PDB-2y4p: Dimeric structure of DAPK-1 catalytic domain

ID or keywords:

Entry

Database: PDB / ID: 2y4p

Title

Dimeric structure of DAPK-1 catalytic domain

Components

DEATH-ASSOCIATED PROTEIN KINASE 1

Keywords

TRANSFERASE / CALMODULIN-BINDING / SERINE/THREONINE-PROTEIN KINASE / NUCLEOTIDE-BINDING / APOPTOSIS / ATP-BINDING

Function / homology

Function and homology information

cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / Caspase activation via Dependence Receptors in the absence of ligand / defense response to tumor cell / calcium/calmodulin-dependent protein kinase activity / regulation of NMDA receptor activity / syntaxin-1 binding / extrinsic apoptotic signaling pathway via death domain receptors ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

de Diego, I. / Lehmann, F. / Wilmanns, M.

Citation

Journal: To be Published
Title: A Journey Through the Dap Kinase Architecture
Authors: De Diego, I. / Kuper, J. / Lehmann, F. / Wilmanns, M.

History

Deposition	Jan 7, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 18, 2012	Provider: repository / Type: Initial release
Revision 1.1	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2y4p.cif.gz	372.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2y4p.ent.gz	309.8 KB	Display	PDB format
PDBx/mmJSON format	2y4p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2y4p_validation.pdf.gz	431.2 KB	Display	wwPDB validaton report
Full document	2y4p_full_validation.pdf.gz	469.8 KB	Display
Data in XML	2y4p_validation.xml.gz	23.2 KB	Display
Data in CIF	2y4p_validation.cif.gz	35 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y4/2y4p ftp://data.pdbj.org/pub/pdb/validation_reports/y4/2y4p	HTTPS FTP

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Related structure data

Related structure data	2y4vC 3zxtC 2w4jS 1ig1 1jkk 1jkl 1jks 1jkt 1p4f 2w4k 2x0g 2xuu 2xzs 2y0a 2yak S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2z77-d 2qm2-2 6h28-d 5ejv-d 6p9f-d 2i32-d 5v6r-2 2jfl-1 1qgj-d 5vlo-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	#68 - Aug 2005 Neurotrophins similarity (5) #122 - Feb 2010 Enhanceosome similarity (4) #56 - Aug 2004 Caspases similarity (2) #177 - Sep 2014 Apoptosomes similarity (1) #250 - Oct 2020 Capsaicin Receptor TRPV1 similarity (1) #224 - Aug 2018 Legumain similarity (1) #223 - Jul 2018 Piezo1 Mechanosensitive Channel similarity (1)

Deposited unit

A: DEATH-ASSOCIATED PROTEIN KINASE 1

B: DEATH-ASSOCIATED PROTEIN KINASE 1

C: DEATH-ASSOCIATED PROTEIN KINASE 1

D: DEATH-ASSOCIATED PROTEIN KINASE 1

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

1

C: DEATH-ASSOCIATED PROTEIN KINASE 1

D: DEATH-ASSOCIATED PROTEIN KINASE 1

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

2

A: DEATH-ASSOCIATED PROTEIN KINASE 1

B: DEATH-ASSOCIATED PROTEIN KINASE 1

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

Unit cell

Length a, b, c (Å)	83.940, 73.700, 120.280
Angle α, β, γ (deg.)	90.00, 101.24, 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	C
1	2	B
2	2	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	3	A	1 - 275
2	1	1	3	C	1 - 275
1	1	2	3	B	1 - 275
2	1	2	3	D	1 - 275

NCS ensembles :

ID
1
2

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.9971, -0.07597, -0.001111), (-0.06837, 0.8908, 0.4491), (-0.03313, 0.4479, -0.8935)	93.57, -27.9, 142.1
2	given	(0.8216, -0.04915, 0.5679), (-0.3813, -0.788, 0.4835), (0.4237, -0.6138, -0.6662)	-15.21, 74.53, 168.6
3	given	(-0.8308, 0.1889, -0.5235), (0.313, -0.6192, -0.7202), (-0.4602, -0.7622, 0.4553)	140.3, 139.4, 118.5

#1: Protein	DEATH-ASSOCIATED PROTEIN KINASE 1 / DAP KINASE 1 Mass: 32725.262 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-285 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P53355, non-specific serine/threonine protein kinase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

