PDB-3gge: Crystal structure of the PDZ domain of PDZ domain-containing prot...

ID or keywords:

Entry

Database: PDB / ID: 3gge

Title

Crystal structure of the PDZ domain of PDZ domain-containing protein GIPC2

Components

PDZ domain-containing protein GIPC2

Keywords

PROTEIN BINDING / PDZ domain / Structural Genomics / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

extracellular exosome / identical protein binding / cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Chaikuad, A. / Hozjan, V. / Yue, W. / Cooper, C. / Elkins, J. / Pike, A.C.W. / Roos, A.K. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. ...

Citation

Journal: To be Published
Title: Crystal structure of the PDZ domain of PDZ domain-containing protein GIPC2
Authors: Chaikuad, A. / Hozjan, V. / Yue, W. / Cooper, C. / Elkins, J. / Pike, A.C.W. / Roos, A.K. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Oppermann, U.

History

Deposition	Feb 27, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 24, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Jan 31, 2018	Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_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_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3gge.cif.gz	71.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3gge.ent.gz	54.4 KB	Display	PDB format
PDBx/mmJSON format	3gge.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gg/3gge ftp://data.pdbj.org/pub/pdb/validation_reports/gg/3gge	HTTPS FTP

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Related structure data

Related structure data	1kwaS S: Starting model for refinement
Similar structure data	7now-2 3qf3-3 3t0f-1 2fep-d 4dy5-d 5ve9-d 6dbf-d 4lpz-1 6u12-d 6p3v-d 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: PDZ domain-containing protein GIPC2

B: PDZ domain-containing protein GIPC2

C: PDZ domain-containing protein GIPC2

hetero molecules

32.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

2

A: PDZ domain-containing protein GIPC2

B: PDZ domain-containing protein GIPC2

C: PDZ domain-containing protein GIPC2

hetero molecules

A: PDZ domain-containing protein GIPC2

B: PDZ domain-containing protein GIPC2

C: PDZ domain-containing protein GIPC2

hetero molecules

defined by software
64.4 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	83.510, 83.510, 160.310
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	91
Space group name H-M	P4₁22

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
2	1	A
3	1	C
1	2	C
2	2	B
3	2	A
1	3	C
2	3	A
3	3	B
1	4	B
2	4	A
3	4	C
1	5	B
2	5	A
3	5	C

NCS domain segments:

Component-ID: 1

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LYS	LYS	ILE	ILE	1	B	B	116 - 131	7 - 22
2	1	LYS	LYS	ILE	ILE	1	A	A	116 - 131	7 - 22
3	1	LYS	LYS	ILE	ILE	1	C	C	116 - 131	7 - 22
1	2	ASP	ASP	TYR	TYR	5	C	C	133 - 138	24 - 29
2	2	ASP	ASP	TYR	TYR	5	B	B	133 - 138	24 - 29
3	2	ASP	ASP	TYR	TYR	5	A	A	133 - 138	24 - 29
1	3	ALA	ALA	ILE	ILE	1	C	C	139 - 170	30 - 61
2	3	ALA	ALA	ILE	ILE	1	A	A	139 - 170	30 - 61
3	3	ALA	ALA	ILE	ILE	1	B	B	139 - 170	30 - 61
1	4	GLY	GLY	LYS	LYS	2	B	B	172 - 180	63 - 71
2	4	GLY	GLY	LYS	LYS	2	A	A	172 - 180	63 - 71
3	4	GLY	GLY	LYS	LYS	2	C	C	172 - 180	63 - 71
1	5	LYS	LYS	LEU	LEU	1	B	B	181 - 195	72 - 86
2	5	LYS	LYS	LEU	LEU	1	A	A	181 - 195	72 - 86
3	5	LYS	LYS	LEU	LEU	1	C	C	181 - 195	72 - 86

NCS ensembles :

ID
1
2
3
4
5

#1: Protein	PDZ domain-containing protein GIPC2 Mass: 10632.248 Da / Num. of mol.: 3 / Fragment: PDZ domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GIPC2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: Q8TF65
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 107 / 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: 4.38 Å³/Da / Density % sol: 71.93 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2M ammonium sulfate; 2.5% v/v propanol; , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.88 Å
Detector	Type: MAR225 CCD / Detector: CCD / Date: Jan 30, 2009 / Details: Dynamically bendable mirror
Radiation	Monochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.88 Å / Relative weight: 1
Reflection	Resolution: 2.6→55.37 Å / Num. all: 18077 / Num. obs: 18077 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / B_iso Wilson estimate: 59.3 Å² / R_merge(I) obs: 0.112 / Net I/σ(I): 12.3
Reflection shell	Resolution: 2.6→2.74 Å / Redundancy: 6.4 % / R_merge(I) obs: 0.767 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2566 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHASER		phasing
REFMAC	5.5.0085	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KWA

