PDB-6roa: Crystal structure of V57G mutant of human cystatin C

ID or keywords:

Entry

Database: PDB / ID: 6roa

Title

Crystal structure of V57G mutant of human cystatin C

Components

Cystatin-C

Keywords

HYDROLASE / hydrolase inhibitor / monomeric structure

Function / homology

Function and homology information

negative regulation of collagen catabolic process / negative regulation of elastin catabolic process / negative regulation of blood vessel remodeling / negative regulation of peptidase activity / peptidase inhibitor activity / negative regulation of extracellular matrix disassembly / regulation of tissue remodeling / endopeptidase inhibitor activity / cysteine-type endopeptidase inhibitor activity / supramolecular fiber organization ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

Orlikowska, M. / Behrendt, I. / Borek, D. / Otwinowski, Z. / Skowron, P. / Szymanska, A.

Citation

Journal: Febs J. / Year: 2020
Title: NMR and crystallographic structural studies of the extremely stable monomeric variant of human cystatin C with single amino acid substitution.
Authors: Maszota-Zieleniak, M. / Jurczak, P. / Orlikowska, M. / Zhukov, I. / Borek, D. / Otwinowski, Z. / Skowron, P. / Pietralik, Z. / Kozak, M. / Szymanska, A. / Rodziewicz-Motowidlo, S.

History

Deposition	May 10, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 7, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 29, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6roa.cif.gz	104.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6roa.ent.gz	81.4 KB	Display	PDB format
PDBx/mmJSON format	6roa.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ro/6roa ftp://data.pdbj.org/pub/pdb/validation_reports/ro/6roa	HTTPS FTP

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Related structure data

Related structure data	6rpvC 3nx0S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3nx0-2 4it7-3 6xvn-d 3gax-1 6btz-2 3c57-d 4it7-2 4it7-4 6bya-2 6myj-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) 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	#224 - Aug 2018 Legumain similarity (5)

Deposited unit

A: Cystatin-C

B: Cystatin-C

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

1

A: Cystatin-C

defined by author
Evidence: gel filtration
13.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Cystatin-C

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

Unit cell

Length a, b, c (Å)	75.828, 75.828, 98.176
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

#1: Protein	Cystatin-C / Cystatin-3 / Gamma-trace / Neuroendocrine basic polypeptide / Post-gamma-globulin Mass: 13323.062 Da / Num. of mol.: 2 / Mutation: V57G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CST3 / Plasmid: pHD313 / Production host: Escherichia coli (E. coli) / Variant (production host): C41(DE3) / References: UniProt: P01034
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.04 Å³/Da / Density % sol: 59.57 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Na acetate, 0.1M Na cacodylate pH 6.5, 30% PEG 8000.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97921 Å / Relative weight: 1
Reflection	Resolution: 2.65→50 Å / Num. obs: 9095 / % possible obs: 96.8 % / Redundancy: 4.7 % / B_iso Wilson estimate: 47.82 Å² / R_merge(I) obs: 0.127 / Net I/σ(I): 13.7
Reflection shell	Resolution: 2.65→2.7 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.565 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 9095 / % possible all: 96.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3NX0

3nx0

Resolution: 2.65→50 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.908 / SU B: 25.648 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.528 / ESU R Free: 0.314 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25238	433	4.8 %	RANDOM
R_work	0.17442	-	-	-
obs	0.17819	8583	96.57 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 49.82 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.4 Å²	0.7 Å²	0 Å²
2-	-	1.4 Å²	-0 Å²
3-	-	-	-4.54 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1714	0	0	43	1757

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	1784
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.715	1.911	2415
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.648	5	222
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.614	23.556	90
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.162	15	301
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.823	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.127	0.2	255
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	1386
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	2.794	2.648	882
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	4.527	3.956	1103
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	5.499	3.156	902
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined	10.854	35.681	2400
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.652→2.721 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.282	33	-
R_work	0.297	623	-
obs	-	-	95.77 %

