PDB-5fpw: proCathepsin B S9 from Trypanosoma congolense

ID or keywords:

Entry

Database: PDB / ID: 5fpw

Title

proCathepsin B S9 from Trypanosoma congolense

Components

PRO CATHEPSIN B S9

Keywords

HYDROLASE / PRO CATHEPSIN B / TRYPANOSOMA CONGOLENSE / TRYPANOSOME

Function / homology

Function and homology information

cysteine-type peptidase activity / proteolysis
Similarity search - Function

Biological species

TRYPANOSOMA CONGOLENSE (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / OTHER / Resolution: 2.1 Å

Authors

Sevajol, M. / Biteau, N. / Baltz, T. / Franzetti, B. / Vellieux, F.M.D.

Citation

Journal: Ph D Thesis
Title: 2.1 Angstrom Crystal Structure of Pro Cathepsin B S9 from Trypanosoma Congolense
Authors: Sevajol, M. / Biteau, N. / Baltz, T. / Franzetti, B. / Vellieux, F.M.D.

History

Deposition	Dec 3, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 17, 2016	Provider: repository / Type: Initial release
Revision 2.0	Mar 6, 2019	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Experimental preparation / Other Category: atom_site / exptl_crystal_grow ...atom_site / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / reflns / struct_biol Item: _atom_site.occupancy / _exptl_crystal_grow.method ..._atom_site.occupancy / _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _reflns.pdbx_Rmerge_I_obs
Revision 2.1	Oct 23, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5fpw.cif.gz	366.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5fpw.ent.gz	299.5 KB	Display	PDB format
PDBx/mmJSON format	5fpw.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5fpw_validation.pdf.gz	442 KB	Display	wwPDB validaton report
Full document	5fpw_full_validation.pdf.gz	446.6 KB	Display
Data in XML	5fpw_validation.xml.gz	43.1 KB	Display
Data in CIF	5fpw_validation.cif.gz	60.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fp/5fpw ftp://data.pdbj.org/pub/pdb/validation_reports/fp/5fpw	HTTPS FTP

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Related structure data

Similar structure data	1pvs-1 3cwd-1 1wx5-2 6hil-4 3kmg-2 1mpg-2 4i04-1 5z0d-d 3pg5-1 6hil-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#142 - Oct 2011 PDB Pioneers similarity (3)

Deposited unit

A: PRO CATHEPSIN B S9

B: PRO CATHEPSIN B S9

C: PRO CATHEPSIN B S9

108 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PRO CATHEPSIN B S9

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

2

B: PRO CATHEPSIN B S9

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

3

C: PRO CATHEPSIN B S9

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

Unit cell

Length a, b, c (Å)	128.790, 223.220, 102.890
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	21
Space group name H-M	C222

Components on special symmetry positions

ID	Model	Components
1	1	A-4022- HOH
2	1	A-4023- HOH
3	1	B-4033- HOH
4	1	B-4100- HOH
5	1	B-4129- HOH
6	1	B-4131- HOH
7	1	C-4077- HOH

#1: Protein	PRO CATHEPSIN B S9 Mass: 36065.629 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA CONGOLENSE (eukaryote) / Strain: IL-1180 / Production host: PICHIA PASTORIS (fungus) / Strain (production host): X-33 / References: UniProt: B2C331, cathepsin B
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 656 / 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: 3.42 Å³/Da / Density % sol: 64.01 % / Description: NONE
Crystal grow	Method: vapor diffusion, hanging drop Details: THE RECOMBINANT PROTEIN (5.5 MG/ML) IN 20 MM NA-ACETATE, PH 4.5, 20 MM NACL IS CRYSTALLIZED BY THE HANGING DROP METHOD USING A PRECIPITANT SOLUTION MADE UP OF 0.2 M MES, PH 6.5, 5% (W/V) PEG ...Details: THE RECOMBINANT PROTEIN (5.5 MG/ML) IN 20 MM NA-ACETATE, PH 4.5, 20 MM NACL IS CRYSTALLIZED BY THE HANGING DROP METHOD USING A PRECIPITANT SOLUTION MADE UP OF 0.2 M MES, PH 6.5, 5% (W/V) PEG 20000, 1.0 M SODIUM IODIDE.