1kwa

Resolution: 2.6→41.76 Å / Cor.coef. F_o:F_c: 0.926 / Cor.coef. F_o:F_c free: 0.892 / SU B: 17.837 / SU ML: 0.194 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 20 / ESU R: 0.322 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26456	920	5.1 %	RANDOM
R_work	0.22302	-	-	-
obs	0.22504	17111	99.28 %	-
all	-	18031	-	-

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: 15.202 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.31 Å²	0 Å²	0 Å²
2-	-	0.31 Å²	0 Å²
3-	-	-	-0.61 Å²

Refine analyze

Luzzati coordinate error obs: 0.446 Å

Refinement step

Cycle: LAST / Resolution: 2.6→41.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2199	0	16	107	2322

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	2239
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1553
X-RAY DIFFRACTION	r_angle_refined_deg	1.458	1.981	2996
X-RAY DIFFRACTION	r_angle_other_deg	0.902	3	3838
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.449	5	279
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.346	26	90
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.468	15	456
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.499	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	339
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2406
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	393
X-RAY DIFFRACTION	r_mcbond_it	0.505	1.5	1383
X-RAY DIFFRACTION	r_mcbond_other	0.113	1.5	585
X-RAY DIFFRACTION	r_mcangle_it	1.068	2	2232
X-RAY DIFFRACTION	r_scbond_it	1.835	3	856
X-RAY DIFFRACTION	r_scangle_it	3.245	4.5	764

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	223	tight positional	0.06	0.05
1	2	B	223	tight positional	0.05	0.05
1	3	C	223	tight positional	0.05	0.05
3	1	A	403	tight positional	0.05	0.05
3	2	B	403	tight positional	0.04	0.05
3	3	C	403	tight positional	0.06	0.05
4	1	A	53	tight positional	0.04	0.05
4	2	B	53	tight positional	0.03	0.05
4	3	C	53	tight positional	0.05	0.05
5	1	A	221	tight positional	0.05	0.05
5	2	B	221	tight positional	0.04	0.05
5	3	C	221	tight positional	0.04	0.05
2	1	A	34	medium positional	0.71	0.5
2	2	B	34	medium positional	0.41	0.5
2	3	C	34	medium positional	0.5	0.5
4	1	A	86	medium positional	0.07	0.5
4	2	B	86	medium positional	0.03	0.5
4	3	C	86	medium positional	0.07	0.5
2	1	A	34	loose positional	1.85	5
2	2	B	34	loose positional	1.85	5
2	3	C	34	loose positional	1.48	5
1	1	A	223	tight thermal	0.1	0.5
1	2	B	223	tight thermal	0.1	0.5
1	3	C	223	tight thermal	0.11	0.5
3	1	A	403	tight thermal	0.1	0.5
3	2	B	403	tight thermal	0.09	0.5
3	3	C	403	tight thermal	0.1	0.5
4	1	A	53	tight thermal	0.13	0.5
4	2	B	53	tight thermal	0.12	0.5
4	3	C	53	tight thermal	0.09	0.5
5	1	A	221	tight thermal	0.11	0.5
5	2	B	221	tight thermal	0.12	0.5
5	3	C	221	tight thermal	0.09	0.5
2	1	A	34	medium thermal	0.25	2
2	2	B	34	medium thermal	0.65	2
2	3	C	34	medium thermal	0.65	2
4	1	A	86	medium thermal	0.13	2
4	2	B	86	medium thermal	0.11	2
4	3	C	86	medium thermal	0.08	2
2	1	A	34	loose thermal	1.31	10
2	2	B	34	loose thermal	0.54	10
2	3	C	34	loose thermal	1.32	10

LS refinement shell

Resolution: 2.6→2.668 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.403	56	-
R_work	0.377	1119	-
obs	-	-	90.11 %

