PDB-4i04: Structure of zymogen of cathepsin B1 from Schistosoma mansoni

ID or keywords:

Entry

Database: PDB / ID: 4i04

Title

Structure of zymogen of cathepsin B1 from Schistosoma mansoni

Components

Cathepsin B-like peptidase (C01 family)

Keywords

HYDROLASE / peptidase / digestive tract

Function / homology

Function and homology information

proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space
Similarity search - Function

Biological species

Schistosoma mansoni (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Rezacova, P. / Jilkova, A. / Brynda, J. / Horn, M. / Mares, M.

Citation

Journal: Structure / Year: 2014
Title: Activation route of the Schistosoma mansoni cathepsin B1 drug target: structural map with a glycosaminoglycan switch
Authors: Jilkova, A. / Horn, M. / Rezacova, P. / Maresova, L. / Fajtova, P. / Brynda, J. / Vondrasek, J. / McKerrow, J.H. / Caffrey, C.R. / Mares, M.

History

Deposition	Nov 16, 2012	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Feb 5, 2014	Provider: repository / Type: Initial release
Revision 1.1	May 25, 2016	Group: Database references
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4i04.cif.gz	498.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4i04.ent.gz	412.2 KB	Display	PDB format
PDBx/mmJSON format	4i04.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4i04_validation.pdf.gz	474 KB	Display	wwPDB validaton report
Full document	4i04_full_validation.pdf.gz	490.5 KB	Display
Data in XML	4i04_validation.xml.gz	49.3 KB	Display
Data in CIF	4i04_validation.cif.gz	70.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i0/4i04 ftp://data.pdbj.org/pub/pdb/validation_reports/i0/4i04	HTTPS FTP

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Related structure data

Related structure data	4i05C 4i07C 3qsdS 3s3q 3s3r C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3jua-2 3jua-1 4p6w-d 6ge4-d 6gee-d 6ge5-d 3cwd-1 6hil-2 4fw3-1 6gpa-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

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 (9)

Deposited unit

A: Cathepsin B-like peptidase (C01 family)

B: Cathepsin B-like peptidase (C01 family)

C: Cathepsin B-like peptidase (C01 family)

D: Cathepsin B-like peptidase (C01 family)

hetero molecules

147 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cathepsin B-like peptidase (C01 family)

hetero molecules

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

2

B: Cathepsin B-like peptidase (C01 family)

hetero molecules

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

3

C: Cathepsin B-like peptidase (C01 family)

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

4

D: Cathepsin B-like peptidase (C01 family)

hetero molecules

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

Unit cell

Length a, b, c (Å)	54.281, 83.172, 84.569
Angle α, β, γ (deg.)	76.97, 86.60, 71.11
Int Tables number	1
Space group name H-M	P1

#1: Protein	Cathepsin B-like peptidase (C01 family) / Cathepsin B1 isotype 1 Mass: 36728.207 Da / Num. of mol.: 4 / Mutation: C100S, T168A, T283A Source method: isolated from a genetically manipulated source Details: zeocin resistance / Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: cb1.1, Smp_103610 / Plasmid: pPICZalpha / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: Q8MNY2, cathepsin B
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.4 Å³/Da / Density % sol: 48.65 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Reservoir: 0.1M Ammonium Acetate, 0.1M Bis-Tris, 17% PEG 10000. Protein buffer and concentration: 5mM Sodium Acetate, pH 5.5, Cpr=5.25mg/ml. Ratio Protein: Reservoir=2:1. Cryocooled in ...Details: Reservoir: 0.1M Ammonium Acetate, 0.1M Bis-Tris, 17% PEG 10000. Protein buffer and concentration: 5mM Sodium Acetate, pH 5.5, Cpr=5.25mg/ml. Ratio Protein: Reservoir=2:1. Cryocooled in mother liquor containing 20% ethylene glycol., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal

Density Matthews: 2.4 Å³/Da / Density % sol: 48.65 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Reservoir: 0.1M Ammonium Acetate, 0.1M Bis-Tris, 17% PEG 10000. Protein buffer and concentration: 5mM Sodium Acetate, pH 5.5, Cpr=5.25mg/ml. Ratio Protein: Reservoir=2:1. Cryocooled in ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.914 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 1, 2011 Details: Double crystal monochromator with 2 sets of Rh-soated silicon and glass mirrors
Radiation	Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.914 Å / Relative weight: 1
Reflection	Resolution: 1.95→50 Å / Num. obs: 78650 / % possible obs: 78.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / B_iso Wilson estimate: 25.2 Å² / R_merge(I) obs: 0.037 / Net I/σ(I): 25.9
Reflection shell	Resolution: 1.95→1.98 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.296 / Mean I/σ(I) obs: 3.1 / % possible all: 42.1

