PDB-1upl: Crystal structure of MO25 alpha

ID or keywords:

Entry

Database: PDB / ID: 1upl

Title

Crystal structure of MO25 alpha

Components

MO25 PROTEIN

Keywords

TRANSFERASE / STRAD / LKB1 / ARMADILLO

Function / homology

Function and homology information

serine/threonine protein kinase complex / negative regulation of potassium ion transmembrane transport / response to thyroid hormone / cellular hypotonic response / Energy dependent regulation of mTOR by LKB1-AMPK / protein kinase activator activity / protein serine/threonine kinase activator activity / response to activity / protein serine/threonine kinase binding / kinase binding ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.6 Å

Authors

Milburn, C.C. / Boudeau, J. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F.

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Crystal Structure of Mo25 Alpha in Complex with the C-Terminus of the Pseudo Kinase Ste-20 Related Adaptor (Strad)
Authors: Milburn, C.C. / Boudeau, J. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F.

History

Deposition	Oct 7, 2003	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 22, 2004	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Apr 10, 2019	Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Source and taxonomy Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / pdbx_unobs_or_zero_occ_atoms / struct_conn Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3	Dec 13, 2023	Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1upl.cif.gz	137.4 KB	Display	PDBx/mmCIF format
PDB format	pdb1upl.ent.gz	109.7 KB	Display	PDB format
PDBx/mmJSON format	1upl.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/up/1upl ftp://data.pdbj.org/pub/pdb/validation_reports/up/1upl	HTTPS FTP

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Related structure data

Related structure data	1upkSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4kzg-6 1yb3-2 6war-1 4kzg-7 6war-8 2as9-d 4kzg-2 2x3c-d 4kzg-3 4kzg-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

Deposited unit

A: MO25 PROTEIN

B: MO25 PROTEIN

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

1

A: MO25 PROTEIN

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

2

B: MO25 PROTEIN

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

Unit cell

Length a, b, c (Å)	70.625, 94.012, 96.327
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	MO25 PROTEIN / MO25 ALPHA / CGI 66 Mass: 40344.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): B834 / References: UniProt: Q9Y376
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 12 / 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 Å³/Da / Density % sol: 38 %

Crystal grow

pH: 6.5
Details: 15 % PEG 20000, 0.1 M MES PH 6.5, 4.4 % GAMMA BUTYROLACTONE

Crystal grow

*PLUS

pH: 6.5 / Method: vapor diffusion, hanging drop

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Details (eV)
1	14.5 mg/ml	protein	1	drop
2	15 %(w/v)	PEG20000	1	reservoir
3	0.1 %	MES	1	reservoir	pH6.5
4	40 %(v/v)	gamma-butyrolactone	1	reservoir

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933
Detector	Type: ADSC Q4 CCD / Detector: CCD / Date: Feb 15, 2003
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 2.6→30 Å / Num. obs: 20073 / % possible obs: 98.6 % / Redundancy: 5.3 % / R_merge(I) obs: 0.118 / Net I/σ(I): 16.3
Reflection shell	Resolution: 2.6→2.69 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.522 / Mean I/σ(I) obs: 2.7 / % possible all: 90.6
Reflection	PLUS Highest resolution: 2.6 Å / Lowest resolution: 30 Å / Redundancy: 5.3 % / Num. measured all: 106613 / R_merge(I) obs*: 0.118
Reflection shell	PLUS % possible obs: 90.6 % / Redundancy: 4.3 % / R_merge(I) obs: 0.522 / Mean I/σ(I) obs*: 2.7

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Processing

Software

Name	Version	Classification
REFMAC	5	refinement
DENZO		data reduction
SCALEPACK		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MAD
Starting model: PDB ENTRY 1UPK

1upk

Resolution: 2.6→25 Å / Cor.coef. F_o:F_c: 0.928 / Cor.coef. F_o:F_c free: 0.895 / SU B: 13.8 / SU ML: 0.301 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28	524	2.6 %	RANDOM
R_work	0.212	-	-	-
obs	0.214	19496	98.6 %	-

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: 18.9 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.29 Å²	0 Å²	0 Å²
2-	-	4.08 Å²	0 Å²
3-	-	-	-1.79 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5107	0	0	12	5119

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	5075
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.647	1.965	6842
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.882	3	612
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.908	15	972
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.118	0.2	788
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	3742
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.293	0.3	2487
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	0.179	0.5	224
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	0.301	0.3	61
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.475	0.5	6
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	1.197	1.4	3082
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.161	2	4968
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.034	2.3	1993
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.29	1.7	1874
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

LS refinement shell

Resolution: 2.6→2.67 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.308	35
R_work	0.221	1269

