PDB-3kfe: Crystal structures of a group II chaperonin from Methanococcus ma...

ID or keywords:

Entry

Database: PDB / ID: 3kfe

Title

Crystal structures of a group II chaperonin from Methanococcus maripaludis

Components

Chaperonin

Keywords

CHAPERONE / double homo-octameric rings / ATP-binding / Nucleotide-binding

Function / homology

Function and homology information

ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / metal ion binding / identical protein binding
Similarity search - Function

Biological species

Methanococcus maripaludis (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.5 Å

Authors

Pereira, J.H. / Ralston, C.Y. / Douglas, N. / Meyer, D. / Knee, K.M. / Goulet, D.R. / King, J.A. / Frydman, J. / Adams, P.D.

Citation

Journal: J.Biol.Chem. / Year: 2010
Title: Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle.
Authors: Pereira, J.H. / Ralston, C.Y. / Douglas, N.R. / Meyer, D. / Knee, K.M. / Goulet, D.R. / King, J.A. / Frydman, J. / Adams, P.D.

History

Deposition	Oct 27, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 23, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 13, 2021	Group: Database references / Derived calculations Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Oct 30, 2024	Group: Data collection / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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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PDBx/mmCIF format	3kfe.cif.gz	1.4 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	3kfe_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	3kfe_full_validation.pdf.gz	2.3 MB	Display
Data in XML	3kfe_validation.xml.gz	154.2 KB	Display
Data in CIF	3kfe_validation.cif.gz	202.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kf/3kfe ftp://data.pdbj.org/pub/pdb/validation_reports/kf/3kfe	HTTPS FTP

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Related structure data

Related structure data	3kfbC 3kfkC C: citing same article (ref.)
Similar structure data	3iyg-d 1a6d-2 1a6e-2 1q3q-3 1q2v-3 1q3r-2 3kfb-d 1q3q-2 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
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (6)

Deposited unit

A: Chaperonin

B: Chaperonin

C: Chaperonin

D: Chaperonin

E: Chaperonin

F: Chaperonin

G: Chaperonin

H: Chaperonin

hetero molecules

449 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	261.450, 161.920, 147.370
Angle α, β, γ (deg.)	90.00, 124.12, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN

Dom-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	SO4	SO4	chain A	A	A - K	11 - 546	11
2	SO4	SO4	chain B	B	B - N	11 - 546	11
3	SO4	SO4	chain C	C	C - Q	11 - 546	11
4	SO4	SO4	chain D	D	D - T	11 - 546	11
5	SO4	SO4	chain E	E	E - W	11 - 546	11
6	SO4	SO4	chain F	F	F - Z	11 - 546	11
7	SO4	SO4	chain G	G	G - CA	11 - 546	11
8	ARG	ARG	chain H	H	H	11 - 511	11 - 489

#1: Protein	Chaperonin / Chaperonin GroEL (Thermosome / HSP60 family) Mass: 55614.137 Da / Num. of mol.: 8 / Mutation: Q264T,E265A,E266S,K267E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanococcus maripaludis (archaea) / Gene: hsp60, MMP1515 / Production host: Escherichia coli (E. coli) / References: UniProt: Q877G8
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.9 Å³/Da / Density % sol: 57.62 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2 M Li2SO4 and 20 % PEG 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.978 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2008
Radiation	Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 3.5→54.49 Å / Num. all: 49417 / Num. obs: 49417 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell	Resolution: 3.5→3.69 Å / % possible all: 92

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
PHENIX	(phenix.refine)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.5→54.49 Å / SU ML: 2.42 / σ(F): 0.02 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2686	2503	5.07 %	RANDOM
R_work	0.2315	-	-	-
obs	0.2334	49417	77.14 %	-
all	-	49417	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 49.424 Å² / k_sol: 0.294 e/Å³

Refinement step

Cycle: LAST / Resolution: 3.5→54.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	29032	0	264	0	29296

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	29408
X-RAY DIFFRACTION	f_angle_d	1.273	39624
X-RAY DIFFRACTION	f_dihedral_angle_d	18.051	11152
X-RAY DIFFRACTION	f_chiral_restr	0.079	4848
X-RAY DIFFRACTION	f_plane_restr	0.003	5080