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Processing

Software

Name	Version	Classification
MarDB		data collection
MOLREP		phasing
REFMAC	5.3.0037	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3QSD

3qsd

Resolution: 1.95→38.4 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.904 / SU B: 8.596 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.254 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25245	3756	5 %	RANDOM
R_work	0.19927	-	-	-
all	0.20195	95142	-	-
obs	0.20195	71614	75.27 %	-

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: 21.792 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	0.01 Å²	0.01 Å²
2-	-	0.01 Å²	0.01 Å²
3-	-	-	-0.01 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→38.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9797	0	24	519	10340

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	10117
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.303	1.935	13662
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.062	5	1234
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.195	23.593	501
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.521	15	1742
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.278	15	84
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	1359
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	7842
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.205	0.2	5058
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.306	0.2	6765
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	723
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	0.181	0.2	84
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.227	0.2	32
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	0.565	1.5	6308
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.911	2	9813
X-RAY DIFFRACTION	r_scbond_it	1.513	3	4506
X-RAY DIFFRACTION	r_scangle_it	2.26	4.5	3842
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.945→1.996 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.285	84	-
R_work	0.247	1585	-
obs	-	-	22.55 %

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	1.2831	-0.395	0.5402	4.7832	-0.906	3.9298	-0.1055	-0.2902	-0.0843	0.4985	0.1815	-0.0004	0.1654	0.0763	-0.0759	-0.0085	0.1144	0.0961	0.165	0.0153	0.0329	24.56	-39.112	-42.537
2	1.4208	0.0871	0.2783	1.5156	0.467	3.1696	0.0847	-0.0456	0.2263	0.1492	0.0728	0.1674	-0.2781	0.0097	-0.1576	-0.034	0.0618	-0.0083	-0.0924	-0.01	0.0271	24.874	-20.328	-60.567
3	1.5287	0.3048	0.994	1.3366	0.2961	0.6539	-0.0002	-0.0399	0.4013	0.2331	0.1449	0.0136	-0.6029	0.13	-0.1446	0.2052	0.0317	-0.0135	0.1226	-0.1031	0.1229	29.986	-13.285	-51.32
4	0.9756	0.0433	0.2067	2.1399	-0.1793	2.1426	-0.0618	-0.2829	0.2505	0.3632	0.0569	-0.2222	-0.5473	0.2574	0.005	0.0586	0.0372	-0.0156	0.0762	-0.0644	0.1119	33.046	-14.17	-53.428
5	1.1395	-0.2129	0.1711	2.2268	-0.1032	1.8842	-0.0115	-0.1573	0.0807	0.3128	0.1427	0.3112	-0.1012	-0.1165	-0.1311	-0.0638	0.1246	0.0503	-0.0013	0.0007	-0.0273	22.514	-31.774	-54.162
6	2.5303	-0.8886	-1.4435	6.2483	1.1193	7.3971	0.091	0.3332	0.2006	-0.4177	0.0035	0.0705	-0.3014	-0.342	-0.0946	-0.1145	-0.0293	-0.0656	0.0342	0.1151	-0.1123	4.894	8.856	-31.058
