PDB-3nkf: Crystal structure of human ligand-free mature caspase-6 with inte...

ID or keywords:

Entry

Database: PDB / ID: 3nkf

Title

Crystal structure of human ligand-free mature caspase-6 with intersubunit linker attached

Components

Caspase-6

Keywords

HYDROLASE / Caspase / protease / apoptosis / zymogen

Function / homology

Function and homology information

caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / cellular response to staurosporine / positive regulation of necroptotic process / Apoptotic cleavage of cellular proteins / TP53 Regulates Transcription of Caspase Activators and Caspases / hepatocyte apoptotic process / pyroptotic inflammatory response / protein autoprocessing ...
Similarity search - Function

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Vaidya, S. / Hardy, J.A.

Citation

Journal: J.Mol.Biol. / Year: 2011
Title: Substrate-Induced Conformational Changes Occur in All Cleaved Forms of Caspase-6.
Authors: Vaidya, S. / Velazquez-Delgado, E.M. / Abbruzzese, G. / Hardy, J.A.

History

Deposition	Jun 18, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 8, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 21, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3nkf.cif.gz	345.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3nkf.ent.gz	283.6 KB	Display	PDB format
PDBx/mmJSON format	3nkf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3nkf_validation.pdf.gz	461.6 KB	Display	wwPDB validaton report
Full document	3nkf_full_validation.pdf.gz	481.9 KB	Display
Data in XML	3nkf_validation.xml.gz	33 KB	Display
Data in CIF	3nkf_validation.cif.gz	44.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nk/3nkf ftp://data.pdbj.org/pub/pdb/validation_reports/nk/3nkf	HTTPS FTP

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Related structure data

Related structure data	2wdp 3k7e
Similar structure data	3k7e-d 3b4v-2 3b4v-1 4ine-d 6dev-d 4b6j-d 6c3k-d 1dlj-1 2yjq-d 3qnw-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) 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	#56 - Aug 2004 Caspases similarity (17) #224 - Aug 2018 Legumain similarity (13) #177 - Sep 2014 Apoptosomes similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #213 - Sep 2017 Sirtuins similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #19 - Jul 2001 Actin similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#56 - Aug 2004
Caspases
similarity (17)
#224 - Aug 2018
Legumain
similarity (13)
#177 - Sep 2014
Apoptosomes
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#213 - Sep 2017
Sirtuins
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#221 - May 2018
Human Papillomavirus and Vaccines
similarity (1)
#234 - Jun 2019
MDM2 and Cancer
similarity (1)
#19 - Jul 2001
Actin
similarity (1)

Deposited unit

A: Caspase-6

B: Caspase-6

C: Caspase-6

D: Caspase-6

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

1

Idetical with deposited unit
defined by software

2

A: Caspase-6

B: Caspase-6

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

3

C: Caspase-6

D: Caspase-6

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

Unit cell

Length a, b, c (Å)	63.290, 90.814, 85.912
Angle α, β, γ (deg.)	90.00, 91.04, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	6	A	32 - 136
2	1	1	6	B	32 - 136
3	1	1	6	C	32 - 136
4	1	1	6	D	32 - 136
1	2	1	6	A	138 - 163
2	2	1	6	B	138 - 163
3	2	1	6	C	138 - 163
4	2	1	6	D	138 - 163
1	3	1	6	A	202 - 217
2	3	1	6	B	202 - 217
3	3	1	6	C	202 - 217
4	3	1	6	D	202 - 217
1	4	1	6	A	225 - 246
2	4	1	6	B	225 - 246
3	4	1	6	C	225 - 246
4	4	1	6	D	225 - 246
1	5	1	6	A	248 - 259
2	5	1	6	B	248 - 259
3	5	1	6	C	248 - 259
4	5	1	6	D	248 - 259
1	6	1	6	A	273 - 291
2	6	1	6	B	273 - 291
3	6	1	6	C	273 - 291
4	6	1	6	D	273 - 291

#1: Protein	Caspase-6 / CASP-6 / Apoptotic protease Mch-2 / Caspase-6 subunit p18 / Caspase-6 subunit p11 Mass: 31943.559 Da / Num. of mol.: 4 / Mutation: Prodomain deleted D179A / Source method: obtained synthetically / Details: E.coli optimized synthetic gene / References: UniProt: P55212, caspase-6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.93 Å³/Da / Density % sol: 36.33 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M CH3COONa.3H2O pH 4.6, 2M NaCl, 3% EtOH, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.98 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 10, 2010
Radiation	Monochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.9→40 Å / Num. all: 21645 / Num. obs: 20897 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3
Reflection shell	Resolution: 2.9→2.96 Å / % possible all: 99.6

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASES		phasing
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.9→29.5 Å / Cor.coef. F_o:F_c: 0.933 / Cor.coef. F_o:F_c free: 0.897 / SU B: 42.273 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R Free: 0.46 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2702	1293	6 %	RANDOM
R_work	0.21584	-	-	-
obs	0.21913	20346	99.72 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 83.636 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.83 Å²	0 Å²	0.51 Å²
2-	-	0.11 Å²	0 Å²
3-	-	-	-2.93 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→29.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6665	0	0	27	6692

