PDB-3thf: Crystal structure of the SD2 domain from Drosophila Shroom

ID or keywords:

Entry

Database: PDB / ID: 3thf

Title

Crystal structure of the SD2 domain from Drosophila Shroom

Components

Protein Shroom

Keywords

ACTIN-BINDING PROTEIN/PROTEIN BINDING / coiled-coil / anti-parallel / helical / Rho-kinase / ACTIN-BINDING / PROTEIN BINDING / CYTOSKELETON REGULATOR / ACTIN-BINDING PROTEIN-PROTEIN BINDING complex

Function / homology

Function and homology information

protein localization involved in establishment of planar polarity / establishment of planar polarity of embryonic epithelium / apical constriction / establishment or maintenance of actin cytoskeleton polarity / embryonic morphogenesis / melanosome organization / protein localization to adherens junction / actomyosin structure organization / apical junction complex / cortical actin cytoskeleton ...
Similarity search - Function

Biological species

Drosophila melanogaster (fruit fly)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.6951 Å

Authors

Mohan, S. / VanDemark, A.P.

Citation

Journal: Mol Biol Cell / Year: 2012
Title: Structure of Shroom domain 2 reveals a three-segmented coiled-coil required for dimerization, Rock binding, and apical constriction.
Authors: Mohan, S. / Rizaldy, R. / Das, D. / Bauer, R.J. / Heroux, A. / Trakselis, M.A. / Hildebrand, J.D. / VanDemark, A.P.

History

Deposition	Aug 18, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 6, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jun 13, 2012	Group: Database references
Revision 1.2	Feb 28, 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	3thf.cif.gz	149.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3thf.ent.gz	120.2 KB	Display	PDB format
PDBx/mmJSON format	3thf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3thf_validation.pdf.gz	443.5 KB	Display	wwPDB validaton report
Full document	3thf_full_validation.pdf.gz	450.3 KB	Display
Data in XML	3thf_validation.xml.gz	13.8 KB	Display
Data in CIF	3thf_validation.cif.gz	17.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/th/3thf ftp://data.pdbj.org/pub/pdb/validation_reports/th/3thf	HTTPS FTP

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Related structure data

Similar structure data	3qrd-d 5mgt-d 4qtf-2 5k69-3 5e1g-3 6nov-d 5du7-5 6puc-1 4hh9-d 5eq4-1 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: Protein Shroom

B: Protein Shroom

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

1

Idetical with deposited unit
defined by author&software

2

A: Protein Shroom

B: Protein Shroom

A: Protein Shroom

B: Protein Shroom

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

Unit cell

Length a, b, c (Å)	72.797, 85.632, 92.977
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Protein Shroom Mass: 21374.182 Da / Num. of mol.: 2 / Fragment: UNP Residues 1393-1576 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG34379, Shroom / Plasmid: pET151 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1Z9P3

#1: Protein

Protein Shroom

Mass: 21374.182 Da / Num. of mol.: 2 / Fragment: UNP Residues 1393-1576
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Drosophila melanogaster (fruit fly) / Gene: CG34379, Shroom / Plasmid: pET151 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1Z9P3

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 3.29 Å³/Da / Density % sol: 62.58 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion / pH: 6 Details: K/Na tartrate, sodium thiocynate, glycerol, pH 6.0, vapor diffusion, temperature 277K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	NSLS	X25	1	0.9792
SYNCHROTRON	NSLS	X25	2	1.1

Detector

Type	ID	Detector	Date	Details
ADSC QUANTUM	1	CCD	Jun 4, 2009
PSI PILATUS 6M	2	PIXEL	Jul 22, 2011	Meridionally-bent fused silica mirror

Radiation

ID	Monochromator	Protocol	Scattering type	Wavelength-ID
1	Double silicon(111) crystal	SINGLE WAVELENGTH	x-ray	1
2	Double silicon(111) crystal	SINGLE WAVELENGTH	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9792	1
2	1.1	1

Reflection

Redundancy: 10 % / Av σ(I) over netI: 36.18 / Number: 76057 / R_merge(I) obs: 0.085 / Χ²: 3.25 / D res high: 3.5 Å / D res low: 30 Å / Num. obs: 7573 / % possible obs: 99.3

