PDB-2vrf: CRYSTAL STRUCTURE OF THE HUMAN BETA-2-SYNTROPHIN PDZ DOMAIN

ID or keywords:

Entry

Database: PDB / ID: 2vrf

Title

CRYSTAL STRUCTURE OF THE HUMAN BETA-2-SYNTROPHIN PDZ DOMAIN

Components

BETA-2-SYNTROPHIN

Keywords

PROTEIN BINDING /

MICROTUBULE /

CYTOSKELETON / ACTIN-BINDING / SNTB2 /

MEMBRANE / CALMODULIN-BINDING / CYTOPLASMIC VESICLE /

ADAPTER PROTEIN

Function / homology

Function and homology information

dystrophin-associated glycoprotein complex / transport vesicle membrane /

actin binding /

microtubule /

calmodulin binding /

focal adhesion /

synapse / structural molecule activity / protein-containing complex /

RNA binding ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Sun, Z. / Roos, A.K. / Pike, A.C.W. / Pilka, E.S. / Cooper, C. / Elkins, J.M. / Murray, J. / Arrowsmith, C.H. / Doyle, D. / Edwards, A. ...

Citation

Journal: To be Published
Title: Crystal Structure of the Human Beta-2-Syntrophin Pdz Domain
Authors: Sun, Z. / Roos, A.K. / Pike, A.C.W. / Pilka, E.S. / Cooper, C. / Elkins, J.M. / Murray, J. / Arrowsmith, C.H. / Doyle, D. / Edwards, A. / von Delft, F. / Bountra, C. / Oppermann, U.

History

Deposition	Mar 31, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 22, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Dec 5, 2012	Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Revision 1.3	Jan 24, 2018	Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2vrf.cif.gz	87.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2vrf.ent.gz	68.4 KB	Display	PDB format
PDBx/mmJSON format	2vrf.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/vr/2vrf ftp://data.pdbj.org/pub/pdb/validation_reports/vr/2vrf	HTTPS FTP

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Related structure data

Related structure data	1qavS 2gzvS S: Starting model for refinement
Similar structure data	3ost-d 1v5t-d 5nsa-d 2mb0-d 4q3h-1 4q3h-2 2cok-d 2wbr-d 4mpa-d 2cp0-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) Search similar-shape structures by Omokage search (details) 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

Related structure data

1qavS

2gzvS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#175 - Jul 2014 Microtubules similarity (1)

Deposited unit

A: BETA-2-SYNTROPHIN

B: BETA-2-SYNTROPHIN

C: BETA-2-SYNTROPHIN

D: BETA-2-SYNTROPHIN

hetero molecules

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

1

A: BETA-2-SYNTROPHIN

hetero molecules

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

2

B: BETA-2-SYNTROPHIN

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

3

C: BETA-2-SYNTROPHIN

hetero molecules

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

4

D: BETA-2-SYNTROPHIN

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

5

A: BETA-2-SYNTROPHIN

B: BETA-2-SYNTROPHIN

hetero molecules

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

6

C: BETA-2-SYNTROPHIN

D: BETA-2-SYNTROPHIN

hetero molecules

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

Unit cell

Length a, b, c (Å)	56.687, 29.503, 128.382
Angle α, β, γ (deg.)	90.00, 95.78, 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:

Ens-ID: 1 / Refine code: 3

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	LYS	LYS	A	A	0 - 120	2 - 11
2	1	MET	MET	LYS	LYS	B	B	0 - 120	2 - 11
3	1	MET	MET	LYS	LYS	C	C	0 - 120	2 - 11
4	1	MET	MET	LYS	LYS	D	D	0 - 120	2 - 11
1	2	GLY	GLY	VAL	VAL	A	A	125 - 204	16 - 95
2	2	GLY	GLY	VAL	VAL	B	B	125 - 204	16 - 95
3	2	GLY	GLY	VAL	VAL	C	C	125 - 204	16 - 95
4	2	GLY	GLY	VAL	VAL	D	D	125 - 204	16 - 95

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.572, 0.544, -0.615), (0.531, -0.326, -0.782), (-0.626, -0.773, -0.102)	31.42341, 11.97262, 32.68468
2	given	(-0.454, 0.036, 0.89), (0.008, 0.999, -0.037), (-0.891, -0.01, -0.454)	49.77926, 12.59265, 63.88924
3	given	(-0.235, -0.959, 0.161), (0.558, -0.269, -0.785), (0.796, -0.095, 0.598)	63.75174, 23.21353, 20.6351