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	6825
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.233	1.942	9209
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.768	5	861
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.486	23.196	291
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.784	15	1098
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.78	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	1024
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	5133
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	13.325	1.5	4325
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	17.476	2	6845
X-RAY DIFFRACTION	r_scbond_it	16.755	3	2500
X-RAY DIFFRACTION	r_scangle_it	23.39	4.5	2364
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 1400 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	loose positional	0.12	5
2	B	loose positional	0.15	5
3	C	loose positional	0.1	5
4	D	loose positional	0.13	5
1	A	loose thermal	8.42	10
2	B	loose thermal	10.57	10
3	C	loose thermal	9.62	10
4	D	loose thermal	8.75	10

LS refinement shell

Resolution: 2.9→2.975 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.398	102	-
R_work	0.32	1485	-
obs	-	-	99.94 %

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	0.1243	-0.0304	-0.0702	0.0611	-0.0478	1.1414	0.0327	0.0917	0.0067	0.0849	0.0352	0.0125	-0.2276	-0.1339	-0.0679	0.293	-0.0055	0.0358	0.1645	-0.0116	0.0748	1.2846	58.5099	47.1132
2	1.2645	-0.6024	4.3348	1.8437	-2.3676	14.9199	-0.1173	-0.1427	0.0306	0.0914	-0.1771	-0.5038	-0.7192	-0.4365	0.2943	0.2565	0.1205	-0.008	0.2526	0.0093	0.2201	2.1426	70.6237	35.5585
3	0.5991	0.5787	0.6739	0.6854	0.4684	1.6141	0.0851	0.0675	0.0165	0.1322	-0.0259	0.0672	-0.0888	-0.0148	-0.0592	0.2623	-0.0261	0.0274	0.1648	-0.0076	0.1106	8.8899	58.6694	40.0807
4	0.7404	-0.4564	0.9391	0.547	-0.1061	2.0468	-0.0338	0.1235	-0.0695	0.148	0.0416	0.0392	-0.0577	0.2004	-0.0078	0.272	-0.0395	0.0314	0.2032	-0.0779	0.0314	12.8791	51.0972	43.5482
5	2.2506	4.12	1.5173	8.7769	1.2161	3.0012	0.3084	0.0915	-0.2553	0.0174	0.4224	0.0554	0.5327	-0.1079	-0.7309	0.3158	-0.1345	-0.0446	0.1972	-0.0772	0.3549	0.493	40.5835	38.8119
6	0.2104	0.0818	0.3984	0.0717	0.1024	1.1104	-0.0623	0.0078	-0.0586	0.0035	0.066	-0.0136	-0.0795	-0.081	-0.0037	0.2571	-0.0239	0.0252	0.17	-0.0155	0.0882	4.9493	46.6403	52.946
7	0.1774	-0.009	-0.303	0.0529	-0.1901	1.654	-0.0922	-0.0552	-0.0868	0.07	0.0125	0.0006	0.1127	0.1648	0.0796	0.3006	-0.0229	-0.0042	0.1703	0.0356	0.0959	22.4259	30.5425	49.4334
8	12.5076	5.313	21.6702	10.9507	9.4768	37.5568	-0.1972	0.1413	-0.0464	-0.3407	0.1558	-0.5351	-0.5657	0.2781	0.0414	0.1606	-0.0807	0.052	0.3926	0.1129	0.0908	43.1936	39.1428	31.9959
9	0.529	-0.2072	-0.0858	0.2628	0.5263	1.3545	0.0375	-0.109	-0.1474	-0.033	0.1502	-0.0232	-0.085	0.2379	-0.1877	0.2203	0.0032	0.0023	0.2247	0.0606	0.1091	34.5734	29.8661	44.4358
10	0.4161	0.0305	-0.587	0.1432	0.0004	0.8569	-0.0161	-0.0303	-0.0694	0.0536	-0.0578	-0.0207	0.0309	0.0748	0.074	0.2526	-0.0217	0.0074	0.1798	0.0134	0.1244	22.1405	32.9697	40.473
11	0.4765	-0.2661	0.038	0.9373	0.3313	0.1624	-0.0253	-0.1301	0.0599	-0.0899	0.0808	-0.1135	-0.0378	0.0237	-0.0555	0.2495	-0.0264	0.0179	0.2603	0.0084	0.0783	30.1212	44.9228	52.2266
12	1.8297	-0.1418	-0.9898	0.0412	0.0769	0.5387	-0.06	-0.1609	0.0619	0.0424	0.0429	0.0393	0.0332	0.1049	0.0171	0.2912	-0.0484	-0.0133	0.1745	0.0291	0.0917	22.5292	43.5592	52.0297
13	0.2163	0.2327	-0.0228	0.5001	-0.1151	0.192	-0.063	0.0593	-0.0702	0.0578	0.0406	-0.1701	-0.0496	0.0901	0.0224	0.1227	0.0197	0.0273	0.1598	-0.0003	0.1832	31.8967	35.9259	86.0098
14	2.5093	4.3518	-1.4272	17.6918	-3.7752	0.9795	-0.472	0.363	-0.2275	0.9359	0.169	-0.6946	0.0848	-0.1291	0.3031	0.5222	-0.1736	-0.0017	0.1726	0.0111	0.3275	41.759	41.8362	95.5718
15	0.0741	-0.056	-0.0832	0.0771	0.0375	0.1147	-0.0544	0.0165	0.014	0.0495	0.0118	-0.0885	0.0431	-0.0411	0.0426	0.1566	-0.0023	-0.0148	0.1682	0.0002	0.2085	29.8247	44.5687	91.9352
16	5.9907	-3.6447	-0.8661	2.5326	0.1154	0.666	0.0158	-0.2374	0.6581	0.1384	0.2553	-0.2872	-0.1994	-0.1175	-0.2711	0.1914	0.0125	0.0474	0.2115	-0.0057	0.2125	20.0256	41.0108	95.9799
17	0.4338	-0.2608	0.0112	0.1701	-0.0111	0.0344	-0.0053	-0.0005	-0.032	-0.0101	0.0317	0.0529	0.0188	0.0579	-0.0264	0.1503	0.0076	0.0088	0.1812	-0.0079	0.1784	18.7836	34.3686	82.8678
18	0.2717	0.1831	-0.061	0.2197	-0.2369	0.4948	-0.0139	0.0165	-0.043	0.0174	-0.0096	0.0084	-0.0009	0.0575	0.0235	0.1247	-0.0163	0.0037	0.1996	0.0012	0.167	20.3628	41.2653	79.11
19	0.1747	-0.0104	-0.0078	0.6488	-0.0323	0.1807	-0.025	0.1118	0.0476	0.0488	0.0343	0.1664	-0.0167	-0.0746	-0.0092	0.0986	0.021	-0.0253	0.1506	-0.0062	0.1973	-3.4308	55.5645	85.7194
20	2.6581	0.4104	0.0253	0.0715	0.0045	0.0004	-0.2632	0.0811	0.0386	-0.0178	0.1466	0.0183	0.0002	-0.0004	0.1166	0.2976	0.0116	0.0108	0.242	0.0324	0.2597	-13.9628	49.2163	95.5603
21	0.0815	-0.0257	-0.1792	0.0995	0.1815	0.5977	0.0029	0.0153	-0.0166	0.0626	-0.0528	0.0627	0.0029	-0.0867	0.0499	0.1539	0.0143	0.0082	0.1688	-0.0125	0.2225	-1.6789	48.4523	93.8673
22	0.0701	0.0609	-0.0679	0.4171	-0.1737	0.1036	-0.0547	0.0075	-0.0459	0.1263	0.0445	0.0508	-0.0115	-0.0045	0.0102	0.1514	0.0006	-0.0096	0.1912	-0.0078	0.2089	4.8385	45.9371	88.8567
23	0.1642	0.0482	-0.0096	0.0327	-0.0729	0.6286	0.0297	0.0888	0.0743	-0.0065	0.0136	-0.004	-0.016	0.0079	-0.0433	0.1563	0.0069	0.0053	0.1745	0.0132	0.177	9.6556	59.9197	80.9314
24	0.3207	0.31	0.0613	0.4191	0.283	0.4848	-0.0224	0.0206	-0.0244	-0.0039	-0.0177	-0.0089	-0.066	-0.0057	0.0401	0.1641	-0.0195	-0.0131	0.187	-0.0094	0.1469	9.577	51.4643	81.0521

