PDB-3qrd: Crystal structure of L68V mutant of human cystatin C

ID or keywords:

Entry

Database: PDB / ID: 3qrd

Title

Crystal structure of L68V mutant of human cystatin C

Components

Cystatin-C

Keywords

HYDROLASE INHIBITOR / cysteine protease inhibitor / 3D domain swapping / protein / Hereditary Cystatin C Amyloid Angiopathy / Protease inhibitor

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: 2.19 Å

Authors

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

Citation

Journal: To be Published
Title: Crystal structure of L68V mutant of human cystatin C
Authors: Orlikowska, M. / Borek, D. / Otwinowski, Z. / Skowron, P. / Szymanska, A.

History

Deposition	Feb 17, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 29, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 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 1.2	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3qrd.cif.gz	102.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3qrd.ent.gz	80.9 KB	Display	PDB format
PDBx/mmJSON format	3qrd.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/qr/3qrd ftp://data.pdbj.org/pub/pdb/validation_reports/qr/3qrd	HTTPS FTP

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Related structure data

Related structure data	3ps8C 1g96S 1r4c 1tij 3gax 3nx0 C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3fld-d 6jo7-1 6z5q-d 7alf-d 3bis-1 5av7-2 4g8k-1 2ght-d 4xoa-4 4xxi-d 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	#224 - Aug 2018 Legumain similarity (5)

Deposited unit

A: Cystatin-C

B: Cystatin-C

C: Cystatin-C

D: Cystatin-C

hetero molecules

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

1

A: Cystatin-C

B: Cystatin-C

hetero molecules

defined by author&software
26.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Cystatin-C

D: Cystatin-C

hetero molecules

defined by author&software
27.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

A: Cystatin-C

B: Cystatin-C

hetero molecules

A: Cystatin-C

B: Cystatin-C

hetero molecules

C: Cystatin-C

D: Cystatin-C

hetero molecules

C: Cystatin-C

D: Cystatin-C

hetero molecules

defined by software
108 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	103.123, 89.876, 65.154
Angle α, β, γ (deg.)	90.00, 107.03, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Cystatin-C / Cystatin-3 / Gamma-trace / Neuroendocrine basic polypeptide / Post-gamma-globulin Mass: 13351.114 Da / Num. of mol.: 4 / Mutation: L68V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CST3 / Plasmid: pHD313 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(de3) / References: UniProt: P01034
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.7 Å³/Da / Density % sol: 54.49 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.18M tri-Sodium citrate, 0.1M TrisHCl pH 8.0, 30% PEG, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97929 Å / Relative weight: 1
Reflection	Resolution: 2.14→50 Å / Num. obs: 28962 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / R_merge(I) obs: 0.057 / R_sym value: 0.057 / Net I/σ(I): 33.889
Reflection shell	Resolution: 2.14→2.24 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.554 / Mean I/σ(I) obs: 2.09 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
HKL-3000		data collection
MOLREP		phasing
REFMAC	5.5.0110	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G96

1g96

Resolution: 2.19→36.45 Å / Cor.coef. F_o:F_c: 0.93 / Cor.coef. F_o:F_c free: 0.846 / SU B: 17.444 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29325	1204	5 %	RANDOM
R_work	0.2137	-	-	-
obs	0.21766	23060	83.06 %	-
all	-	28962	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 16.196 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.13 Å²	0 Å²	-1.49 Å²
2-	-	1.32 Å²	0 Å²
3-	-	-	-1.06 Å²

Refinement step

Cycle: LAST / Resolution: 2.19→36.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3409	0	42	108	3559

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	3559
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.283	1.941	4801
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.558	5	437
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.957	23.736	174
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.158	15	593
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.73	15	29
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	514
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	2715
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	4.109	1.5	2181
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	5.536	2	3517
X-RAY DIFFRACTION	r_scbond_it	9.635	3	1378
X-RAY DIFFRACTION	r_scangle_it	12.062	4.5	1283
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.19→2.249 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.257	26	-
R_work	0.22	516	-
obs	-	-	25.53 %