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	3655	X-RAY DIFFRACTION	POSITIONAL	0.042
1	2	B	3655	X-RAY DIFFRACTION	POSITIONAL	0.042
1	3	C	3655	X-RAY DIFFRACTION	POSITIONAL	0.046
1	4	D	3655	X-RAY DIFFRACTION	POSITIONAL	0.044
1	5	E	3655	X-RAY DIFFRACTION	POSITIONAL	0.042
1	6	F	3655	X-RAY DIFFRACTION	POSITIONAL	0.044
1	7	G	3655	X-RAY DIFFRACTION	POSITIONAL	0.047
1	8	H	3655	X-RAY DIFFRACTION	POSITIONAL	0.046

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.5-3.5673	0.3725	112	0.3513	2077	X-RAY DIFFRACTION	62
3.5673-3.6401	0.3713	114	0.3307	2051	X-RAY DIFFRACTION	61
3.6401-3.7193	0.3152	98	0.2916	2162	X-RAY DIFFRACTION	64
3.7193-3.8058	0.3544	115	0.2792	2232	X-RAY DIFFRACTION	66
3.8058-3.9009	0.2632	105	0.2523	2208	X-RAY DIFFRACTION	66
3.9009-4.0064	0.2692	135	0.2318	2375	X-RAY DIFFRACTION	70
4.0064-4.1242	0.2651	123	0.2174	2447	X-RAY DIFFRACTION	72
4.1242-4.2573	0.2616	150	0.2054	2549	X-RAY DIFFRACTION	76
4.2573-4.4094	0.225	128	0.2075	2623	X-RAY DIFFRACTION	78
4.4094-4.5858	0.2242	156	0.1956	2635	X-RAY DIFFRACTION	79
4.5858-4.7944	0.2413	155	0.1968	2818	X-RAY DIFFRACTION	83
4.7944-5.047	0.256	148	0.1841	2781	X-RAY DIFFRACTION	83
5.047-5.363	0.2606	131	0.1948	2796	X-RAY DIFFRACTION	82
5.363-5.7766	0.285	155	0.2138	2800	X-RAY DIFFRACTION	82
5.7766-6.3572	0.2825	171	0.2174	2990	X-RAY DIFFRACTION	89
6.3572-7.2752	0.239	156	0.1982	3103	X-RAY DIFFRACTION	91
7.2752-9.159	0.1833	171	0.1669	3131	X-RAY DIFFRACTION	92
9.159-54.5004	0.2626	180	0.2513	3136	X-RAY DIFFRACTION	91