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	2.077	2.2704	3.3853	9.7218	7.8554	7.908	0.3989	-0.6277	0.3512	0.7024	-0.5174	-0.3933	0.764	-0.9397	0.1185	0.3351	-0.0296	0.0895	0.242	-0.0935	0.1624	-37.4177	-1.3469	13.7717
2	0.0351	-0.0707	0.3921	0.9722	1.1376	9.0162	-0.03	0.044	0.0652	0.3046	-0.0687	-0.4178	0.0654	0.4157	0.0986	0.2423	-0.0083	-0.0828	0.1305	0.0563	0.2721	-29.2751	1.0893	5.7179
3	4.6894	5.0131	-3.736	5.4591	-4.483	5.3907	-0.2103	0.1235	-0.0337	-0.2324	0.1097	-0.0513	0.01	0.1411	0.1007	0.2807	0.0188	0.0674	0.1421	0.0259	0.1238	-27.483	8.1246	-6.7809
4	9.7639	4.579	-5.3948	6.0069	-4.5328	4.2891	0.0646	-0.4126	-0.1982	0.4209	-0.2365	-0.1728	-0.349	0.3135	0.172	0.1609	-0.0411	-0.067	0.1173	-0.0411	0.1052	-30.9336	12.2085	3.3268
5	1.906	0.7287	0.0187	9.6713	1.9511	6.7011	-0.0191	0.1208	-0.4412	0.0734	-0.0653	0.1859	-0.1341	-0.2277	0.0844	0.1372	-0.0663	0.0004	0.087	0.0084	0.179	-40.1977	-6.5981	7.0927
6	6.033	9.3652	-3.8285	15.3157	-6.4077	2.7093	0.0325	-0.052	0.1641	0.0353	0.0437	0.2195	-0.0003	-0.0308	-0.0762	0.1521	-0.0152	0.0303	0.1183	-0.0189	0.1513	-36.2338	9.2318	2.8155
7	4.5429	4.7952	-2.4111	5.0724	-2.6235	1.8577	0.176	-0.5113	-0.3931	0.0869	-0.5683	-0.4419	0.3682	0.789	0.3923	0.3572	0.3779	0.0764	0.6343	0.0076	0.3827	-20.1182	15.3404	-2.1657
8	30.9808	1.0558	20.3143	0.0711	0.7051	13.3252	0.6159	0.3328	-0.6836	0.1581	-0.1046	0.0835	0.5215	0.2151	-0.5113	0.8862	0.2169	0.0953	0.3358	-0.2307	0.7732	-16.1093	12.0837	3.1753
9	6.0896	-6.2864	-0.4248	7.2051	3.26	11.2173	-0.4367	-0.076	0.2045	0.4267	0.2171	-0.1261	-0.1723	0.5301	0.2196	0.2161	-0.1267	0.0095	0.1517	0.0062	0.262	-26.4051	21.7959	3.7398
10	3.981	7.0767	-0.0899	12.6029	-0.2045	3.4466	0.2047	0.0204	0.2267	0.3245	0.0881	0.3636	-0.0997	-0.173	-0.2927	0.1157	-0.0165	0.0083	0.1346	-0.0279	0.1821	-35.0768	18.6842	-1.1367
11	0.6921	-0.4534	0.8217	5.9945	-3.508	2.7034	0.1116	-0.0962	-0.1274	-0.2771	0.0944	0.347	0.0588	-0.0586	-0.206	0.212	-0.0346	-0.0448	0.1269	0.0142	0.1315	-35.8329	-4.5942	1.6153
12	5.3152	-5.1784	5.1426	9.7451	-9.817	9.8915	0.1266	0.3723	-0.129	-0.2222	-0.3445	-0.2106	0.2221	0.3385	0.2179	0.2668	0.0116	-0.0449	0.0638	-0.0559	0.112	-30.7619	-10.5867	1.8275
13	4.5845	-1.5653	2.6982	17.7448	1.8021	2.0221	-0.5907	-0.5842	0.1623	-0.2928	0.4223	0.5228	-0.3916	-0.3108	0.1684	0.2603	0.0478	-0.0354	0.2224	-0.0172	0.1128	-39.8562	8.1894	-4.1221
14	9.5917	-3.9801	2.2643	4.2773	-0.2416	0.7351	-0.2637	-0.1282	-0.0897	-1.0117	0.4657	-0.511	-0.3609	0.0094	-0.202	0.4835	-0.1599	0.2418	0.414	0.0446	0.1652	-21.8299	32.804	5.2012
15	1.5324	1.5593	-3.7893	4.0317	-0.8294	13.1361	-0.2158	-0.0971	-0.1631	-0.3199	0.0972	-0.3506	0.4073	0.5556	0.1186	0.1074	-0.0237	-0.023	0.3697	-0.13	0.2297	-16.5539	23.9591	11.0267
16	3.0443	6.3539	-1.767	13.7603	-1.3779	11.747	0.1089	-0.0399	-0.3521	0.303	-0.057	-0.7942	0.3098	0.1906	-0.0518	0.1603	0.0045	-0.0198	0.1578	0.0474	0.2059	-20.3889	19.8171	22.1218
17	2.4537	0.5497	3.3154	11.6076	1.169	4.5046	0.0604	0.0752	-0.2191	0.7276	0.1746	-0.0206	0.0318	0.1334	-0.235	0.2038	-0.0761	-0.0389	0.2589	0.0015	0.1421	-24.8861	12.2599	25.5864
18	1.7394	1.4712	-1.9035	5.1585	-1.495	4.4588	-0.0144	0.2855	0.0854	-0.5357	-0.1097	0.627	-0.093	-0.0968	0.1241	0.1374	-0.0281	-0.0855	0.1638	-0.014	0.0999	-25.2421	28.2887	11.2965
19	4.5376	0.8588	0.8108	0.4617	-1.041	4.9181	0.2089	0.125	0.4672	0.0921	-0.0344	0.1511	-0.1913	0.2489	-0.1745	0.1502	-0.0355	0.0545	0.1742	-0.0004	0.1759	-17.4175	35.0944	13.8945
20	2.0248	7.6696	-3.8188	37.1741	-20.1746	13.3017	-0.0859	0.156	0.1804	0.0239	0.3012	0.3049	-0.2365	-0.2748	-0.2154	0.1094	0.0033	0.0119	0.0876	0.0048	0.161	-30.1229	20.9525	16.6897
21	2.9989	7.0396	1.7138	21.7199	-0.7666	5.3972	0.7121	0.0398	0.0949	0.6073	-0.9949	0.0092	1.3409	1.0376	0.2828	0.398	0.1964	0.0154	0.3466	0.0182	0.1569	-24.0519	7.6119	20.8516
22	38.0948	-10.2207	-6.2647	2.7433	1.682	1.0318	0.4355	2.4809	-1.2081	-0.099	-0.6507	0.3399	-0.0511	-0.3811	0.2152	0.3607	0.3416	0.2005	0.7297	0.2215	0.3584	-19.2917	6.7048	15.2919
23	0.1452	-0.3052	1.0038	4.7447	0.6039	8.7671	0.0299	-0.0009	-0.0116	-0.049	-0.0431	0.1835	0.3316	-0.0464	0.0132	0.2304	-0.0258	0.0213	0.1376	-0.0129	0.2151	-34.1608	9.7054	16.855
24	8.2494	2.5956	-1.1814	12.1261	0.0254	0.1841	-0.323	0.2217	0.098	-0.24	0.3333	0.5054	0.0383	-0.0134	-0.0103	0.2337	-0.0063	0.0188	0.1159	-0.0473	0.1394	-33.9248	20.5796	19.1774
25	4.5224	2.3883	-2.0841	1.8618	0.1482	3.6118	0.4835	-0.4766	0.1063	0.1441	-0.17	-0.0599	-0.3558	0.3881	-0.3135	0.2319	-0.049	0.0247	0.1946	0.0212	0.1522	-13.0094	32.2122	16.3315
26	12.56	2.7223	0.807	2.4638	0.9597	0.3823	-0.0846	-0.2788	-0.1595	0.0857	0.0209	0.1678	0.026	0.0365	0.0637	0.2392	-0.0301	-0.0009	0.2038	0.028	0.0683	-23.596	28.1286	22.0014

