PDB-3kd7: Designed TPR module (CTPR390) in complex with its peptide-ligand ...

ID or keywords:

Entry

Database: PDB / ID: 3kd7

Title

Designed TPR module (CTPR390) in complex with its peptide-ligand (Hsp90 peptide)

Components

CTPR390
Hsp90 MEEVD peptide

Keywords

DE NOVO PROTEIN /

Designed protein / tetratricopeptide repeat (TPR) /

Hsp90 binding / repeat protein / TPR-ligand complex / superhelical structure

Function / homology

Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat /

Alpha Horseshoe / Mainly Alpha / DSCR1

Function and homology information

Biological species

UNIDENTIFIED (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.85 Å

Authors

Cortajarena, A.L. / Wang, J. / Regan, L.

Citation

Journal: Febs J. / Year: 2010
Title: Crystal structure of a designed tetratricopeptide repeat module in complex with its peptide ligand.
Authors: Cortajarena, A.L. / Wang, J. / Regan, L.

History

Deposition	Oct 22, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 2, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	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_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3kd7.cif.gz	120 KB	Display	PDBx/mmCIF format
PDB format	pdb3kd7.ent.gz	96.7 KB	Display	PDB format
PDBx/mmJSON format	3kd7.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/kd/3kd7 ftp://data.pdbj.org/pub/pdb/validation_reports/kd/3kd7	HTTPS FTP

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Related structure data

Related structure data	1na0S 1elr 1elw 1na3 2avp 2c2l 3fwv S: Starting model for refinement
Similar structure data	4fg3-d 4f1b-d 4ins-d 5co6-d 3n55-d 5m9g-d 5m9c-d 4f0o-d 4ey1-d 3njj-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) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

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	#70 - Oct 2005 Designer Proteins similarity (2) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

A: CTPR390

B: CTPR390

C: CTPR390

D: CTPR390

E: CTPR390

G: Hsp90 MEEVD peptide

H: Hsp90 MEEVD peptide

I: Hsp90 MEEVD peptide

J: Hsp90 MEEVD peptide

K: Hsp90 MEEVD peptide

75.1 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CTPR390

H: Hsp90 MEEVD peptide

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

2

B: CTPR390

G: Hsp90 MEEVD peptide

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

3

C: CTPR390

I: Hsp90 MEEVD peptide

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

4

D: CTPR390

J: Hsp90 MEEVD peptide

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

5

E: CTPR390

K: Hsp90 MEEVD peptide

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

Unit cell

Length a, b, c (Å)	100.674, 100.674, 161.574
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
1	2	G
2	2	H
3	2	I
4	2	J
5	2	K

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	ASP	ASP	LEU	LEU	4	A	A	24 - 106	24 - 106
2	1	ASP	ASP	LEU	LEU	4	B	B	24 - 106	24 - 106
3	1	ASP	ASP	LEU	LEU	4	C	C	24 - 106	24 - 106
4	1	ASP	ASP	LEU	LEU	4	D	D	24 - 106	24 - 106
5	1	ASP	ASP	LEU	LEU	4	E	E	24 - 106	24 - 106
1	2	ACE	ACE	ASP	ASP	1	G	F	0 - 5	1 - 6
2	2	ACE	ACE	ASP	ASP	1	H	G	0 - 5	1 - 6
3	2	ACE	ACE	ASP	ASP	1	I	H	0 - 5	1 - 6
4	2	ACE	ACE	ASP	ASP	1	J	I	0 - 5	1 - 6
5	2	ACE	ACE	ASP	ASP	1	K	J	0 - 5	1 - 6

NCS ensembles :

ID
1
2

#1: Protein	CTPR390 Mass: 14371.691 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) UNIDENTIFIED (others) / Plasmid: pProEX-HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Protein/peptide	Hsp90 MEEVD peptide Mass: 647.695 Da / Num. of mol.: 5 / Source method: obtained synthetically Details: This sequence comprises the 5 C-terminal residues of Hsp90 References: UniProt: Q9H2A1*PLUS
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.1 Å³/Da / Density % sol: 41.38 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 10 Details: 50 mM NaH2PO4, 20% (w/v) PEG 20000, 50 mM CAPS, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1001 Å
Detector	Detector: CCD / Date: Apr 20, 2004
Radiation	Monochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1001 Å / Relative weight: 1
Reflection	Resolution: 2.85→76.7 Å / Num. all: 13878 / Num. obs: 13180 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / R_merge(I) obs: 0.075 / R_sym value: 0.075 / Net I/σ(I): 21.18
Reflection shell	Resolution: 2.85→2.95 Å / Redundancy: 5.28 % / R_merge(I) obs: 0.397 / Mean I/σ(I) obs: 1.16 / R_sym value: 0.397 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
MOLREP		phasing
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1NA0