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	3.3924	-1.1868	0.055	2.4145	-0.7545	1.4803	-0.0764	-0.2407	0.4285	0.1149	0.107	-0.0554	-0.0227	-0.0644	-0.0305	0.2331	-0.0578	0.0291	0.1918	-0.1176	0.2392	13.6631	33.1878	29.0017
2	2.0134	-0.3794	-1.3631	2.2749	-0.6658	1.5703	-0.0258	-0.2024	0.0806	0.1359	-0.0138	-0.0744	-0.0973	0.0721	0.0396	0.2447	-0.0323	0.0089	0.2249	-0.0342	0.2006	19.2424	24.2796	25.185
3	1.5693	-0.4635	-0.2523	2.4035	-0.1786	1.65	-0.0211	-0.0428	0.0626	0.1226	-0.1751	-0.0047	0.0203	-0.0331	0.1962	0.2267	-0.0139	0.0215	0.2444	-0.0271	0.2218	22.208	17.0398	16.6918
4	2.1592	-0.8819	-0.7167	3.195	-0.0707	1.4317	-0.0033	-0.0068	0.0302	-0.0762	-0.0642	-0.0505	-0.0685	-0.1523	0.0675	0.2295	-0.0278	0.003	0.221	-0.0085	0.1956	28.6076	10.9112	10.8544
5	2.7431	0.0136	-0.3504	2.0818	-0.9983	2.3888	-0.0492	-0.052	-0.0432	-0.0467	0.0316	0.0581	-0.0114	-0.088	0.0176	0.2312	-0.0022	-0.0085	0.1858	-0.0076	0.2198	36.0903	4.6584	5.3494
6	2.2669	0.0498	0.2495	4.6829	0.6877	0.5483	0.1197	-0.1076	-0.046	0.0607	-0.0965	-0.0045	0.17	0.0339	-0.0231	0.2706	0.024	0.0136	0.1913	0.014	0.219	45.7333	0.5197	-1.5438
7	4.5723	2.9703	2.6504	13.2436	3.2923	3.5244	0.2003	0.005	-0.423	0.3439	-0.2221	-0.7321	0.0448	0.1008	0.0218	0.0714	0.0022	-0.0205	0.2187	0.0383	0.2705	56.9501	2.7775	-0.165
8	6.0761	-3.3835	-0.6679	4.6943	0.3168	1.7976	-0.0047	-0.2976	0.3321	0.3662	0.0859	-0.0452	-0.357	0.1633	-0.0812	0.2705	-0.023	0.0233	0.1626	-0.0585	0.1821	44.5709	48.3009	98.7397
9	2.1159	0.3221	0.4007	1.6835	0.812	-0.2453	0.0671	0.1146	0.0739	0.0958	-0.1818	0.0453	0.0199	0.1454	0.1147	0.2504	0.0152	-0.004	0.1509	-0.0204	0.2326	40.2713	43.1371	89.8982
10	1.9597	1.3136	-0.1962	0.3533	0.8486	1.4073	-0.0697	0.09	-0.0374	-0.0563	0.145	0.0184	0.0801	0.0412	-0.0753	0.2103	0.0169	0.0012	0.2521	-0.0013	0.2522	37.599	34.8784	83.0536
11	1.6023	0.1974	1.3837	1.658	0.8684	3.0245	0.0106	0.0812	0.013	0.1801	0.103	-0.109	-0.0072	0.0405	-0.1136	0.2037	0.0011	-0.0065	0.2096	0.0376	0.2352	31.1793	28.7576	75.9846
12	2.6347	1.057	0.769	1.6566	0.2072	1.9531	0.0079	-0.0412	-0.0125	0.0572	-0.0905	0.0198	0.1313	0.1285	0.0826	0.2179	0.0075	0.0018	0.2059	-0.0013	0.2235	23.8486	24.028	69.6912
13	1.5815	0.3067	0.6396	2.1631	-0.6446	6.1199	-0.1499	0.0995	0.0745	-0.1011	-0.1051	0.1531	0.4992	-0.3249	0.255	0.248	-0.0533	0.0131	0.1933	-0.0488	0.2321	14.297	17.7136	64.146
14	3.8901	-0.3536	-2.9891	4.3838	2.4552	9.0801	-0.1761	0.0137	0.3536	0.0442	-0.1168	0.3793	0.261	-0.5703	0.2929	0.0128	-0.0523	0.022	0.215	-0.0711	0.3026	3.3584	20.313	65.9903

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	13 - 78
2	X-RAY DIFFRACTION	2	A	79 - 124
3	X-RAY DIFFRACTION	3	A	125 - 164
4	X-RAY DIFFRACTION	4	A	165 - 208
5	X-RAY DIFFRACTION	5	A	209 - 253
6	X-RAY DIFFRACTION	6	A	254 - 298
7	X-RAY DIFFRACTION	7	A	299 - 333
8	X-RAY DIFFRACTION	8	B	13 - 78
9	X-RAY DIFFRACTION	9	B	79 - 124
10	X-RAY DIFFRACTION	10	B	125 - 164
11	X-RAY DIFFRACTION	11	B	165 - 208
12	X-RAY DIFFRACTION	12	B	209 - 253
13	X-RAY DIFFRACTION	13	B	254 - 298
14	X-RAY DIFFRACTION	14	B	299 - 333

Refinement

*PLUS

R_factor R_free: 0.279

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	r_bond_d	0.019
X-RAY DIFFRACTION	r_angle_d
X-RAY DIFFRACTION	r_angle_deg	1.9

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