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	14.4173	0.166	4.674	10.2591	-1.5039	17.8369	0.4682	0.0185	-0.2581	0.0314	-0.4596	-1.3281	0.8739	1.1293	-0.0086	0.2405	0.0816	0.0871	0.1081	0.0548	0.3103	35.3838	32.0439	-41.7721
2	48.3853	11.4241	-6.7708	25.3454	1.5842	29.2048	-0.2193	1.7046	-0.4422	-1.2999	0.2641	-0.1157	0.4773	-0.6777	-0.0449	0.2382	0.0465	0.0818	0.1252	-0.0205	0.0823	25.713	29.0952	-48.3381
3	14.318	-4.3016	-8.8957	10.5109	-0.7615	6.8951	0.2165	-0.6577	0.2768	0.019	0.2782	0.8839	-0.1497	0.0855	-0.4947	0.1883	-0.078	-0.0287	1.0489	-0.2127	0.2785	13.1584	32.0802	-38.3875
4	5.1375	-1.4643	2.4296	5.3705	-1.3467	3.7278	-0.1933	-0.4396	0.5714	0.3506	-0.1173	0.2793	-0.1881	-0.5616	0.3106	0.1979	-0.0242	0.0618	0.1422	-0.0579	0.1897	22.5968	35.3031	-40.856
5	3.3006	0.0954	1.7851	3.3138	1.0165	4.5948	0.0935	-0.2448	-0.0069	0.3394	-0.18	-0.2938	0.0351	0.2451	0.0864	0.1265	-0.0376	0.0789	0.0819	0.0404	0.1967	42.7804	5.2169	-14.0927
6	21.9588	5.5024	-8.8855	5.3462	-4.1233	17.3271	0.1714	-1.257	-1.4805	0.9705	-0.163	-0.3868	1.3111	0.137	-0.0083	0.6001	-0.0524	0.013	0.1528	0.1287	0.3094	44.085	-4.0664	-2.6464
7	4.5732	-0.7832	2.8154	3.9315	0.9432	8.0964	-0.1999	-0.2295	0.211	0.4873	-0.055	0.2203	-0.784	-0.5671	0.2548	0.1851	0.0495	0.043	0.0472	-0.0528	0.202	35.1341	9.2796	-19.9485
8	19.8502	4.3042	1.9409	7.2719	0.9136	14.5771	0.0966	-1.5328	-0.5272	0.7844	-0.1643	-0.3615	0.3572	-0.4998	0.0677	0.2284	-0.0139	0.1046	0.1437	-0.0081	0.204	32.3494	-43.0476	-30.8437
9	6.0711	0.6022	5.5449	16.5388	-10.5083	28.6776	-0.0508	-0.1636	0.4577	0.1896	-0.0103	0.5966	-0.311	-0.6009	0.061	0.0971	0.0531	0.0608	0.0954	-0.0838	0.2794	28.3721	-37.0445	-41.3649
10	3.4038	-0.3694	1.2499	5.729	-0.3158	5.37	0.1208	0.4294	0.154	-0.4109	-0.1781	-0.0909	0.2021	0.3001	0.0573	0.0769	0.0115	0.0997	0.0852	-0.0321	0.2186	32.4984	-39.902	-46.4509
11	6.8113	-0.5602	2.7317	3.6436	1.1642	5.0479	0.3775	1.079	0.6491	0.0648	-0.5033	-0.1782	-0.2498	0.5316	0.1258	0.1352	0.0718	0.0706	0.3543	0.08	0.1383	52.6758	-10.0298	-21.5942
12	27.286	-12.9988	-2.2626	13.3148	1.0663	26.0832	-0.5729	-0.1954	0.2326	1.9639	0.3586	-0.0617	0.6762	0.7366	0.2143	0.4523	0.0051	0.0145	0.3042	-0.0158	0.1511	62.7029	-9.9245	-10.8546
13	7.1693	0.4812	2.3072	5.8527	0.7761	7.6833	-0.14	0.8422	0.54	-0.3169	0.0267	-0.1302	-0.6103	0.6526	0.1133	0.1806	0.0772	0.0564	0.2861	0.0494	0.1805	51.639	-9.8819	-22.4144
14	8.9765	4.6794	-2.1584	32.2514	-12.6378	11.8725	0.4901	1.2953	0.2176	-0.6401	-0.2639	0.3658	0.241	0.5616	-0.2262	0.1235	0.1665	0.0488	0.4636	-0.0695	0.1523	50.4136	-14.2996	-27.9121
15	76.5315	2.9571	20.665	7.2066	-2.4468	12.0031	1.6333	1.45	-1.1854	-0.5286	-0.6999	0.0684	1.9926	0.5019	-0.9334	0.974	0.0619	-0.1497	0.4307	-0.1845	0.6218	88.5988	4.9982	-2.0351
16	7.9281	32.3215	0.3198	203.9193	2.9534	0.0557	-4.5629	2.7929	-1.5836	-0.4114	4.8103	3.5179	0.2505	0.0208	-0.2474	6.3915	-2.4931	2.8103	2.7681	-1.2622	2.8473	94.7824	11.5512	-0.9114
17	5.1609	-3.9827	-0.0342	8.7552	13.077	30.4039	0.0316	-0.2701	0.124	-0.4303	0.2226	-0.2856	-1.0129	-0.1084	-0.2542	0.3121	-0.1547	-0.0084	0.2789	0.0659	0.2872	87.6875	21.7323	6.3385
18	3.4093	-0.3644	2.4806	3.2884	1.0852	8.2695	0.1344	-0.1525	-0.2625	0.2238	0.0371	0.1097	0.8699	-0.4119	-0.1715	0.185	-0.1122	0.0697	0.2308	0.0778	0.203	86.5059	15.5624	10.0482
19	7.0272	1.5456	1.2063	1.1711	0.0637	1.6906	-0.0196	0.0423	0.7827	-0.0689	0.0764	0.2576	-0.1785	0.1801	-0.0568	0.2868	-0.0986	0.0607	0.1212	0.0178	0.2604	60.2009	19.5052	-14.7886
20	9.8883	1.41	-2.4249	12.6519	2.4747	33.992	-0.1315	-0.4204	1.3197	-0.4463	0.0976	0.6517	-2.1275	-0.3637	0.0339	0.409	-0.1327	-0.0572	0.1768	0.0891	0.6101	47.5422	23.8669	-17.3562
21	16.6148	-4.4654	-3.5985	5.4147	1.3873	5.4216	0.1219	0.0967	0.0135	0.0442	-0.2032	0.4528	0.0324	-0.2761	0.0813	0.37	-0.2596	0.0069	0.1995	0.0079	0.3078	63.4166	20.7667	-12.0927
22	38.046	-28.3603	-14.0283	23.7288	11.772	11.4889	-0.9359	-1.5319	1.497	0.3821	1.1387	-0.6916	-0.2331	0.8491	-0.2028	0.4694	-0.1518	-0.0688	0.3489	-0.1374	0.5147	62.6827	26.6575	-4.4981
23	57.6997	-39.0882	33.1507	26.5828	-22.3236	19.407	-1.0876	-0.7744	0.8136	0.8776	0.6705	-0.5567	-0.7042	-0.1514	0.4171	0.6003	0.0201	0.0272	0.4031	-0.0656	0.3607	80.992	-15.062	21.3034
24	20.6385	-4.6537	-13.749	5.4753	5.3497	10.9138	-0.1719	-0.4583	-0.2665	0.5575	0.0548	-0.0992	0.4826	0.4492	0.117	0.2948	0.1279	-0.0339	0.1193	0.036	0.2493	93.0449	-27.0905	14.6834
25	2.4591	-0.2567	1.5429	0.0636	-0.2212	1.2239	0.0699	0.0498	0.154	-0.012	-0.035	-0.0203	-0.0671	-0.0021	-0.0348	0.2655	0.0833	0.107	0.1082	0.0068	0.2635	81.1027	-24.2697	5.4325
26	10.4399	-3.5702	-6.273	6.4512	1.4467	3.8685	-0.1956	0.1475	-0.2009	-0.2872	0.083	0.0506	0.1737	-0.0623	0.1126	0.1661	0.0671	0.0001	0.3418	-0.0559	0.0842	61.9394	-24.7561	-20.9874
27	1.3574	-0.3258	-1.4929	1.6761	0.8203	10.6459	0.0415	0.0592	0.1667	0.0171	0.1323	-0.162	0.3313	0.3361	-0.1738	0.1663	0.0805	0.0748	0.2006	-0.0313	0.1819	71.7506	-26.6462	-3.8647