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	31 - 91
2	X-RAY DIFFRACTION	2	A	92 - 102
3	X-RAY DIFFRACTION	3	A	103 - 200
4	X-RAY DIFFRACTION	4	A	201 - 213
5	X-RAY DIFFRACTION	5	A	214 - 221
6	X-RAY DIFFRACTION	6	A	222 - 292
7	X-RAY DIFFRACTION	7	B	32 - 55
8	X-RAY DIFFRACTION	8	B	56 - 61
9	X-RAY DIFFRACTION	9	B	62 - 101
10	X-RAY DIFFRACTION	10	B	102 - 215
11	X-RAY DIFFRACTION	11	B	216 - 258
12	X-RAY DIFFRACTION	12	B	259 - 290
13	X-RAY DIFFRACTION	13	C	32 - 92
14	X-RAY DIFFRACTION	14	C	93 - 103
15	X-RAY DIFFRACTION	15	C	104 - 160
16	X-RAY DIFFRACTION	16	C	161 - 201
17	X-RAY DIFFRACTION	17	C	202 - 259
18	X-RAY DIFFRACTION	18	C	260 - 294
19	X-RAY DIFFRACTION	19	D	31 - 92
20	X-RAY DIFFRACTION	20	D	93 - 103
21	X-RAY DIFFRACTION	21	D	104 - 148
22	X-RAY DIFFRACTION	22	D	149 - 215
23	X-RAY DIFFRACTION	23	D	216 - 259
24	X-RAY DIFFRACTION	24	D	267 - 291

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Yorodumi