PDB-2vkn: YEAST SHO1 SH3 DOMAIN COMPLEXED WITH A PEPTIDE FROM PBS2

ID or keywords:

Entry

Database: PDB / ID: 2vkn

Title

YEAST SHO1 SH3 DOMAIN COMPLEXED WITH A PEPTIDE FROM PBS2

Components

MAP KINASE KINASE PBS2
PROTEIN SSU81

Keywords

MEMBRANE PROTEIN /

MEMBRANE /

SH3 DOMAIN /

S. CEREVISIAE /

TRANSMEMBRANE

Function / homology

Function and homology information

: / : / HICS complex / : / Oxidative Stress Induced Senescence / signal transduction involved in filamentous growth /

Clathrin-mediated endocytosis / NatB complex / PI5P Regulates TP53 Acetylation / : ...
Similarity search - Function

Biological species

SACCHAROMYCES CEREVISIAE (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Kursula, P. / Kursula, I. / Song, Y.H. / Paraskevopoulos, K. / Wilmanns, M.

Citation

Journal: To be Published
Title: Structural Genomics of Yeast SH3 Domains
Authors: Kursula, P. / Kursula, I. / Pinotsis, N. / Song, Y.H. / Lehmann, F. / Zou, P. / Wilmanns, M.

History

Deposition	Dec 20, 2007	Deposition site: PDBE / Processing site: PDBE
Supersession	Feb 5, 2008	ID: 2QK6
Revision 1.0	Feb 5, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Jan 30, 2019	Group: Data collection / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3	Dec 13, 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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PDBx/mmCIF format	2vkn.cif.gz	30.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2vkn.ent.gz	20.7 KB	Display	PDB format
PDBx/mmJSON format	2vkn.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/vk/2vkn ftp://data.pdbj.org/pub/pdb/validation_reports/vk/2vkn	HTTPS FTP

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Related structure data

Related structure data	2v1qC 2v1rC 2qk6 PDB Unreleased entryS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2gbk-4 4x3i-d 1rgw-d 2rot-d 4qqg-3 1rlq-d 2kg9-d 5ami-3 3a9f-1 1rlp-d 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	#19 - Jul 2001 Actin similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1) #28 - Apr 2002 Anthrax Toxin similarity (1) #70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: PROTEIN SSU81

C: MAP KINASE KINASE PBS2

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	67.490, 67.490, 33.170
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

#1: Protein	PROTEIN SSU81 / SHO1 OSMOSENSOR / SHO1 Mass: 8204.886 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN, RESIDUES 298-367 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P40073
#2: Protein/peptide	MAP KINASE KINASE PBS2 / POLYMYXIN B RESISTANCE PROTEIN 2 / SUPPRESSOR OF FLUORIDE SENSITIVITY 4 / PBS2 Mass: 1204.438 Da / Num. of mol.: 1 / Fragment: PROLINE-RICH DOMAIN, RESIDUES 2-13 / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) References: UniProt: P08018, mitogen-activated protein kinase kinase
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.34 Å³/Da / Density % sol: 47.08 % / Description: NONE
Crystal grow	Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2.3M AMMONIUM SULPHATE, 0.1M TRIS-HCL, PH 8.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.25
Detector	Type: MARRESEARCH / Detector: CCD / Date: Nov 14, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.25 Å / Relative weight: 1
Reflection	Resolution: 2.05→20 Å / Num. obs: 5525 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / R_merge(I) obs: 0.08 / Net I/σ(I): 14.8
Reflection shell	Resolution: 2.05→2.1 Å / Redundancy: 5.5 % / R_merge(I) obs: 0.62 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QK6

2qk6
PDB Unreleased entry

Resolution: 2.05→10 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.93 / SU B: 10.906 / SU ML: 0.139 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.238	243	4.4 %	RANDOM
R_work	0.168	-	-	-
obs	0.171	5233	99.8 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 28.6 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.85 Å²	0.42 Å²	0 Å²
2-	-	0.85 Å²	0 Å²
3-	-	-	-1.27 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→10 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	605	0	15	37	657

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	642
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	434
X-RAY DIFFRACTION	r_angle_refined_deg	1.444	1.999	877
X-RAY DIFFRACTION	r_angle_other_deg	0.928	3	1058
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.575	5	75
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	43.012	25	34
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.186	15	100
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.028	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	88
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	703
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	123
X-RAY DIFFRACTION	r_nbd_refined	0.167	0.2	103
X-RAY DIFFRACTION	r_nbd_other	0.193	0.2	432
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	288
X-RAY DIFFRACTION	r_nbtor_other	0.088	0.2	354
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.2	24
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	0.138	0.2	7
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.167	0.2	22
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.118	0.2	5
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	1.368	2	483
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.986	4	611
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.389	6	317
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.746	8	265
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: 2.05→2.1 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.293	15
R_work	0.312	377