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	10 - 19
2	X-RAY DIFFRACTION	2	A	20 - 25
3	X-RAY DIFFRACTION	3	A	26 - 40
4	X-RAY DIFFRACTION	4	A	41 - 58
5	X-RAY DIFFRACTION	5	A	59 - 81
6	X-RAY DIFFRACTION	6	A	82 - 92
7	X-RAY DIFFRACTION	7	A	93 - 120
8	X-RAY DIFFRACTION	8	B	12 - 22
9	X-RAY DIFFRACTION	9	B	23 - 33
10	X-RAY DIFFRACTION	10	B	34 - 57
11	X-RAY DIFFRACTION	11	B	58 - 76
12	X-RAY DIFFRACTION	12	B	77 - 82
13	X-RAY DIFFRACTION	13	B	83 - 106
14	X-RAY DIFFRACTION	14	B	107 - 120
15	X-RAY DIFFRACTION	15	C	13 - 19
16	X-RAY DIFFRACTION	16	C	20 - 24
17	X-RAY DIFFRACTION	17	C	25 - 38
18	X-RAY DIFFRACTION	18	C	39 - 55
19	X-RAY DIFFRACTION	19	C	56 - 80
20	X-RAY DIFFRACTION	20	C	81 - 87
21	X-RAY DIFFRACTION	21	C	88 - 113
22	X-RAY DIFFRACTION	22	C	114 - 120
23	X-RAY DIFFRACTION	23	D	10 - 20
24	X-RAY DIFFRACTION	24	D	21 - 40
25	X-RAY DIFFRACTION	25	D	41 - 73
26	X-RAY DIFFRACTION	26	D	74 - 91
27	X-RAY DIFFRACTION	27	D	92 - 120

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi