6867	-0.7187	1.0777	2.218	-0.6219	2.5552	0.0245	-0.3111	0.2559	0.3613	-0.0043	-0.0159	-0.3352	-0.0321	-0.0202	0.1503	-0.0215	0.0341	0.0698	-0.0932	0.0631	31.7836	34.4991	32.3358
3	9.8459	2.3403	3.8808	26.3061	-17.3685	23.2659	0.4357	-0.5525	-0.2242	1.1265	-0.5382	-0.4779	0.2392	-0.6775	0.1025	0.2657	-0.0346	0.0286	0.047	-0.003	0.0422	23.2005	17.878	39.1217
4	0.3577	0.053	-0.847	3.0336	0.7032	3.4131	0.0141	-0.0113	0.1301	0.1813	-0.0012	0.11	0.1239	-0.3425	-0.0129	0.0327	0.0142	0.0253	0.1154	-0.0373	0.118	20.554	27.6524	25.7871
5	15.3364	8.0383	2.0544	11.7848	-0.0254	0.4356	0.1302	-1.0654	-0.8843	0.3597	0.4208	0.0794	0.1411	-0.1564	-0.551	0.3497	0.0482	-0.089	0.2388	0.265	0.2057	27.0124	14.644	28.5507
6	2.0864	0.151	-1.3299	2.3591	0.8554	4.8258	-0.0432	-0.0189	-0.2184	0.0873	-0.0109	0.0617	0.3754	-0.2825	0.0541	0.0331	-0.0571	-0.0154	0.1112	0.0128	0.1242	21.5346	16.9876	15.7107
7	2.5118	1.1707	0.8602	1.7887	-0.8004	2.2173	-0.0785	0.0824	-0.1124	-0.0191	0.0251	-0.0459	0.0589	-0.0961	0.0534	0.0265	-0.0009	0.0237	0.1308	-0.0172	0.0812	25.8114	19.1582	6.5024
8	2.154	0.8667	1.344	24.1001	39.1716	63.6706	-1.6429	0.5998	-0.0752	-0.4064	1.6066	0.1967	2.1615	1.9361	0.0362	0.3527	-0.1432	0.0927	0.4454	-0.1524	0.3325	41.7846	9.7896	1.4362
9	14.1561	-6.219	10.3701	4.9436	-5.0773	7.7196	-0.0226	0.4487	-0.1265	-0.2984	-0.1377	-0.1262	0.1956	0.301	0.1603	0.0116	-0.0007	0.0488	0.139	-0.0005	0.1015	37.2324	19.8523	2.2855
10	0.9619	-0.0938	-0.3943	0.7923	0.2487	2.2225	0.0317	-0.014	0.1844	0.0252	0.0345	-0.1417	-0.2872	0.1612	-0.0661	0.0404	-0.0536	-0.007	0.0999	-0.0073	0.1338	45.1574	31.4702	16.0042
11	27.9602	11.2983	-8.145	7.0112	0.4082	7.9686	-0.3863	-0.7589	1.9659	-0.4632	0.8645	0.5057	-0.0489	0.2871	-0.4782	0.0557	-0.0827	-0.1428	0.1638	-0.2703	0.2853	50.3763	40.8687	35.3305
12	12.3964	-3.1749	5.2021	3.4585	-2.4741	4.9082	-0.1081	0.6752	-0.7442	-1.2738	-0.0917	0.0376	0.953	0.0378	0.1998	0.8213	-0.0742	0.0707	-0.1514	-0.0825	-0.1187	41.2322	-12.3982	6.8353
13	3.0392	-1.6292	-1.0593	4.3725	-0.0291	6.0123	-0.1341	-0.2299	-0.5906	-1.4155	0.0582	0.4909	1.4309	-0.7794	0.076	0.7588	-0.2486	-0.0187	-0.2629	0.0032	0.0315	37.5998	-16.9512	13.991
14	22.6057	-3.8959	-7.8328	3.9163	1.2144	5.6179	-0.1764	0.8644	-2.0886	-0.2583	-0.8022	0.6879	1.6816	-1.7364	0.9786	0.6099	-0.3115	0.0418	-0.0741	0.109	0.2006	35.7424	-22.0559	22.1733
15	7.1645	-3.3147	-2.6599	7.4213	0.0366	6.1615	-0.2319	-0.2219	0.0063	-0.3638	0.2765	0.4237	0.5934	-0.4969	-0.0446	0.1623	-0.0539	0.0856	0.0161	0.1012	0.0129	39.2468	-8.3212	28.2751
16	3.0973	2.0079	-1.6262	5.1023	-2.2943	4.7516	-0.0316	-0.0347	-0.0384	-0.1168	-0.1354	0.1097	0.5059	-0.0771	0.167	0.1183	0.0076	0.0613	0.0508	0.058	0.0396	41.5832	-7.059	33.0629
17	6.6282	-4.7419	2.8284	8.4247	-2.5336	8.1319	-0.4253	-0.3243	-0.5329	0.3088	0.1295	0.043	0.8065	-0.2803	0.2958	0.1528	-0.0494	-0.0541	0.0607	-0.0106	0.1255	40.9078	18.7781	31.4844
18	1.0717	0.4037	-0.713	2.9831	-1.8351	4.0957	-0.0382	-0.1426	-0.0378	0.1167	-0.3288	-0.4573	0.0054	0.4868	0.367	-0.0284	0.0269	0.0133	0.1299	0.1339	0.1245	54.1084	4.8275	24.4645
19	4.8739	1.7547	0.2781	4.7669	-0.7911	4.9146	-0.1054	0.4095	-0.2425	-1.133	-0.1731	-0.5374	1.3547	0.3551	0.2785	0.4228	0.1617	0.2575	-0.081	0.042	-0.0755	54.0014	-6.0835	5.0144

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	12 - 20	12 - 20
2	X-RAY DIFFRACTION	2	A	A	21 - 78	21 - 78
3	X-RAY DIFFRACTION	3	A	A	79 - 86	79 - 86
4	X-RAY DIFFRACTION	4	A	A	87 - 124	87 - 124
5	X-RAY DIFFRACTION	5	A	A	125 - 150	125 - 150
6	X-RAY DIFFRACTION	6	A	A	151 - 201	151 - 201
7	X-RAY DIFFRACTION	7	A	A	202 - 233	202 - 233
8	X-RAY DIFFRACTION	8	A	A	234 - 240	234 - 240
9	X-RAY DIFFRACTION	9	A	A	241 - 255	241 - 255
10	X-RAY DIFFRACTION	10	A	A	256 - 338	256 - 338
11	X-RAY DIFFRACTION	11	A	A	339 - 347	339 - 347
12	X-RAY DIFFRACTION	12	B	B	13 - 39	13 - 39
13	X-RAY DIFFRACTION	13	B	B	40 - 87	40 - 87
14	X-RAY DIFFRACTION	14	B	B	88 - 103	88 - 103
15	X-RAY DIFFRACTION	15	B	B	104 - 151	104 - 151
16	X-RAY DIFFRACTION	16	B	B	152 - 189	152 - 189
17	X-RAY DIFFRACTION	17	B	B	190 - 198	190 - 198
18	X-RAY DIFFRACTION	18	B	B	199 - 287	199 - 287
19	X-RAY DIFFRACTION	19	B	B	288 - 342	288 - 342

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