7	2.3108	0.0474	-0.9989	1.7247	0.1296	2.7064	-0.0595	0.0771	-0.1905	-0.1216	0.109	0.1263	0.3256	-0.1626	-0.0495	-0.1373	-0.0301	-0.0152	-0.1674	0.0172	-0.1006	4.057	-12.353	-13.894
8	3.6404	0.4563	-0.4388	4.8469	1.9375	2.4697	0.0009	-0.0142	-0.356	-0.1996	0.0623	-0.1093	0.8311	-0.1182	-0.0631	-0.0403	-0.0344	0.04	-0.0593	-0.0119	-0.0457	10.493	-20.093	-21.795
9	2.3126	-0.3205	-0.8517	2.1412	0.0902	2.5484	-0.0932	0.158	-0.2567	-0.2255	0.0585	-0.2272	0.4126	0.1963	0.0346	-0.0717	-0.0135	-0.0052	-0.0896	-0.0229	-0.0669	13.143	-18.079	-19.267
10	1.3364	0.3641	-0.3853	2.4347	0.0992	2.96	-0.0944	0.1668	0.0189	-0.2055	0.1987	0.2418	0.0222	-0.2709	-0.1044	-0.204	-0.027	-0.0318	-0.1025	0.0451	-0.1578	2.08	-0.998	-19.022
11	4.7116	-0.5253	0.3089	3.8276	-2.1538	5.0252	0.1144	0.1093	0.3049	0.0294	-0.1034	-0.3264	-0.4543	0.401	-0.011	-0.1172	-0.1147	0.0419	-0.1141	-0.0337	-0.0221	17.939	40.857	-69.994
12	2.3373	-0.3959	0.0618	2.1185	0.1452	3.0627	-0.0006	-0.139	-0.1004	-0.0568	0.0887	0.1645	0.1892	-0.053	-0.0881	-0.1444	-0.0164	-0.0329	-0.1894	0.0719	-0.1411	7.889	16.783	-59.705
13	2.1189	0.1461	0.0301	3.6201	-0.8248	3.4804	0.0802	-0.289	0.0175	0.0918	-0.15	-0.5565	0.1961	0.7097	0.0698	-0.1607	0.0245	-0.0522	0.0394	0.0303	-0.061	22.217	15.124	-50.803
14	1.3372	-0.6146	0.2435	2.3886	-1.1837	2.324	0.1188	-0.0256	-0.1035	-0.2449	0.0863	0.1835	0.1776	-0.0112	-0.205	-0.1563	-0.0381	-0.025	-0.1819	-0.0022	-0.1577	8.739	21.682	-64.539
15	2.0084	-0.3826	-0.4086	4.1783	-1.2419	2.6832	0.2126	-0.0525	-0.0484	-0.2955	0.09	0.1557	0.0667	-0.1426	-0.3027	-0.1891	-0.0321	-0.0305	-0.1929	0.0152	-0.1624	7.572	24.264	-64.684
16	3.799	0.1366	1.1489	4.6126	-1.104	4.3648	0.1568	-0.1045	-0.4175	0.1366	-0.0467	-0.3387	0.1356	0.6987	-0.1101	-0.1595	0.0561	-0.1183	-0.0206	-0.0969	0.0315	24.696	7.139	-3.528
17	1.5224	0.518	0.3234	2.5177	0.6599	1.7492	-0.0467	0.1703	0.0683	-0.2082	0.1239	0.2621	-0.3492	0.0016	-0.0773	-0.0343	0.0147	0.0299	-0.1041	0.0349	-0.0781	12.772	30.003	-13.213
18	2.6007	-0.5549	-0.7244	4.8007	0.2367	3.3984	0.0719	0.37	0.0241	-0.2552	0.074	-0.4117	-0.3524	0.4674	-0.1459	-0.0079	-0.1208	0.0535	0.0752	-0.0338	-0.0786	26.413	30.325	-20.252
19	1.6057	0.84	0.0606	2.8162	-0.6637	1.2701	0.0341	0.2331	0.1072	-0.0236	0.1066	0.0087	-0.3006	0.2017	-0.1408	-0.0713	0.007	0.0207	-0.1031	-0.0414	-0.1272	17.246	25.079	-12.27
20	2.7632	-0.6922	2.4303	8.2661	-3.4797	4.9289	0.1368	0.1241	0.2621	0.5253	-0.0379	0.2196	-0.5001	-0.0095	-0.0989	-0.036	0.0451	0.1157	-0.1473	-0.046	-0.1221	12.795	29.354	-5.587

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	9 - 50
2	X-RAY DIFFRACTION	2	A	51 - 117
3	X-RAY DIFFRACTION	3	A	118 - 150
4	X-RAY DIFFRACTION	4	A	151 - 240
5	X-RAY DIFFRACTION	5	A	241 - 323
6	X-RAY DIFFRACTION	6	B	8 - 42
7	X-RAY DIFFRACTION	7	B	43 - 119
8	X-RAY DIFFRACTION	8	B	120 - 147
9	X-RAY DIFFRACTION	9	B	148 - 237
10	X-RAY DIFFRACTION	10	B	246 - 323
11	X-RAY DIFFRACTION	11	C	6 - 42
12	X-RAY DIFFRACTION	12	C	43 - 123
13	X-RAY DIFFRACTION	13	C	128 - 209
14	X-RAY DIFFRACTION	14	C	210 - 282
15	X-RAY DIFFRACTION	15	C	294 - 323
16	X-RAY DIFFRACTION	16	D	6 - 46
17	X-RAY DIFFRACTION	17	D	47 - 120
18	X-RAY DIFFRACTION	18	D	121 - 194
19	X-RAY DIFFRACTION	19	D	195 - 295
20	X-RAY DIFFRACTION	20	D	308 - 323

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