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
9.41	30	97.5	1	0.051	7.239	9.1
7.5	9.41	99	1	0.051	4.234	10
6.57	7.5	99.7	1	0.071	4.201	10.3
5.97	6.57	99.5	1	0.081	3.523	9.4
5.55	5.97	100	1	0.088	2.729	10.1
5.22	5.55	100	1	0.063	1.868	10
4.96	5.22	100	1	0.051	1.82	10.2
4.75	4.96	99.5	1	0.053	1.69	10.3
4.56	4.75	99.5	1	0.06	1.673	10.5
4.41	4.56	99.7	1	0.056	1.621	10.3
4.27	4.41	100	1	0.049	1.283	10.5
4.15	4.27	99.7	1	0.054	1.368	10.4
4.04	4.15	99.7	1	0.051	1.641	10.7
3.94	4.04	100	1	0.061	1.698	10.5
3.85	3.94	95.6	1	0.364	13.732	8.1
3.77	3.85	99.2	1	0.07	1.679	10
3.69	3.77	99.4	1	0.068	1.569	10.2
3.62	3.69	99.5	1	0.361	12.673	9.4
3.56	3.62	99.5	1	0.083	1.426	10.2
3.5	3.56	100	1	0.082	1.446	10.7

Reflection

Resolution: 2.695→50 Å / Num. all: 16922 / Num. obs: 16446 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.5 % / B_iso Wilson estimate: 77.2 Å² / R_merge(I) obs: 0.069 / Χ²: 1.13 / Net I/σ(I): 9.7

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.695-2.75	8.1	0.463	815	0.619	1,2	99.9
2.75-2.8	8.6	0.421	800	0.565	1,2	100
2.8-2.85	8.8	0.294	797	0.657	1,2	100
2.85-2.91	8.7	0.24	804	0.734	1,2	100
2.91-2.97	8.5	0.213	812	0.797	1,2	100
2.97-3.04	8	0.173	809	0.827	1,2	100
3.04-3.12	8.8	0.164	802	0.827	1,2	100
3.12-3.2	8.6	0.142	819	0.844	1,2	99.9
3.2-3.3	8.1	0.129	803	1.018	1,2	100
3.3-3.4	7.9	0.115	823	1.135	1,2	100
3.4-3.52	9	0.097	798	1.173	1,2	100
3.52-3.66	9	0.081	817	1.203	1,2	100
3.66-3.83	8.6	0.071	836	1.29	1,2	100
3.83-4.03	8.7	0.061	816	1.241	1,2	100
4.03-4.29	8.9	0.05	822	1.309	1,2	99.9
4.29-4.62	8.5	0.049	817	1.451	1,2	100
4.62-5.08	8.9	0.057	833	1.689	1,2	99.9
5.08-5.81	8.3	0.06	850	1.47	1,2	100
5.81-7.32	8.3	0.051	855	1.287	1,2	99.9
7.32-50	7.7	0.044	918	2.325	1,2	99.5

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Phasing

Phasing	Method: SAD

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHELX		phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
CBASS		data collection
SHELXD		phasing
PHENIX	1.6.2_432	refinement

Refinement

Method to determine structure:

SAD / Resolution: 2.6951→47.633 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.43 / σ(F): 0 / Phase error: 30.99 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2838	1157	7.26 %	Random
R_work	0.2278	-	-	-
all	0.2317	16370	-	-
obs	0.2317	15941	95.92 %	-

Solvent computation

Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 62.691 Å² / k_sol: 0.365 e/Å³

Displacement parameters

B_iso max: 180.16 Å² / B_iso mean: 75.6584 Å² / B_iso min: 20 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	20.0033 Å²	0 Å²	-0 Å²
2-	-	11.3694 Å²	0 Å²
3-	-	-	-31.3727 Å²

Refinement step

Cycle: LAST / Resolution: 2.6951→47.633 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2749	0	0	0	2749

Refine LS restraints

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	f_angle_deg	0.6
X-RAY DIFFRACTION	f_bond_d	0.1
X-RAY DIFFRACTION	f_dihedral_angle_d	16.731
X-RAY DIFFRACTION	fhirality	0.041
X-RAY DIFFRACTION	flanairty	0.001