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	2.4496	-1.0647	0.6163	2.1188	-0.4944	1.8123	-0.1554	-0.0579	-0.03	-0.1109	0.029	0.2271	-0.1597	0.0381	0	0.4817	-0.1114	0.1263	0.3421	-0.1098	0.3202	-1.4914	100.4955	79.9817
2	0.7638	1.4817	-0.9048	-0.0532	-0.5974	0.3646	-0.134	0.4639	-0.3793	-0.0471	0.223	-0.5847	0.0541	0.0355	-0	0.6659	-0.0952	0.0929	0.4637	-0.1669	0.4769	19.0265	84.9903	72.6566
3	0.5996	-1.8568	-0.318	1.1867	0.4738	0.6213	0.0544	0.917	-0.2835	-1.3566	0.4144	-0.9977	0.4069	0.081	-0	1.8505	-0.3221	0.5106	0.956	-0.3157	1.3098	26.9808	70.9544	48.4278
4	0.833	0.3981	0.1515	2.378	1.1231	1.7523	0.0027	-0.1644	-0.3196	0.0692	0.0762	0.0447	-0.2737	0.3973	0	0.417	-0.1591	0.041	0.424	-0.0301	0.4021	7.0915	60.524	88.2474
5	1.1127	0.2695	-0.1296	-0.4025	-0.8434	0.638	0.1292	0.2348	-0.3071	-0.1345	-0.0388	-0.1008	0.1058	0.3902	0	0.4723	0.0733	0.1314	0.5635	-0.0947	0.7347	17.7492	43.1066	70.988
6	0.6642	1.0749	-0.3615	0.5152	0.7938	0.7692	0.5827	0.2888	-0.0621	-0.8588	-0.2139	-0.1032	-0.1292	0.0992	-0	1.4329	0.1093	0.2957	0.9457	0.0322	0.9534	20.3969	41.3514	42.0526
7	0.7347	1.0594	0.4046	1.3748	0.2384	2.3221	-0.1054	0.0093	-0.0802	0.1025	-0.0683	0.1204	0.148	-0.2452	0	0.3267	0.0119	-0.0044	0.3184	0.1372	0.4788	-6.4576	23.3457	74.4478
8	1.0919	-0.6368	-0.6322	0.9188	-0.3094	-0.3074	0.5198	0.4405	0.1866	-0.4126	-0.26	0.15	0.6719	-0.3491	-0	0.5931	0.044	0.0304	0.6404	0.0101	0.6063	-4.0209	13.8278	49.5801
9	0.2503	-0.5793	0.3539	-0.4693	-0.9898	0.2265	0.9085	2.3844	1.525	-0.7675	-0.5493	-0.6881	0.2926	0.8427	-0	1.2414	0.0423	0.1359	2.9788	0.5294	1.4428	0.7547	25.2442	23.2342
10	1.1124	-0.1409	1.119	0.858	0.0631	2.9984	-0.0169	0.3419	-0.0699	-0.0336	0.0809	-0.1953	0.2734	-0.0247	-0	0.3896	0.0128	0.0037	0.4529	-0.0967	0.6628	-35.285	10.5233	46.9385
11	1.1492	0.196	-0.2869	0.5437	-0.0238	0.4608	0.4536	0.3488	0.01	-0.4758	-0.1502	0.1038	0.3508	0.3271	-0	0.8076	0.1751	-0.0098	1.1162	-0.2663	0.635	-34.637	14.7568	20.543
12	-0.3242	-0.0691	-0.1891	0.4581	-0.2485	0.2132	-0.4685	-0.4343	0.3481	-1.5493	-0.0253	-0.0645	-0.896	0.1498	-0	1.8359	-0.0119	-0.0075	1.966	0.2487	1.4551	-20.6548	32.9723	2.6564
13	1.8855	0.1778	0.7307	1.0693	-0.5681	1.7902	0.0781	0.2257	-0.1528	-0.1377	-0.0064	0.0698	0.0438	-0.009	0	0.4143	0.0782	0.0107	0.4277	-0.2062	0.4114	-61.7763	30.7106	21.5469
14	1.0811	-1.1772	-0.1884	0.093	1.1062	0.4746	-0.0033	0.4233	0.0825	-0.4221	0.1816	0.1961	-0.2302	0.3478	0	0.763	0.0323	0.0547	0.9143	-0.0756	0.4541	-55.0482	46.0001	0.6615
15	-0.0304	0.6435	0.6459	0.2718	-0.5813	0.1608	-0.7123	0.1684	-0.4187	-0.2912	0.7102	-0.9381	-0.2335	1.2561	0	1.4287	-0.1415	0.2908	1.775	-0.2372	1.8412	-31.0393	59.8885	-8.1714
16	2.4262	0.0012	-0.3969	3.1766	-0.1906	1.1971	-0.0815	0.3759	0.0875	0.2484	0.0454	-0.1132	-0.3081	0.1286	-0	0.4513	0.037	0.0139	0.5821	-0.0653	0.3367	-70.0653	70.9843	12.8756
17	0.9704	-0.6049	-0.5231	0.5292	-0.0191	0.9795	0.4045	-0.082	0.1804	0.3537	-0.3222	-0.0752	0.3566	0.3122	-0	0.6222	0.0028	-0.0509	0.9466	0.253	0.9229	-53.5337	88.6248	1.45
18	0.3499	0.6479	-0.1207	-0.0274	0.9165	0.1851	-0.6059	1.2671	-0.5312	-0.1991	0.6078	-0.2255	-0.066	0.8012	0	1.4278	-0.4252	-0.0242	1.9036	0.0796	1.8493	-24.7802	90.6934	-2.5913
19	2.7751	-0.7552	0.2881	3.0394	0.9825	1.5547	0.0635	-0.0255	0.3786	0.3959	0.031	-0.548	-0.0934	0.2463	0	0.5299	0.029	-0.041	0.4983	0.1312	0.4453	-56.1609	108.1864	26.5377
20	-0.2455	-0.2582	-0.1227	0.2592	0.4404	0.1936	0.0182	-0.1521	0.1949	0.2341	-0.0661	-0.4731	0.5157	0.8946	0	0.7029	-0.1259	-0.0376	1.4728	0.0876	1.2642	-31.704	118.362	22.9346
21	0.4001	0.3136	-0.3433	-0.012	-0.3396	0.0456	-0.0082	-0.0469	-0.5958	-0.2478	0.2781	-0.0929	0.5799	0.0353	0	1.2897	-0.0168	-0.1844	2.2758	-0.2104	1.7665	-5.4585	107.7449	16.1748
22	2.0879	-0.2671	1.5127	0.2339	0.6735	2.4581	-0.0874	0.3263	0.0549	-0.0259	0.3128	-0.1767	-0.1433	0.5179	0	0.8389	-0.0198	-0.1508	0.738	-0.045	0.7706	-27.5755	120.6338	54.3011
23	0.3818	-0.1523	0.0054	-0.0571	0.5794	0.6996	-0.4802	0.6413	0.0451	-0.1827	0.2287	0.1125	-0.0243	0.7347	-0	0.9019	-0.2939	0.0055	1.633	0.0649	1.0057	-1.2362	116.3861	52.5953
24	0.6614	-0.2652	-0.3847	0.1151	-0.1485	0.4067	0.4104	0.4212	-0.2088	0.2908	-0.4872	0.1351	0.352	-0.2149	-0	1.3712	0.2269	-0.0223	2.0091	-0.0482	1.0788	16.0809	98.3249	37.7184

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 11:141 or resid 400:519)	A	11 - 141
2	X-RAY DIFFRACTION	1	chain A and (resid 11:141 or resid 400:519)	A	400 - 519
3	X-RAY DIFFRACTION	2	chain A and (resid 362:399 or resid 142:210)	A	362 - 399
4	X-RAY DIFFRACTION	2	chain A and (resid 362:399 or resid 142:210)	A	142 - 210
5	X-RAY DIFFRACTION	3	chain A and resid 211:361	A	211 - 361
6	X-RAY DIFFRACTION	4	chain B and (resid 11:141 or resid 400:519)	B	11 - 141
7	X-RAY DIFFRACTION	4	chain B and (resid 11:141 or resid 400:519)	B	400 - 519
8	X-RAY DIFFRACTION	5	chain B and (resid 362:399 or resid 142:210)	B	362 - 399
9	X-RAY DIFFRACTION	5	chain B and (resid 362:399 or resid 142:210)	B	142 - 210
10	X-RAY DIFFRACTION	6	chain B and resid 211:361	B	211 - 361
11	X-RAY DIFFRACTION	7	chain C and (resid 11:141 or resid 400:519)	C	11 - 141
12	X-RAY DIFFRACTION	7	chain C and (resid 11:141 or resid 400:519)	C	400 - 519
13	X-RAY DIFFRACTION	8	chain C and (resid 362:399 or resid 142:210)	C	362 - 399
14	X-RAY DIFFRACTION	8	chain C and (resid 362:399 or resid 142:210)	C	142 - 210
15	X-RAY DIFFRACTION	9	chain C and resid 211:361	C	211 - 361
16	X-RAY DIFFRACTION	10	chain D and (resid 11:141 or resid 400:519)	D	11 - 141
17	X-RAY DIFFRACTION	10	chain D and (resid 11:141 or resid 400:519)	D	400 - 519
18	X-RAY DIFFRACTION	11	chain D and (resid 362:399 or resid 142:210)	D	362 - 399
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