#1: Protein	BETA-2-SYNTROPHIN / 59 KDA DYSTROPHIN-ASSOCIATED PROTEIN A1 BASIC COMPONENT 2 / SYNTROPHIN-3 / SNT3 / SYNTROPHIN-LIKE / SNTL Mass: 10346.122 Da / Num. of mol.: 4 / Fragment: PDZ DOMAIN, RESIDUES 112-200 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q13425
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.59 Å³/Da / Density % sol: 52.45 % / Description: NONE
Crystal grow	pH: 8.2 / Details: 1.4 M NA-CITRATE, HEPES PH 8.2

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9919
Detector	Type: MARRESEARCH / Detector: CCD / Date: Mar 9, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9919 Å / Relative weight: 1
Reflection	Resolution: 2→63 Å / Num. obs: 29264 / % possible obs: 99.6 % / Observed criterion σ(I): 2.1 / Redundancy: 3.4 % / B_iso Wilson estimate: 21 Å² / R_merge(I) obs: 0.12 / Net I/σ(I): 7.2
Reflection shell	Resolution: 2→2.11 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.69 / Mean I/σ(I) obs: 2.1 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
REFMAC	5.4.0066	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1QAV, 2GZV

1qav

2gzv

Resolution: 2→56.43 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.92 / SU B: 9.714 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.247	1146	3.9 %	RANDOM
R_work	0.184	-	-	-
obs	0.186	28082	99.5 %	-

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: 24.4 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.21 Å²	0 Å²	-1.43 Å²
2-	-	-1.66 Å²	0 Å²
3-	-	-	-0.83 Å²

Refinement step

Cycle: LAST / Resolution: 2→56.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2857	0	12	165	3034

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	2886
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2062
X-RAY DIFFRACTION	r_angle_refined_deg	1.391	1.992	3873
X-RAY DIFFRACTION	r_angle_other_deg	0.833	3	5011
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.881	5	376
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.676	22.252	111
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.821	15	551
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.465	15	37
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	467
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3173
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	560
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	2.264	3	1875
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.711	5	3001
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	6.321	8	1011
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	10.101	11	872
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

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

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	529	tight positional	0.25	0.05
2	B	529	tight positional	0.31	0.05
3	C	529	tight positional	0.21	0.05
4	D	529	tight positional	0.31	0.05
1	A	597	loose positional	0.98	5
2	B	597	loose positional	0.97	5
3	C	597	loose positional	0.82	5
4	D	597	loose positional	1.05	5
1	A	529	tight thermal	11.69	10
2	B	529	tight thermal	8.25	10
3	C	529	tight thermal	6.36	10
4	D	529	tight thermal	5.47	10
1	A	597	loose thermal	11.57	30
2	B	597	loose thermal	8.84	30
3	C	597	loose thermal	6.43	30
4	D	597	loose thermal	5.19	30

LS refinement shell

Resolution: 2→2.05 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.272	89
R_work	0.244	1995