DEATH-ASSOCIATED PROTEIN KINASE 1 / DAP KINASE 1

Mass: 32725.262 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

HOMO SAPIENS (human) / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P53355, non-specific serine/threonine protein kinase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.78 Å³/Da / Density % sol: 55.75 % / Description: NONE
Crystal grow	pH: 8 Details: 0.1 M TRIS PH 8.0, 0.1 M MGCL2, 15% (W/V) PEG 4000, 0.5 MM AMPPCP, 0.5 MM PMSF.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 15, 2010 / Details: MIRRORS
Radiation	Monochromator: SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 2.65→62.51 Å / Num. obs: 41340 / % possible obs: 98.3 % / Observed criterion σ(I): 3.1 / Redundancy: 3.7 % / B_iso Wilson estimate: 48.3 Å² / R_merge(I) obs: 0.11 / Net I/σ(I): 10.1
Reflection shell	Resolution: 2.65→2.79 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.5 / Mean I/σ(I) obs: 3.1 / % possible all: 97.8

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0102	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W4J

2w4j

Resolution: 2.65→117.97 Å / Cor.coef. F_o:F_c: 0.895 / Cor.coef. F_o:F_c free: 0.84 / SU B: 31.574 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R: 0.59 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. THE FOLLOWING RESIDUE RANGES ARE DISORDERED AND EXCLUDED FROM MODEL: CHAIN A RESIDUES 1-3, 23, 48-57, 170-179, 276- ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.31242	2087	5 %	RANDOM
R_work	0.25163	-	-	-
obs	0.25465	39240	98.03 %	-

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: 45.954 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.48 Å²	0 Å²	0.83 Å²
2-	-	2.01 Å²	0 Å²
3-	-	-	1.79 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→117.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7171	0	0	175	7346

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.036	0.022	7313
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.787	1.971	9891
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.79	5	878
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.02	24.971	348
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	24.401	15	1305
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	25.869	15	33
X-RAY DIFFRACTION	r_chiral_restr	0.18	0.2	1127
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	5441
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	0.257	1.5	4448
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.35	2	7192
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0	3	2865
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	0	4.5	2699
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
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

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	995	tight positional	0.31	0.05
1	2	C	995	tight positional	0.31	0.05
2	1	B	712	tight positional	0.27	0.05
2	2	D	712	tight positional	0.27	0.05
1	1	A	1007	loose positional	0.52	5
1	2	C	1007	loose positional	0.52	5
2	1	B	714	loose positional	0.48	5
2	2	D	714	loose positional	0.48	5
1	1	A	995	tight thermal	0	0.5
1	2	C	995	tight thermal	0	0.5
2	1	B	712	tight thermal	0	0.5
2	2	D	712	tight thermal	0	0.5
1	1	A	1007	loose thermal	0	10
1	2	C	1007	loose thermal	0	10
2	1	B	714	loose thermal	0	10
2	2	D	714	loose thermal	0	10

LS refinement shell

Resolution: 2.65→2.719 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.341	150	-
R_work	0.328	2879	-
obs	-	-	97.46 %