1na0

Resolution: 2.85→50 Å / Cor.coef. F_o:F_c: 0.885 / Cor.coef. F_o:F_c free: 0.875 / SU B: 39.581 / SU ML: 0.363 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.479 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28255	696	5 %	RANDOM
R_work	0.27055	-	-	-
obs	0.27114	13180	97.26 %	-
all	-	13878	-	-

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: 35.289 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.31 Å²	-1.16 Å²	0 Å²
2-	-	-2.31 Å²	0 Å²
3-	-	-	3.47 Å²

Refinement step

Cycle: LAST / Resolution: 2.85→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4416	0	0	17	4433

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.022	4521
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.708	1.944	6109
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.838	5	518
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.298	25.762	269
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.23	15	728
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.565	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.054	0.2	556
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	3652
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.156	0.2	1981
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.302	0.2	2995
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.121	0.2	99
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	0.132	0.2	65
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.104	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	2.735	2	2716
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	4.193	3	4119
X-RAY DIFFRACTION	r_scbond_it	2.622	2	2222
X-RAY DIFFRACTION	r_scangle_it	3.939	3	1990
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
2	1	G	45	tight positional	0.01	0.05
2	2	H	45	tight positional	0.01	0.05
2	3	I	45	tight positional	0.01	0.05
2	4	J	45	tight positional	0.01	0.05
2	5	K	45	tight positional	0.01	0.05
1	1	A	630	medium positional	0.54	0.5
1	2	B	630	medium positional	0.39	0.5
1	3	C	630	medium positional	0.27	0.5
1	4	D	630	medium positional	0.28	0.5
1	5	E	630	medium positional	0.27	0.5
2	1	G	45	tight thermal	0.01	0.5
2	2	H	45	tight thermal	0.01	0.5
2	3	I	45	tight thermal	0.01	0.5
2	4	J	45	tight thermal	0.01	0.5
2	5	K	45	tight thermal	0.01	0.5
1	1	A	630	medium thermal	0.27	2
1	2	B	630	medium thermal	0.22	2
1	3	C	630	medium thermal	0.18	2
1	4	D	630	medium thermal	0.2	2
1	5	E	630	medium thermal	0.21	2

LS refinement shell

Resolution: 2.85→2.924 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.407	66	-
R_work	0.436	995	-
obs	-	-	99.81 %

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	38.674	31.2568	-18.6843	26.6033	-24.1182	69.6536	0.1391	1.6075	1.0828	1.8295	1.131	0.8219	0.9247	-0.9085	-1.27	0.8135	0.0517	0.3581	0.4078	-0.126	0.7058	-56.4795	-12.0904	14.1321
2	12.2844	5.9957	-0.1345	3.3105	1.2043	4.2001	-0.3217	-0.4755	-0.387	0.5201	0.4437	-0.0938	0.2731	-0.5304	-0.122	0.4051	-0.0729	0.0755	0.3028	0.1357	0.2801	-46.3131	-6.0947	14.5746
3	5.5199	0.6272	-0.9233	6.2998	-3.6945	5.0857	0.1648	-0.2714	-0.1314	0.1828	0.3655	0.853	0.3554	-0.2746	-0.5303	0.1678	0.0723	0.0359	0.2273	0.1286	0.3516	-43.3298	-1.0666	-1.905
4	9.0082	-4.4959	7.8038	10.9327	-3.9531	6.7608	-1.4585	0.5737	1.3232	1.8749	0.2166	-0.1211	0.1427	0.4243	1.2419	0.4905	0.2872	0.0073	0.5539	-0.0372	0.5997	-17.9015	-12.2894	2.6151
5	12.9589	-9.4441	-1.6834	7.2689	-0.6863	9.6944	0.027	-0.1096	-0.1326	0.0545	0.1705	-0.6237	0.5423	1.2632	-0.1976	0.2706	0.2762	-0.1077	0.5584	-0.0356	0.3768	-19.0211	-4.6722	-5.0986
6	4.5907	-3.6505	0.8898	3.1149	0.6128	8.3949	0.046	0.069	0.1892	-0.2414	0.1322	-0.8048	0.2353	1.4176	-0.1782	0.3017	0.1746	0.1176	0.695	0.0435	0.4514	-16.3297	-0.1978	-16.1433
7	16.5658	-5.7342	8.2787	5.2016	-7.146	9.8328	-1.8932	0.2514	-1.3906	0.3911	0.4055	-0.9912	-0.0574	-0.6734	1.4878	0.6287	-0.0501	0.3437	0.2266	0.0357	0.6258	-51.2116	-8.0869	-30.3891
8	2.6146	-2.6398	-3.0215	12.5377	-1.0162	5.1669	-0.4716	-0.0356	-1.4287	-0.109	-0.1663	-0.0271	1.155	-0.4743	0.6379	0.3775	-0.0577	0.109	0.5132	0.0588	0.549	-56.9254	-7.4449	-25.0961
9	7.7275	-7.1212	4.4337	8.8636	-5.53	5.713	-0.4026	0.0914	-0.2343	-0.0021	0.4002	0.3868	0.0987	-0.4323	0.0025	0.3997	0.0128	0.0156	0.5546	0.0059	0.1887	-65.0527	7.116	-28.6532
10	2.9177	11.3927	-1.1874	44.4859	-4.6365	0.4832	2.4213	-0.1895	2.7952	0.7124	0.6369	1.5755	2.2293	-0.406	-3.0582	0.4765	-0.1754	0.0472	0.7081	-0.1822	0.8777	-41.1487	14.3913	-4.1279
11	7.0768	6.805	0.5277	6.6165	0.0548	2.8522	0.1673	0.1032	0.8918	-0.0086	0.0053	1.5355	0.4542	-0.0339	-0.1725	0.2072	0.0493	-0.0052	0.3914	0.2618	0.5779	-35.6786	18.7584	-8.602
12	13.396	-0.0951	1.9664	7.1755	0.2803	0.7789	-0.1335	-0.9696	1.2875	0.3991	0.4559	0.3742	-0.2082	0.2097	-0.3224	0.3602	-0.0349	0.0323	0.5395	0.0073	0.3874	-22.2516	27.0368	-2.3855
13	26.466	-9.7593	10.4835	18.87	0.5298	10.2968	0.3733	0.145	-0.6733	-0.1089	-0.3755	0.208	0.3144	0.6187	0.0023	0.4284	0.2536	0.17	0.6284	0.0677	-0.1074	-22.567	-2.8729	-25.2724
14	8.4321	-3.7522	5.015	3.4379	-2.5218	3.0302	-0.0294	0.0246	-0.4673	0.455	0.1738	-0.3692	0.0807	1.2875	-0.1444	0.6308	0.3233	0.3179	0.5644	-0.0504	0.3168	-22.2036	-4.9452	-32.1494
15	6.0543	0.8	0.8219	3.5843	-0.1733	0.7433	-0.409	0.323	-1.2741	-0.2583	0.3043	0.1668	0.683	0.0742	0.1047	0.7523	0.145	0.2781	0.3398	-0.1214	0.5321	-38.2961	-10.695	-34.1447

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	7 - 12
2	X-RAY DIFFRACTION	2	A	13 - 36
3	X-RAY DIFFRACTION	3	A	37 - 108
4	X-RAY DIFFRACTION	4	B	23 - 41
5	X-RAY DIFFRACTION	5	B	42 - 70
6	X-RAY DIFFRACTION	6	B	71 - 107
7	X-RAY DIFFRACTION	7	C	7 - 22
8	X-RAY DIFFRACTION	8	C	23 - 46
9	X-RAY DIFFRACTION	9	C	47 - 107
10	X-RAY DIFFRACTION	10	D	7 - 15
11	X-RAY DIFFRACTION	11	D	16 - 46
12	X-RAY DIFFRACTION	12	D	47 - 107
13	X-RAY DIFFRACTION	13	E	8 - 21
14	X-RAY DIFFRACTION	14	E	22 - 46
15	X-RAY DIFFRACTION	15	E	47 - 107

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