Crystal

Density Matthews: 3.42 Å³/Da / Density % sol: 64.01 % / Description: NONE

Crystal grow

Method: vapor diffusion, hanging drop
Details: THE RECOMBINANT PROTEIN (5.5 MG/ML) IN 20 MM NA-ACETATE, PH 4.5, 20 MM NACL IS CRYSTALLIZED BY THE HANGING DROP METHOD USING A PRECIPITANT SOLUTION MADE UP OF 0.2 M MES, PH 6.5, 5% (W/V) PEG ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 1
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.1→39.03 Å / Num. obs: 85254 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 99 % / B_iso Wilson estimate: 32.46 Å² / R_merge(I) obs: 0.015

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure: OTHER
Starting model: NONE

Resolution: 2.1→39.029 Å / SU ML: 0.24 / σ(F): 1.99 / Phase error: 22.47 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2162	4263	5 %
R_work	0.1791	-	-
obs	0.1809	85242	98.5 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.1→39.029 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6910	0	0	656	7566

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	7126
X-RAY DIFFRACTION	f_angle_d	0.923	9698
X-RAY DIFFRACTION	f_dihedral_angle_d	15.906	4146
X-RAY DIFFRACTION	f_chiral_restr	0.057	1009
X-RAY DIFFRACTION	f_plane_restr	0.006	1242

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.1-2.1239	0.351	140	0.2857	2670	X-RAY DIFFRACTION	99
2.1239-2.1488	0.3138	145	0.2752	2749	X-RAY DIFFRACTION	99
2.1488-2.175	0.2929	140	0.2565	2662	X-RAY DIFFRACTION	99
2.175-2.2026	0.2603	142	0.2511	2694	X-RAY DIFFRACTION	99
2.2026-2.2316	0.3037	142	0.2507	2706	X-RAY DIFFRACTION	99
2.2316-2.2621	0.2905	141	0.2416	2677	X-RAY DIFFRACTION	99
2.2621-2.2944	0.2912	143	0.2363	2718	X-RAY DIFFRACTION	99
2.2944-2.3287	0.2597	141	0.2343	2671	X-RAY DIFFRACTION	99
2.3287-2.3651	0.2518	140	0.2043	2672	X-RAY DIFFRACTION	99
2.3651-2.4038	0.2385	142	0.2191	2696	X-RAY DIFFRACTION	99
2.4038-2.4453	0.2661	142	0.1956	2687	X-RAY DIFFRACTION	99
2.4453-2.4897	0.2379	143	0.1936	2726	X-RAY DIFFRACTION	99
2.4897-2.5376	0.2201	142	0.1944	2683	X-RAY DIFFRACTION	99
2.5376-2.5894	0.2679	142	0.1979	2701	X-RAY DIFFRACTION	99
2.5894-2.6457	0.2535	142	0.2049	2699	X-RAY DIFFRACTION	99
2.6457-2.7072	0.2486	141	0.2031	2692	X-RAY DIFFRACTION	99
2.7072-2.7749	0.2131	141	0.1921	2672	X-RAY DIFFRACTION	99
2.7749-2.8499	0.2469	142	0.1911	2702	X-RAY DIFFRACTION	99
2.8499-2.9338	0.2268	143	0.1887	2700	X-RAY DIFFRACTION	99
2.9338-3.0284	0.2346	140	0.1905	2671	X-RAY DIFFRACTION	98
3.0284-3.1366	0.2206	143	0.1772	2717	X-RAY DIFFRACTION	99
3.1366-3.2621	0.2309	141	0.1666	2685	X-RAY DIFFRACTION	98
3.2621-3.4105	0.2149	143	0.1701	2698	X-RAY DIFFRACTION	98
3.4105-3.5902	0.2123	143	0.1666	2723	X-RAY DIFFRACTION	98
3.5902-3.815	0.1635	141	0.145	2685	X-RAY DIFFRACTION	98
3.815-4.1092	0.1727	143	0.1435	2715	X-RAY DIFFRACTION	98
4.1092-4.5222	0.1822	141	0.1356	2672	X-RAY DIFFRACTION	98
4.5222-5.1753	0.1576	144	0.1317	2734	X-RAY DIFFRACTION	97
5.1753-6.5154	0.1915	142	0.1691	2713	X-RAY DIFFRACTION	97
6.5154-39.0358	0.2042	148	0.1889	2789	X-RAY DIFFRACTION	95