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	9.1382	-2.4065	-2.491	8.6652	-2.7538	11.5133	0.3043	0.5471	-0.0995	-0.2389	0.0324	0.471	0.2612	-0.3394	-0.3366	0.1736	-0.0524	0.039	0.1152	0.0687	0.4175	19.9285	30.2538	117.0913
2	2.702	0.2304	-0.0676	4.9864	-1.4104	2.051	0.0336	-0.0449	-0.2197	-0.0299	-0.0389	0.1137	0.0351	-0.0146	0.0053	0.0642	0.0251	0.063	0.1151	0.0023	0.125	25.0531	45.4145	109.6006
3	26.512	3.7951	-2.808	0.5449	-0.4033	0.2987	0.1716	-0.7643	0.3113	0.0383	-0.1404	0.0364	-0.0257	0.1011	-0.0312	0.193	-0.0549	0.0161	0.3603	0.1673	0.3673	49.8603	50.186	109.905
4	4.9231	-1.0738	-0.7916	3.4208	-0.578	3.9341	0.0943	0.3387	0.1793	-0.1014	-0.0821	-0.0997	-0.3252	0.1542	-0.0122	0.0563	-0.0319	0.0216	0.0638	0.0252	0.0866	33.9824	57.935	94.8389
5	11.1024	0.6498	-0.3889	0.6267	1.0721	2.4037	0.4612	-1.0689	-0.592	0.3372	-0.3587	-0.0021	0.2208	-0.6224	-0.1026	0.5645	-0.1299	0.0064	0.5255	0.2849	0.4683	64.3807	41.4461	125.3093
6	11.7857	2.4438	-1.2267	2.9393	0.5389	3.7384	0.4071	-0.4514	-0.8499	0.3705	-0.0499	-0.4559	-0.0672	0.2658	-0.3572	0.2021	-0.0326	-0.1087	0.117	0.148	0.3724	75.9629	42.324	116.51
7	13.1229	0.6704	9.1108	0.2592	0.3626	6.4152	0.7004	0.0641	-0.6019	0.0362	-0.3602	-0.0938	0.5864	0.1924	-0.3401	0.2315	-0.0273	0.0268	0.4858	0.1292	0.3414	55.6533	44.4211	110.6443
8	10.08	-0.1452	0.0756	2.7105	-0.3334	3.8089	0.084	0.7001	-0.5486	-0.1543	-0.0012	-0.177	0.1045	-0.0174	-0.0829	0.0532	0.0072	-0.0421	0.1002	-0.0106	0.1127	73.3682	48.2219	103.648
9	3.5496	2.5976	0.1654	4.2571	0.9017	2.4719	0.0357	0.246	-0.5472	-0.2542	-0.0337	-0.3477	0.1509	0.2863	-0.002	0.2798	-0.0117	-0.0319	0.4387	-0.0009	0.3252	61.9679	46.5827	49.9862
10	4.4026	-0.3027	0.3125	2.814	1.1961	3.1429	0.0437	-0.0527	-0.1298	0.036	0.0911	-0.3283	0.1557	0.286	-0.1347	0.0687	-0.0448	0.0043	0.2045	0.0415	0.1279	66.1322	57.263	64.5434
11	20.4754	-0.9611	-5.7848	0.0667	0.3128	1.714	0.1144	-0.0542	1.1863	-0.0326	0.0916	-0.0007	-0.0735	0.1563	-0.2059	0.1016	-0.0744	-0.0007	0.384	0.0528	0.4421	36.3139	59.9641	64.5147
12	6.8315	1.2634	-1.0744	3.4351	-0.8386	6.1544	0.0157	-0.684	0.0023	0.2931	-0.1232	0.107	-0.1231	0.1947	0.1075	0.0313	0.024	-0.0014	0.2444	-0.0368	0.063	55.1733	59.3681	81.2775
13	3.7109	1.4574	-2.8319	4.3844	-2.2883	4.7629	0.4465	0.9544	0.5104	-0.923	-0.1473	-0.3323	-0.4233	-0.1115	-0.2992	0.5358	0.1537	0.1625	0.6107	0.0438	0.3389	22.3244	56.8496	46.147
14	5.4018	-0.8435	0.7431	4.9908	0.1338	5.1004	0.1631	0.2047	-0.0184	-0.3275	-0.0323	0.3919	-0.0411	-0.3266	-0.1308	0.1256	-0.0178	0.01	0.1915	-0.0153	0.1197	16.3135	52.7357	54.2194
15	7.1594	-0.0914	6.5803	0.9622	-0.4461	7.5276	0.3641	-0.0539	-0.3376	-0.2669	-0.0212	0.0585	0.3872	-0.1876	-0.343	0.1986	-0.0104	0.0678	0.2745	-0.0103	0.1835	29.7691	53.8343	58.9334
16	6.4347	0.0202	-0.1492	2.5343	0.1694	4.1123	-0.0034	-0.2716	-0.0677	0.188	-0.0292	0.0147	0.2145	-0.2277	0.0326	0.0443	-0.011	-0.0208	0.0894	0.0342	0.0481	15.3697	55.6413	69.0508

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 39
2	X-RAY DIFFRACTION	2	A	40 - 158
3	X-RAY DIFFRACTION	3	A	159 - 193
4	X-RAY DIFFRACTION	4	A	194 - 275
5	X-RAY DIFFRACTION	5	B	57 - 102
6	X-RAY DIFFRACTION	6	B	103 - 148
7	X-RAY DIFFRACTION	7	B	155 - 192
8	X-RAY DIFFRACTION	8	B	193 - 275
9	X-RAY DIFFRACTION	9	C	2 - 71
10	X-RAY DIFFRACTION	10	C	72 - 162
11	X-RAY DIFFRACTION	11	C	163 - 196
12	X-RAY DIFFRACTION	12	C	197 - 275
13	X-RAY DIFFRACTION	13	D	55 - 113
14	X-RAY DIFFRACTION	14	D	114 - 149
15	X-RAY DIFFRACTION	15	D	150 - 192
16	X-RAY DIFFRACTION	16	D	193 - 276

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+
Jul 12, 2017. Major update of PDB

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Yorodumi