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Refine-ID	Num. reflection obs
2.6951-2.8177	0.5162	119	0.42	X-RAY DIFFRACTION	1530
2.8177-2.9622	0.3803	141	0.295	X-RAY DIFFRACTION	1781
2.9622-3.152	0.339	153	0.2615	X-RAY DIFFRACTION	1801
3.152-3.3953	0.3059	136	0.2514	X-RAY DIFFRACTION	1868
3.3953-3.7369	0.2927	165	0.2329	X-RAY DIFFRACTION	1892
3.7369-4.2774	0.2492	154	0.1996	X-RAY DIFFRACTION	1914
4.2774-5.3878	0.2187	149	0.1844	X-RAY DIFFRACTION	1941
5.3878-47.6399	0.2872	144	0.2206	X-RAY DIFFRACTION	2057

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	-0.1345	-0.0153	0.2529	0.1055	-0.7368	1.607	-0.1968	-0.0858	-0.1817	-0.5994	-0.8757	-0.579	1.4369	1.2374	-0.0144	0.8039	-0.0342	-0.021	0.4795	0.2162	0.4374	21.6207	-10.9203	-16.9868
2	0.9719	-0.3427	0.6529	2.763	-0.8617	1.6315	-0.4527	0.014	0.0366	0.0566	-0.3846	-0.1464	0.3409	0.8987	-0.0346	0.0343	0.0326	-0.0248	0.1903	-0.005	0.2749	22.0269	9.8721	-31.3996
3	0.5928	0.0775	-0.3611	0.7185	-0.5892	0.606	-0.3372	-0.0518	0.2412	-0.8118	-0.3574	0.2885	-1.116	-1.1174	0.0009	0.5448	0.1462	-0.1129	0.4579	-0.0753	0.4013	24.0064	20.6703	27.4928
4	0.6613	0.2938	-0.5964	0.7974	-0.9327	1.1391	-0.1965	0.1111	-0.0165	-0.185	-0.1069	-0.2426	-0.0859	-0.0392	-0.0001	0.1701	-0.0539	0.0772	0.2338	-0.1443	0.3555	43.2915	17.85	35.3998
5	0.2716	-0.239	-0.0232	0.0209	0.0583	0.2403	-0.1225	-0.2574	0.0484	-0.0287	0.2879	-0.2273	1.5457	0.9143	-0	0.6354	0.1076	0.1115	0.4301	-0.0707	0.3844	52.0297	10.9304	26.9372
6	1.5553	-0.4282	-0.5607	1.301	0.7561	0.4854	-0.2037	0.1557	-0.1531	-0.4084	-0.3405	0.0676	-0.051	0.2932	0.0008	0.3757	-0.0048	-0.0587	0.3158	-0.0288	0.356	32.4022	17.529	40.3367
7	0.0631	-0.1732	0.0168	0.3236	0.205	0.2909	-1.012	-0.2637	0.7307	0.2958	-0.2204	0.2867	-1.0242	0.6393	-0.0039	0.851	0.0421	-0.0982	0.7243	-0.0846	0.474	23.8056	20.1961	-12.1371
8	0.1196	0.2115	0.652	0.3938	-0.7984	2.4024	0.1136	-0.4704	-0.2401	0.3507	-0.2324	0.2504	1.0068	-0.7488	-0.2052	0.3168	-0.0185	-0.0616	0.3176	0.1162	0.2805	17.6525	2.3606	-28.6904

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 1396:1440)	A	1396 - 1440
2	X-RAY DIFFRACTION	2	(chain A and resid 1441:1482)	A	1441 - 1482
3	X-RAY DIFFRACTION	3	(chain A and resid 1483:1523)	A	1483 - 1523
4	X-RAY DIFFRACTION	4	(chain A and resid 1524:1570)	A	1524 - 1570
5	X-RAY DIFFRACTION	5	(chain B and resid 1397:1440)	B	1397 - 1440
6	X-RAY DIFFRACTION	6	(chain B and resid 1441:1482)	B	1441 - 1482
7	X-RAY DIFFRACTION	7	(chain B and resid 1483:1512)	B	1483 - 1512
8	X-RAY DIFFRACTION	8	(chain B and resid 1513:1570)	B	1513 - 1570

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