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	3.718	2.4379	-1.4895	12.004	-6.7163	5.3132	-0.0056	0.373	-0.2015	-0.5123	-0.2102	-0.6671	0.1538	0.2696	0.2158	0.2865	-0.0033	-0.0212	0.2781	-0.014	0.1169	22.738	30.802	14.833
2	5.5414	-0.9509	4.4644	9.6347	-3.8058	9.0824	0.1509	0.6715	0.4623	-0.2028	0.0832	0.6295	-0.2573	0.1124	-0.2341	0.2024	0.0556	0.0558	0.2332	0.1358	0.2621	14.638	36.81	18.583
3	6.9158	2.3599	2.7187	6.3143	3.3236	9.5915	-0.0605	1.2557	0.622	-0.8626	0.2168	0.0225	-0.1398	-0.0662	-0.1563	0.4451	0.0448	0.0001	0.5546	0.2233	0.2112	17.063	33.506	10.049
4	4.6993	-0.5035	0.0193	9.72	-2.1354	2.8195	0.1508	0.4536	-0.0861	-0.3467	0.302	0.6689	0.1873	-0.3203	-0.4528	0.3156	-0.0124	-0.0785	0.3087	0.0688	0.0988	12.411	26.677	14.974
5	0.6706	2.117	0.7539	10.4136	-2.5097	7.8434	0.0539	-0.0949	-0.1654	0.445	-0.2774	-0.7681	-0.1868	0.3792	0.2234	0.2549	0.0835	-0.0093	0.4654	0.0715	0.2874	26.902	46.884	7.647
6	9.3906	-4.3483	-1.8329	7.8296	0.8369	6.5462	0.1861	0.3488	0.2089	-0.1327	-0.2472	0.3454	-0.3115	-0.3435	0.0611	0.1013	-0.087	-0.0431	0.1646	0.0624	0.1337	-6.417	64.1	14.118
7	10.3228	-1.4595	0.8412	1.8772	0.3655	1.5678	-0.1058	-0.2392	-0.1975	0.234	0.0518	0.057	0.0656	-0.0491	0.054	0.2347	-0.0622	-0.0023	0.1798	0.0395	0.0731	-0.512	58.886	21.876
8	6.3546	4.914	-2.3592	9.3532	-0.1258	2.8304	-0.1497	-0.1999	-0.2478	-0.3483	0.1737	-0.2583	0.3246	0.0848	-0.0239	0.1059	-0.0586	-0.0186	0.1913	0.0114	0.0194	4.068	61.761	13.454
9	9.8358	-0.1436	3.1291	2.073	-1.1479	2.0093	-0.1307	-0.2131	0.7418	0.0361	0.0796	0.3126	-0.4479	-0.1989	0.0511	0.4037	-0.0003	0.0101	0.1802	-0.0067	0.107	-0.202	69.018	16.164
10	1.5774	-5.8502	2.3794	22.115	-8.0648	5.2819	0.2431	0.1594	-0.0362	-0.7562	-0.5023	0.2272	0.3306	0.5716	0.2592	0.3127	0.0085	-0.0037	0.3316	0.1017	0.451	5.006	42.419	15.352
11	2.2672	-2.179	-4.8278	4.6486	9.8303	20.9839	0.154	0.1614	-0.0781	-0.3336	-0.3401	0.1371	-0.6683	-0.878	0.1861	0.2393	-0.0338	-0.0434	0.2076	0.0507	0.162	14.614	68.839	1.463
12	6.0806	1.0296	-1.7602	3.3273	-1.1129	6.6176	-0.1484	-0.506	-0.2112	0.1548	0.0049	-0.3844	0.4403	1.0075	0.1435	0.1531	0.036	-0.034	0.2302	0.0104	0.0551	24.815	57.131	0.387
13	9.7274	4.0582	-2.6821	4.724	0.0211	2.7332	0.0022	-0.1389	0.1807	-0.069	-0.0048	0.0235	0.1423	0.1913	0.0027	0.1599	0.0023	-0.0309	0.1921	0.0224	0.0205	18.819	59.901	-0.305
14	1.8171	-0.9134	-0.6527	3.1369	3.9147	7.616	-0.1943	0.0472	-0.0696	-0.2898	0.1914	0.0223	0.1022	0.3101	0.0029	0.1983	-0.0611	0.0046	0.2634	0.0257	0.0061	18.751	58.965	-1.212

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-1 - 124
2	X-RAY DIFFRACTION	2	A	125 - 154
3	X-RAY DIFFRACTION	3	A	155 - 174
4	X-RAY DIFFRACTION	4	A	175 - 195
5	X-RAY DIFFRACTION	5	A	196 - 204
6	X-RAY DIFFRACTION	6	B	113 - 127
7	X-RAY DIFFRACTION	7	B	128 - 154
8	X-RAY DIFFRACTION	8	B	155 - 174
9	X-RAY DIFFRACTION	9	B	175 - 196
10	X-RAY DIFFRACTION	10	B	197 - 204
11	X-RAY DIFFRACTION	11	C	-1 - 120
12	X-RAY DIFFRACTION	12	C	121 - 146
13	X-RAY DIFFRACTION	13	C	147 - 174
14	X-RAY DIFFRACTION	14	C	175 - 204

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Yorodumi