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	18.8452	-6.2237	4.4596	2.1752	-0.1585	15.4722	-0.586	0.3048	0.8898	-0.1795	0.3379	-0.2913	-0.6801	1.376	0.2481	0.0604	-0.0498	0.0255	0.0533	0.0356	0.1139	21.282	-27.967	3.757
2	3.8367	2.66	-4.1958	35.0126	-2.2311	8.2534	0.248	0.0994	-0.2442	0.3305	-0.4153	1.1334	-0.3032	-1.8094	0.1674	-0.1127	0.0803	0.0152	0.2486	-0.0127	0.0281	3.079	-24.801	1.24
3	28.4446	-8.8166	-2.3808	78.0838	15.7589	3.1937	-2.6849	-2.0347	3.0777	0.0567	0.6391	4.4458	-1.0595	0.1	2.0457	0.3971	0.2425	-0.0833	0.3387	0.2622	0.3869	6.283	-9.796	0.702
4	2.2957	2.8565	2.178	30.5406	5.2906	6.5407	0.1529	0.2643	-0.1129	-0.8643	-0.2965	-0.1339	-1.0693	-1.589	0.1436	0.032	0.1493	0.0494	0.2227	0.0724	0.0475	6.357	-21.711	-2.154
5	19.1471	7.6766	15.9252	7.7797	7.1796	14.3155	0.1434	0.6794	-0.3288	-0.0735	0.1792	-0.2658	-0.1909	0.1062	-0.3226	0.0049	-0.0192	0.0626	0.0973	0.0168	0.0926	13.697	-27.096	-1.728
6	11.2342	-0.6884	0.2481	12.0103	-10.8404	17.7563	-0.2775	-0.5029	0.75	0.6146	0.1958	-0.2131	-1.6498	0.728	0.0817	0.1012	-0.0206	-0.0226	0.0627	-0.0972	0.1032	14.298	-20.268	11.297
7	5.2464	-0.3074	0.877	5.5932	2.3804	28.3563	0.0979	0.1073	-0.0752	-0.2577	0.0837	-0.4515	-1.4034	0.7122	-0.1816	0.009	-0.0067	0.0139	-0.0269	0.0322	0.1631	15.599	-21.365	0.472
8	1.2831	-1.4489	-3.5023	12.7704	7.4956	19.0456	0.2361	0.3694	0.2868	-0.4115	0.1114	0.5869	-1.6518	-0.5906	-0.3475	0.0519	0.017	0.0124	0.0639	0.0793	0.1086	13.736	-18.73	-3.677
9	5.6184	-2.0476	-3.4424	6.9647	8.423	10.3728	-0.0205	-0.5319	0.1352	0.1964	0.3637	-0.0298	0.1606	-0.6899	-0.3433	-0.0192	-0.0108	0.0439	0.1129	0.0341	0.1395	8.501	-26.797	6.19
10	28.8571	8.8561	12.9723	17.4457	-1.7357	20.5735	0.1344	1.3243	-1.1615	-0.9229	0.2332	-1.5468	0.2026	2.0043	-0.3676	-0.0276	0.0221	0.0952	0.1616	-0.151	0.0881	23.331	-31.808	2.874
11	35.7112	12.2121	15.2092	5.1887	2.5137	13.6099	-0.1011	0.562	0.5652	0.3541	0.3883	0.3938	-0.2586	-0.0043	-0.2872	-0.2796	0.0968	0.1133	0.0815	-0.0122	-0.0622	1.0386	-21.0616	8.9383

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 8
2	X-RAY DIFFRACTION	2	A	9 - 14
3	X-RAY DIFFRACTION	3	A	15 - 21
4	X-RAY DIFFRACTION	4	A	22 - 27
5	X-RAY DIFFRACTION	5	A	28 - 34
6	X-RAY DIFFRACTION	6	A	35 - 40
7	X-RAY DIFFRACTION	7	A	41 - 45
8	X-RAY DIFFRACTION	8	A	46 - 53
9	X-RAY DIFFRACTION	9	A	54 - 60
10	X-RAY DIFFRACTION	10	A	61 - 66
11	X-RAY DIFFRACTION	11	C	3 - 11

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