PDB-8ccu: Cathepsin B1 from Schistosoma mansoni in complex with gallinamide...

ID or keywords:

Entry

Database: PDB / ID: 8ccu

Title

Cathepsin B1 from Schistosoma mansoni in complex with gallinamide analog 1

Components

Cathepsin B-like peptidase (C01 family)

Keywords

HYDROLASE /

cysteine protease /

cathepsin B / SmCB1 /

Schistosoma mansoni / protease inhibitor peptidomimetic / gallinamide A

Function / homology

Function and homology information

cysteine-type endopeptidase activity /

Biological species

Schistosoma mansoni (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Rubesova, P. / Brynda, J. / Gerwick, W.H. / Mares, M.

Funding support

Czech Republic, 2items

Citation

Journal: To Be Published
Title: Cathepsin B1 from Schistosoma mansoni in complex with gallinamide analog 1
Authors: Rubesova, P. / Brynda, J. / Gerwick, W.H. / Mares, M.

History

Deposition	Jan 27, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 7, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8ccu.cif.gz	78.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8ccu.ent.gz		Display	PDB format
PDBx/mmJSON format	8ccu.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cc/8ccu ftp://data.pdbj.org/pub/pdb/validation_reports/cc/8ccu	HTTPS FTP

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Related structure data

Related structure data	8cc2
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
Related items in Molecule of the Month	#142 - Oct 2011 PDB Pioneers similarity (9)

Deposited unit

AAA: Cathepsin B-like peptidase (C01 family)

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: homology

Unit cell

Length a, b, c (Å)	33.081, 79.031, 90.584
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Cathepsin B-like peptidase (C01 family) / Cathepsin B1 isotype 1 Mass: 28507.256 Da / Num. of mol.: 1 / Mutation: T168A, T283A Source method: isolated from a genetically manipulated source Details: the first amino acid has number 70, numbering is the same as in 4I07 and 8CC2 Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: cb1.1, Smp_103610 / Plasmid: pPICZ(alpha) A / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: Q8MNY2
#2: Chemical	ChemComp-U9X / [(2~{S})-1-[[(2~{S})-1-[[(2~{S})-5-[(2~{S})-3-methoxy-2-(2-methylpropyl)-5-oxidanylidene-2~{H}-pyrrol-1-yl]-5-oxidanylidene-pentan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl] (2~{S},3~{S})-2-(dimethylamino)-3-methyl-pentanoate Mass: 636.863 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₄H₆₀N₄O₇ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.08 Å³/Da / Density % sol: 40.81 %
Crystal grow	Temperature: 278.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.2 M ammonium acetate, 0.1 M sodium citrate, 30% PEG 3350, streak seeding

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.1 / Wavelength: 0.918 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.918 Å / Relative weight: 1

Reflection

Resolution: 1.6→50 Å / Num. obs: 32051 / % possible obs: 99.4 % / Redundancy: 5.9 % / CC_1/2: 0.997 / R_merge(I) obs: 0.115 / R_rim(I) all: 0.126 / Net I/σ(I): 10.65

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID	% possible all
1.6-1.7	0.944	4938	0.482	1.11	1	96.5
1.7-1.81	0.671	4827	0.801	0.737	1	99.9
1.81-1.96	0.409	4505	0.932	0.444	1	99.9
1.96-2.14	0.234	4160	0.974	0.255	1	99.9
2.14-2.4	0.16	3785	0.987	0.173	1	99.9
2.4-2.77	0.116	3365	0.992	0.126	1	100
2.77-3.38	0.071	2856	0.997	0.077	1	99.9
3.38-4.77	0.049	2274	0.998	0.053	1	99.8
4.77-50	0.043	1341	0.998	0.048	1	99.6

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0257	refinement
XSCALE		data scaling
XDS	20210323	data reduction
MOLREP	11.7.02	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→45.292 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.958 / SU B: 2.11 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.089
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1937	1601	5 %
R_work	0.1597	30418	-
all	0.161	-	-
obs	-	32019	99.392 %