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	4.2458	-0.4127	0.5539	2.7962	0.2466	1.9197	0.0088	0.0869	-0.1485	-0.0444	-0.0392	-0.0783	0.0675	0.0663	0.0305	0.0727	-0.0156	0.0179	0.1102	0.0313	0.1653	7.706	8.0296	-0.9403
2	1.3913	0.1185	0.3058	2.6467	-0.7045	3.6408	-0.0143	0.0459	0.0531	0.0093	-0.088	-0.3302	-0.2485	0.1736	0.1023	-0.0392	-0.0163	0.0119	0.0704	-0.0002	0.1135	12.3693	11.5896	0.1836
3	6.1701	0.0111	2.5281	2.6618	-0.6034	3.464	0.1689	0.1439	-0.3652	0.0453	-0.0953	-0.2263	0.1587	0.1538	-0.0735	0.0222	-0.0137	-0.0008	0.0362	0.0035	0.1422	8.1681	0.2201	1.7286
4	19.8237	10.9567	13.4999	6.0895	7.5424	9.3877	-0.0083	-0.174	0.246	0.1639	-0.0401	-0.1315	-0.2235	0.1108	0.0484	0.0502	0.0181	0.0098	0.0651	-0.0063	0.1079	15.1867	17.9393	12.2793
5	3.0494	5.8123	1.3814	16.197	6.4018	3.4009	0.3135	-0.2732	-0.4841	0.3771	-0.2292	-0.5253	0.2706	-0.1697	-0.0843	0.0717	0.0071	-0.0485	0.1182	0.0202	0.1512	34.897	7.8387	22.3123
6	9.5571	2.9679	1.1517	3.5578	0.496	3.4257	0.2038	-0.1857	-0.0887	0.0326	-0.1287	0.0313	0.0172	-0.0799	-0.0751	0.0503	-0.008	0.0006	0.0975	-0.004	0.0994	29.9543	16.47	17.1434
7	5.7486	1.676	1.3636	2.8173	1.6105	3.6392	0.5881	-0.913	-0.0739	0.8815	-0.4429	-0.118	0.3435	-0.4183	-0.1452	0.0576	-0.1528	-0.0052	0.0918	0.0213	0.0106	26.6681	12.838	25.316
8	22.5006	3.2307	22.8974	7.6682	1.576	33.5203	0.1728	-0.2702	-0.0839	0.1163	-0.0964	-0.6203	0.2267	0.6317	-0.0764	0.0116	0.0345	0.0643	0.0922	-0.0101	0.1275	21.8041	4.723	0.8872
9	10.0775	4.2228	-1.8056	5.7713	-1.1232	6.0826	0.0965	-0.1204	0.1863	0.0811	-0.0248	0.226	-0.0096	-0.155	-0.0717	0.2285	0.0658	-0.003	0.0469	-0.019	0.0708	46.9003	22.834	61.0094
10	4.0418	-0.619	-1.8706	4.4911	1.8076	7.1432	0.1447	0.1333	0.0853	-0.3035	-0.1179	0.1681	-0.0928	-0.4778	-0.0269	0.2493	0.0269	-0.0216	0.0214	0.0202	-0.0459	43.8509	22.0773	51.6292
11	2.1145	0.5181	0.044	3.1671	-1.0693	6.3173	0.0197	-0.0119	-0.0221	-0.3533	-0.0187	0.1852	0.3173	-0.108	-0.0011	0.3241	0.0273	0.032	-0.0274	-0.0077	-0.0285	48.2891	15.2205	55.226
12	0.3858	1.1972	-2.391	5.3537	-12.258	29.1044	0.0315	0.042	0.0496	0.1608	-0.1784	-0.1717	-0.455	0.541	0.1468	0.2031	-0.004	0.0116	0.0926	-0.0122	0.0593	54.2741	30.1624	44.4913
13	5.3828	3.1601	-1.2538	12.8562	-5.0953	8.8957	0.0784	0.1764	0.1217	-0.0145	-0.0442	0.0221	0.0599	0.2155	-0.0342	0.0566	0.0254	-0.0127	0.1688	-0.045	0.05	53.2401	24.1473	21.8951
14	4.2129	0.0391	1.5277	3.4234	-1.1831	9.9393	-0.0143	-0.1825	0.0984	0.3318	0.0326	-0.126	-0.0393	0.1458	-0.0183	0.1421	-0.0376	0.0597	0.0126	-0.0341	0.0216	52.0189	29.0214	31.2144
15	3.2986	1.3616	0.8181	2.9379	0.4154	5.8235	0.1978	0.0922	0.0782	0.207	-0.0058	-0.2145	0.3828	0.7705	-0.1921	0.0912	0.0396	0.0092	0.0898	-0.0138	-0.0208	58.1462	25.1203	27.821
16	6.6374	1.9073	-12.1208	1.0243	-3.0047	24.4266	-0.3275	-0.0594	-0.1622	0.1279	0.1544	0.1011	1.0081	-0.5031	0.1731	0.2247	-0.0124	-0.035	0.0587	0.0091	0.0638	44.9662	17.1851	38.0467

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-1 - 134
2	X-RAY DIFFRACTION	2	A	135 - 164
3	X-RAY DIFFRACTION	3	A	165 - 192
4	X-RAY DIFFRACTION	4	A	193 - 204
5	X-RAY DIFFRACTION	5	B	-1 - 120
6	X-RAY DIFFRACTION	6	B	121 - 161
7	X-RAY DIFFRACTION	7	B	162 - 197
8	X-RAY DIFFRACTION	8	B	198 - 204
9	X-RAY DIFFRACTION	9	C	-1 - 125
10	X-RAY DIFFRACTION	10	C	126 - 157
11	X-RAY DIFFRACTION	11	C	158 - 192
12	X-RAY DIFFRACTION	12	C	193 - 204
13	X-RAY DIFFRACTION	13	D	-1 - 125
14	X-RAY DIFFRACTION	14	D	126 - 154
15	X-RAY DIFFRACTION	15	D	155 - 192
16	X-RAY DIFFRACTION	16	D	193 - 204

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi