PDB-4q2o: PDLIM4 PDZ in Complex with a Phage-Derived Peptide

ID or keywords:

Entry

Database: PDB / ID: 4q2o

Title

PDLIM4 PDZ in Complex with a Phage-Derived Peptide

Components

PDZ and LIM domain protein 4

Keywords

PROTEIN BINDING / PDZ

Function / homology

Function and homology information

recycling endosome lumen / muscle structure development / excitatory chemical synaptic transmission / muscle alpha-actinin binding / filamentous actin / alpha-actinin binding / stress fiber / early endosome lumen / adherens junction / Z disc ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Appleton, B.A. / Wiesmann, C.

Citation

Journal: J.Mol.Biol. / Year: 2014
Title: A structural portrait of the PDZ domain family.
Authors: Ernst, A. / Appleton, B.A. / Ivarsson, Y. / Zhang, Y. / Gfeller, D. / Wiesmann, C. / Sidhu, S.S.

History

Deposition	Apr 9, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 10, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 26, 2014	Group: Database references
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references / 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 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_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_ref_seq_dif.details
Revision 1.3	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4q2o.cif.gz	212.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4q2o.ent.gz	173.3 KB	Display	PDB format
PDBx/mmJSON format	4q2o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4q2o_validation.pdf.gz	473.1 KB	Display	wwPDB validaton report
Full document	4q2o_full_validation.pdf.gz	481.7 KB	Display
Data in XML	4q2o_validation.xml.gz	20 KB	Display
Data in CIF	4q2o_validation.cif.gz	28.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q2/4q2o ftp://data.pdbj.org/pub/pdb/validation_reports/q2/4q2o	HTTPS FTP

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Related structure data

Related structure data	4q2nC 4q2pC 4q2qC 2v1wS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6q0n-d 6q0u-d 2vph-d 3s63-d 6q3u-d 3ntk-2 6ak2-d 3owr-2 6jie-d 3e2i-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: PDZ and LIM domain protein 4

B: PDZ and LIM domain protein 4

C: PDZ and LIM domain protein 4

D: PDZ and LIM domain protein 4

E: PDZ and LIM domain protein 4

F: PDZ and LIM domain protein 4

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

1

A: PDZ and LIM domain protein 4

B: PDZ and LIM domain protein 4

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

2

C: PDZ and LIM domain protein 4

D: PDZ and LIM domain protein 4

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

3

E: PDZ and LIM domain protein 4

F: PDZ and LIM domain protein 4

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

Unit cell

Length a, b, c (Å)	33.710, 64.610, 126.220
Angle α, β, γ (deg.)	90.000, 93.050, 90.000
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	D
4	1	E
5	1	F
6	1	C
1	2	A
2	2	B
3	2	D
4	2	E
5	2	F
6	2	C

NCS domain segments:

Refine code: 3

Dom-ID	Component-ID	Ens-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	1	HIS	HIS	GLY	GLY	A	A	3 - 20	6 - 23
2	1	1	HIS	HIS	GLY	GLY	B	B	3 - 20	6 - 23
3	1	1	HIS	HIS	GLY	GLY	D	D	3 - 20	6 - 23
4	1	1	HIS	HIS	GLY	GLY	E	E	3 - 20	6 - 23
5	1	1	HIS	HIS	GLY	GLY	F	F	3 - 20	6 - 23
6	1	1	HIS	HIS	GLY	GLY	C	C	3 - 20	6 - 23
1	2	1	PRO	PRO	GLY	GLY	A	A	26 - 71	29 - 74
2	2	1	PRO	PRO	GLY	GLY	B	B	26 - 71	29 - 74
3	2	1	PRO	PRO	GLY	GLY	D	D	26 - 71	29 - 74
4	2	1	PRO	PRO	GLY	GLY	E	E	26 - 71	29 - 74
5	2	1	PRO	PRO	GLY	GLY	F	F	26 - 71	29 - 74
6	2	1	PRO	PRO	GLY	GLY	C	C	26 - 71	29 - 74
1	3	1	ASP	ASP	PRO	PRO	A	A	74 - 83	77 - 86
2	3	1	ASP	ASP	PRO	PRO	B	B	74 - 83	77 - 86
3	3	1	ASP	ASP	PRO	PRO	D	D	74 - 83	77 - 86
4	3	1	ASP	ASP	PRO	PRO	E	E	74 - 83	77 - 86
5	3	1	ASP	ASP	PRO	PRO	F	F	74 - 83	77 - 86
6	3	1	ASP	ASP	PRO	PRO	C	C	74 - 83	77 - 86
1	1	2	GLU	GLU	LEU	LEU	A	A	91 - 95	94 - 98
2	1	2	GLU	GLU	LEU	LEU	B	B	91 - 95	94 - 98
3	1	2	GLU	GLU	LEU	LEU	D	D	91 - 95	94 - 98
4	1	2	GLU	GLU	LEU	LEU	E	E	91 - 95	94 - 98
5	1	2	GLU	GLU	LEU	LEU	F	F	91 - 95	94 - 98
6	1	2	GLU	GLU	LEU	LEU	C	C	91 - 95	94 - 98

NCS ensembles :

ID
1
2

#1: Protein	PDZ and LIM domain protein 4 / LIM protein RIL / Reversion-induced LIM protein Mass: 10303.676 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDLIM4, RIL / Production host: Escherichia coli (E. coli) / References: UniProt: P50479
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	PHAGE-DERIVED PEPTIDE LIGAND WAS FUSED TO THE C TERMINUS OF THE LINKER

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.22 Å³/Da / Density % sol: 44.6 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion / pH: 4.6 Details: 25% PEG 4000, 0.1 M sodium acetate (pH 4.6), 0.1 M Sodium citrate tribasic, 0.2 M ammonium sulfate, VAPOR DIFFUSION, temperature 292K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 0.98

Detector

Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 6, 2007

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 2.1→50 Å / Num. obs: 31772 / % possible obs: 99.3 % / Redundancy: 4 % / R_merge(I) obs: 0.04 / R_sym value: 0.036 / Χ²: 1.037 / Net I/σ(I): 26.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.1-2.18	3.6	0.384	3156	0.955	1	99.8
2.18-2.26	4	0.322	3218	1.35	1	100
2.26-2.37	4.1	0.306	3138	1.163	1	100
2.37-2.49	4.1	0.15	3186	0.943	1	100
2.49-2.65	4.1	0.11	3179	1.007	1	100
2.65-2.85	4.2	0.068	3214	1.055	1	100
2.85-3.14	4.2	0.047	3193	0.967	1	100
3.14-3.59	4.1	0.038	3202	0.981	1	100
3.59-4.52	4.1	0.03	3206	1.025	1	99.7
4.52-50	3.9	0.03	3080	0.912	1	93.3

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3.11	data extraction
HKL-2000		data collection
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2v1w

2v1w

Resolution: 2.1→20 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.916 / Occupancy max: 1 / Occupancy min: 1 / SU B: 24.062 / SU ML: 0.278 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.292	1565	5 %	RANDOM
R_work	0.2478	-	-	-
obs	0.2501	31009	97.73 %	-

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 max: 98.44 Å² / B_iso mean: 73.699 Å² / B_iso min: 39.8 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.18 Å²	0 Å²	-0.16 Å²
2-	-	0.52 Å²	0 Å²
3-	-	-	-0.72 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3910	0	0	61	3971

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	3999
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	2728
X-RAY DIFFRACTION	r_angle_refined_deg	1.434	1.97	5437
X-RAY DIFFRACTION	r_angle_other_deg	1.015	3.003	6628
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.603	5	516
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	25.435	21.739	138
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.529	15	612
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.726	15	34
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	625
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	4413
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	773
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	653
X-RAY DIFFRACTION	r_nbd_other	0.186	0.2	2597
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	1795
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	2340
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.15	0.2	97
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.155	0.2	27
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.211	0.2	40
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.079	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	2.593	2.5	2718
X-RAY DIFFRACTION	r_mcbond_other	0.296	2.5	1070
X-RAY DIFFRACTION	r_mcangle_it	3.84	5	4191
X-RAY DIFFRACTION	r_scbond_it	3.463	2.5	1476
X-RAY DIFFRACTION	r_scangle_it	4.962	5	1246

Refine LS restraints NCS

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

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	430	TIGHT POSITIONAL	0.07	0.05
1	B	430	TIGHT POSITIONAL	0.06	0.05
1	D	430	TIGHT POSITIONAL	0.05	0.05
1	E	430	TIGHT POSITIONAL	0.05	0.05
1	F	430	TIGHT POSITIONAL	0.05	0.05
1	C	430	TIGHT POSITIONAL	0.05	0.05
1	A	457	LOOSE POSITIONAL	0.64	5
1	B	457	LOOSE POSITIONAL	0.6	5
1	D	457	LOOSE POSITIONAL	0.56	5
1	E	457	LOOSE POSITIONAL	0.66	5
1	F	457	LOOSE POSITIONAL	0.54	5
1	C	457	LOOSE POSITIONAL	0.64	5
1	A	430	TIGHT THERMAL	0.17	0.5
1	B	430	TIGHT THERMAL	0.18	0.5
1	D	430	TIGHT THERMAL	0.1	0.5
1	E	430	TIGHT THERMAL	0.13	0.5
1	F	430	TIGHT THERMAL	0.13	0.5
1	C	430	TIGHT THERMAL	0.14	0.5
1	A	457	LOOSE THERMAL	2.99	10
1	B	457	LOOSE THERMAL	3.24	10
1	D	457	LOOSE THERMAL	2.79	10
1	E	457	LOOSE THERMAL	2.81	10
1	F	457	LOOSE THERMAL	2.5	10
1	C	457	LOOSE THERMAL	2.59	10
2	A	29	TIGHT POSITIONAL	0.04	0.05
2	B	29	TIGHT POSITIONAL	0.03	0.05
2	D	29	TIGHT POSITIONAL	0.04	0.05
2	E	29	TIGHT POSITIONAL	0.05	0.05
2	F	29	TIGHT POSITIONAL	0.05	0.05
2	C	29	TIGHT POSITIONAL	0.05	0.05
2	A	40	LOOSE POSITIONAL	0.2	5
2	B	40	LOOSE POSITIONAL	0.39	5
2	D	40	LOOSE POSITIONAL	0.28	5
2	E	40	LOOSE POSITIONAL	0.34	5
2	F	40	LOOSE POSITIONAL	0.2	5
2	C	40	LOOSE POSITIONAL	0.41	5
2	A	29	TIGHT THERMAL	0.13	0.5
2	B	29	TIGHT THERMAL	0.1	0.5
2	D	29	TIGHT THERMAL	0.14	0.5
2	E	29	TIGHT THERMAL	0.1	0.5
2	F	29	TIGHT THERMAL	0.18	0.5
2	C	29	TIGHT THERMAL	0.06	0.5
2	A	40	LOOSE THERMAL	1.73	10
2	B	40	LOOSE THERMAL	1.07	10
2	D	40	LOOSE THERMAL	1.56	10
2	E	40	LOOSE THERMAL	2.23	10
2	F	40	LOOSE THERMAL	4.74	10
2	C	40	LOOSE THERMAL	1.85	10

LS refinement shell

Resolution: 2.1→2.143 Å / Total num. of bins used: 25

	R_factor	Num. reflection	% reflection
R_free	0.382	77	-
R_work	0.312	1465	-
all	-	1542	-
obs	-	-	83.8 %

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	5.1729	-2.0713	1.3298	5.2139	-0.6792	13.3561	-0.0336	0.1738	0.2491	0.2033	0.0808	0.1272	-0.2729	1.5375	-0.0472	-0.3427	0.0992	0.0597	-0.0983	-0.0395	-0.2332	-6.0273	15.3738	-26.9282
2	6.7904	-2.2161	0.1649	5.1481	0.0779	7.656	0.1121	0.1974	0.0193	-0.1796	0.0434	0.2279	0.431	-0.1311	-0.1555	-0.2013	0.1734	-0.0116	-0.3003	0.0221	-0.2982	-20.145	5.9551	-46.9297
3	8.6175	0.9489	2.6561	6.7136	0.3495	18.4803	-0.464	0.9181	0.2601	-0.023	0.2057	0.3247	-0.4901	1.1274	0.2583	-0.22	-0.1545	-0.067	-0.2827	0.0268	-0.2193	-8.7483	4.9617	17.828
4	12.6688	-1.1241	1.4125	10.0828	-4.6543	14.5802	0.3884	-0.3162	-0.4365	-0.2428	-0.5265	-0.3177	0.6767	1.0199	0.1381	-0.0032	0.2444	-0.0012	-0.0184	-0.029	-0.293	-0.1688	3.4384	-7.0385
5	5.372	3.2834	0.1318	9.4267	0.7119	9.5809	-0.2245	0.2004	0.4349	-0.0952	0.1296	0.5846	-0.1161	0.4037	0.0948	-0.1178	-0.2711	-0.0811	0.0271	0.07	-0.1986	1.7933	17.1166	36.486
6	9.3697	2.2551	-2.0459	5.5676	-3.4109	12.9311	-0.4691	-0.1145	-0.582	-0.1844	0.0996	-0.3824	0.9351	-0.1642	0.3695	-0.0578	-0.1719	0.08	-0.2565	-0.0122	-0.2446	14.8805	4.3545	55.775

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 84
2	X-RAY DIFFRACTION	1	B	90 - 95
3	X-RAY DIFFRACTION	2	B	1 - 83
4	X-RAY DIFFRACTION	2	A	87 - 95
5	X-RAY DIFFRACTION	3	C	1 - 83
6	X-RAY DIFFRACTION	3	D	90 - 95
7	X-RAY DIFFRACTION	4	D	1 - 83
8	X-RAY DIFFRACTION	4	C	91 - 95
9	X-RAY DIFFRACTION	5	E	3 - 83
10	X-RAY DIFFRACTION	5	F	88 - 95
11	X-RAY DIFFRACTION	6	F	1 - 87
12	X-RAY DIFFRACTION	6	E	91 - 95

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