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: 17.476 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.135 Å²	-0 Å²	0 Å²
2-	-	0.28 Å²	0 Å²
3-	-	-	-0.146 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→45.292 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1995	0	46	261	2302

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	2200
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	1983
X-RAY DIFFRACTION	r_angle_refined_deg	1.703	1.677	2982
X-RAY DIFFRACTION	r_angle_other_deg	1.485	1.626	4640
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.644	5	273
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.944	22.342	111
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.936	15	381
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	11.228	15	1
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.199	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	278
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	2493
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	469
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	438
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	0.2	1850
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	1055
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	921
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.175	0.2	178
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.211	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.08	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.144	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.193	0.2	61
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.205	0.2	17
X-RAY DIFFRACTION	r_mcbond_it	1.431	1.539	1062
X-RAY DIFFRACTION	r_mcbond_other	1.423	1.538	1061
X-RAY DIFFRACTION	r_mcangle_it	2.122	2.303	1339
X-RAY DIFFRACTION	r_mcangle_other	2.124	2.304	1340
X-RAY DIFFRACTION	r_scbond_it	2.781	1.913	1138
X-RAY DIFFRACTION	r_scbond_other	2.78	1.915	1139
X-RAY DIFFRACTION	r_scangle_it	4.292	2.726	1641
X-RAY DIFFRACTION	r_scangle_other	4.29	2.728	1642
X-RAY DIFFRACTION	r_lrange_it	5.214	19.062	2615
X-RAY DIFFRACTION	r_lrange_other	5.117	18.61	2551

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
1.6-1.642	0.374	112	0.317	2121	0.319	2361	0.717	0.731	94.5786	0.315
1.642-1.686	0.319	111	0.294	2103	0.295	2253	0.755	0.79	98.269	0.287
1.686-1.735	0.275	111	0.249	2121	0.25	2235	0.843	0.853	99.8658	0.242
1.735-1.789	0.229	107	0.208	2024	0.209	2133	0.903	0.904	99.9062	0.197
1.789-1.847	0.211	105	0.18	2007	0.181	2113	0.931	0.934	99.9527	0.163
1.847-1.912	0.22	101	0.168	1912	0.171	2015	0.921	0.939	99.9007	0.148
1.912-1.984	0.186	98	0.151	1867	0.153	1966	0.957	0.954	99.9491	0.133
1.984-2.065	0.206	95	0.148	1810	0.151	1907	0.943	0.96	99.8951	0.13
2.065-2.156	0.194	90	0.137	1704	0.14	1794	0.954	0.968	100	0.119
2.156-2.261	0.176	87	0.134	1655	0.136	1743	0.961	0.969	99.9426	0.116
2.261-2.383	0.18	84	0.124	1586	0.127	1672	0.961	0.97	99.8804	0.107
2.383-2.527	0.198	78	0.127	1497	0.131	1577	0.957	0.971	99.8732	0.11
2.527-2.701	0.219	74	0.131	1399	0.135	1473	0.953	0.97	100	0.114
2.701-2.917	0.17	70	0.14	1323	0.141	1393	0.96	0.969	100	0.125
2.917-3.194	0.162	64	0.15	1218	0.151	1285	0.967	0.968	99.7665	0.139
3.194-3.569	0.178	59	0.146	1118	0.147	1177	0.967	0.971	100	0.139
3.569-4.117	0.129	52	0.131	996	0.131	1048	0.981	0.981	100	0.131
4.117-5.031	0.122	45	0.132	849	0.132	898	0.986	0.984	99.5546	0.138
5.031-7.072	0.187	36	0.205	680	0.204	716	0.966	0.968	100	0.207
7.072-45.292	0.332	22	0.222	417	0.228	443	0.905	0.943	99.0971	0.239

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