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	0.8628	0.0073	-0.1332	1.1863	-0.3875	0.9057	0.0578	0.0422	-0.0078	0.0101	-0.0773	-0.0238	-0.1217	-0.125	0.0089	0.3155	0.0791	-0.015	0.2051	-0.0116	0.2131	52.4093	11.7653	31.882
2	2.4703	-0.2872	-0.1948	1.439	-0.6943	2.6214	0.1018	0.2227	-0.3485	-0.3379	-0.1414	-0.1093	0.2642	-0.0993	0.1096	0.447	0.145	0.0128	0.2655	-0.0007	0.2883	56.5094	13.8556	13.4543
3	0.9196	0.1271	0.0384	1.6792	-0.3347	0.9557	0.0464	-0.0656	0.0244	0.0758	-0.0286	-0.0392	-0.1553	-0.1378	0.0005	0.3359	0.0925	-0.0024	0.2103	0.0114	0.2175	49.6904	11.3741	39.1294
4	1.2884	0.0528	-0.1197	1.2532	-0.2455	0.9238	-0.0589	-0.0089	0.0989	-0.056	0.05	-0.0414	-0.1622	-0.1466	0.0281	0.1344	-0.0043	-0.0048	0.3721	-0.0017	0.1813	81.4812	65.4182	32.1556
5	1.5541	-0.1641	-0.6743	0.7946	-0.4177	1.9084	-0.0655	-0.2936	-0.0737	0.0284	-0.0005	-0.1035	-0.0327	-0.001	0.0635	0.1575	-0.0207	0.0049	0.4479	-0.0141	0.2639	78.5439	53.4598	45.2009
6	1.3577	0.2818	-0.0474	1.3093	0.1902	0.9767	-0.0334	0.0766	0.0335	-0.0949	0.0399	-0.0563	-0.0984	-0.1421	0.0338	0.1773	0.0103	0.0105	0.3965	0.0038	0.232	80.3807	64.6135	30.1523
7	1.4615	-0.0969	0.3762	0.85	-0.0162	1.1017	-0.0121	0.0284	0.0207	0.0501	0.0218	0.0498	0.2628	-0.0321	0.0065	0.3109	0.0918	0.0191	0.209	0.0035	0.2079	34.1051	37.3182	0.4105
8	0.8241	-0.1237	0.4185	1.6256	-0.1165	1.6307	-0.103	-0.0516	0.1131	0.1826	0.0273	-0.0319	0.0251	0.0349	0.0944	0.3116	0.1169	-0.0081	0.2301	0.0129	0.268	43.4942	42.0266	9.5275
9	1.5197	-0.3972	-0.0319	1.0942	-0.1518	0.7271	0.0129	0.09	0.0701	0.0323	-0.0021	0.0414	0.1284	-0.0338	0.0163	0.3285	0.0832	-0.0126	0.2173	0.0159	0.2418	31.0901	37.8932	-4.2772

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 8:154)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 155:206)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 207:313)
4	X-RAY DIFFRACTION	4	(CHAIN B AND RESID 1008:1095)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID 1096:1222)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 1223:1314)
7	X-RAY DIFFRACTION	7	(CHAIN C AND RESID 2008:2123)
8	X-RAY DIFFRACTION	8	(CHAIN C AND RESID 2124:2234)
9	X-RAY DIFFRACTION	9	(CHAIN C AND RESID 2235:2314)

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