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	12 - 21
2	X-RAY DIFFRACTION	2	A	22 - 32
3	X-RAY DIFFRACTION	3	A	33 - 40
4	X-RAY DIFFRACTION	4	A	41 - 51
5	X-RAY DIFFRACTION	5	A	52 - 62
6	X-RAY DIFFRACTION	6	A	63 - 70
7	X-RAY DIFFRACTION	7	A	71 - 76
8	X-RAY DIFFRACTION	8	A	77 - 81
9	X-RAY DIFFRACTION	9	A	82 - 89
10	X-RAY DIFFRACTION	10	A	90 - 97
11	X-RAY DIFFRACTION	11	A	98 - 105
12	X-RAY DIFFRACTION	12	A	106 - 112
13	X-RAY DIFFRACTION	13	A	113 - 120
14	X-RAY DIFFRACTION	14	B	12 - 20
15	X-RAY DIFFRACTION	15	B	21 - 29
16	X-RAY DIFFRACTION	16	B	30 - 36
17	X-RAY DIFFRACTION	17	B	37 - 43
18	X-RAY DIFFRACTION	18	B	44 - 56
19	X-RAY DIFFRACTION	19	B	57 - 64
20	X-RAY DIFFRACTION	20	B	65 - 70
21	X-RAY DIFFRACTION	21	B	71 - 76
22	X-RAY DIFFRACTION	22	B	77 - 81
23	X-RAY DIFFRACTION	23	B	82 - 91
24	X-RAY DIFFRACTION	24	B	92 - 97
25	X-RAY DIFFRACTION	25	B	98 - 108
26	X-RAY DIFFRACTION	26	B	109 - 120

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