PDB-3kfb: Crystal structure of a group II chaperonin from Methanococcus mar...

ID or keywords:

Entry

Database: PDB / ID: 3kfb

Title

Crystal structure 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 / identical protein binding
Similarity search - Function

Biological species

Methanococcus maripaludis (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.2 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3kfb.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb3kfb.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	3kfb.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/kf/3kfb ftp://data.pdbj.org/pub/pdb/validation_reports/kf/3kfb	HTTPS FTP

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Related structure data

Related structure data	3kfeC 3kfkC 1a6d 1q3s C: citing same article (ref.)
Similar structure data	3j3x-d 4v81-1 3rus-1 4v94-1 3ruv-1 0767 4v8r-1 5646 1q3q-1 3917 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
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (6) #108 - Dec 2008 Hsp90 similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#32 - Aug 2002
Chaperones
similarity (6)
#108 - Dec 2008
Hsp90
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#182 - Feb 2015
Insulin receptor
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#238 - Oct 2019
Ribonucleotide Reductase
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)
#50 - Feb 2004
Glycolytic Enzymes
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#80 - Aug 2006
AAA+ Proteases
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: Chaperonin

B: Chaperonin

C: Chaperonin

D: Chaperonin

E: Chaperonin

F: Chaperonin

G: Chaperonin

H: Chaperonin

hetero molecules

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

1

A: Chaperonin

B: Chaperonin

C: Chaperonin

D: Chaperonin

E: Chaperonin

F: Chaperonin

G: Chaperonin

H: Chaperonin

hetero molecules

A: Chaperonin

B: Chaperonin

C: Chaperonin

D: Chaperonin

E: Chaperonin

F: Chaperonin

G: Chaperonin

H: Chaperonin

hetero molecules

defined by author&software
941 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	260.694, 162.220, 184.733
Angle α, β, γ (deg.)	90.00, 135.05, 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:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID
1	1	1	chain 'A' and (resseq 11:519 ) and (not element H) and (not element D)	A
2	1	1	chain 'B' and (resseq 11:519 ) and (not element H) and (not element D)	B
3	1	1	chain 'C' and (resseq 11:519 ) and (not element H) and (not element D)	C
4	1	1	chain 'D' and (resseq 11:519 ) and (not element H) and (not element D)	D
5	1	1	chain 'E' and (resseq 11:519 ) and (not element H) and (not element D)	E
6	1	1	chain 'F' and (resseq 11:519 ) and (not element H) and (not element D)	F
7	1	1	chain 'G' and (resseq 11:519 ) and (not element H) and (not element D)	G
8	1	1	chain 'H' and (resseq 11:519 ) and (not element H) and (not element D)	H

#1: Protein	Chaperonin / / Chaperonin GroEL (Thermosome / HSP60 family) Mass: 58290.262 Da / Num. of mol.: 8 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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Mass: 506.196 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₂P₃ / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.96 Å³/Da / Density % sol: 58.43 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 200 mM sodium fluoride 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: 8.2.2 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2009
Radiation	Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.2→48.84 Å / Num. all: 74731 / Num. obs: 74731 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell	Resolution: 3.2→3.3144 Å / % possible all: 83.52

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.4_162)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.2→48.84 Å / SU ML: 0.31 / σ(F): 0.1 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2395	3760	5.03 %
R_work	0.2097	-	-
obs	0.2112	74731	83.52 %
all	-	74731	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 36.403 Å² / k_sol: 0.307 e/Å³

Refinement step

Cycle: LAST / Resolution: 3.2→48.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	30560	0	256	0	30816

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	31008
X-RAY DIFFRACTION	f_angle_d	1.201	41768
X-RAY DIFFRACTION	f_dihedral_angle_d	17.217	11880
X-RAY DIFFRACTION	f_chiral_restr	0.068	5072
X-RAY DIFFRACTION	f_plane_restr	0.003	5376

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	3820	X-RAY DIFFRACTION	POSITIONAL	0.036
1	2	B	3820	X-RAY DIFFRACTION	POSITIONAL	0.036
1	3	C	3820	X-RAY DIFFRACTION	POSITIONAL	0.041
1	4	D	3820	X-RAY DIFFRACTION	POSITIONAL	0.038
1	5	E	3820	X-RAY DIFFRACTION	POSITIONAL	0.023
1	6	F	3820	X-RAY DIFFRACTION	POSITIONAL	0.037
1	7	G	3820	X-RAY DIFFRACTION	POSITIONAL	0.042
1	8	H	3820	X-RAY DIFFRACTION	POSITIONAL	0.038

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 (%)
3.2-3.3144	0.4397	199	0.3752	3640	X-RAY DIFFRACTION	43
3.3144-3.447	0.3528	287	0.3295	5359	X-RAY DIFFRACTION	63
3.447-3.6039	0.3196	364	0.2977	6547	X-RAY DIFFRACTION	78
3.6039-3.7938	0.2966	407	0.2554	7336	X-RAY DIFFRACTION	87
3.7938-4.0314	0.2722	393	0.221	7449	X-RAY DIFFRACTION	87
4.0314-4.3425	0.2438	394	0.1873	7851	X-RAY DIFFRACTION	92
4.3425-4.7791	0.1972	412	0.1684	8117	X-RAY DIFFRACTION	96
4.7791-5.4699	0.1895	414	0.1533	8143	X-RAY DIFFRACTION	95
5.4699-6.8884	0.2243	411	0.1816	8058	X-RAY DIFFRACTION	94
6.8884-48.8472	0.167	479	0.1663	8471	X-RAY DIFFRACTION	98

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	1.3076	-0.7137	0.333	1.7772	0.1945	0.8023	-0.0455	-0.3003	0.213	0.0573	0.0994	-0.1674	0.0658	0.1372	-0.0575	0.1523	-0.0927	0.0035	0.1332	-0.0414	0.0569	25.3055	-101.347	84.7181
2	0.0617	0.2002	0.2899	2.7342	0.5626	0.9163	-0.1034	0.3195	0.2439	-0.185	-0.0061	0.3552	0.0802	-0.393	0.0098	0.0528	-0.0212	0.0001	0.2176	0.1634	0.1314	5.0026	-85.7972	76.9588
3	0.067	0.2501	-0.4708	0.6902	-0.7273	1.3468	0.1074	0.0751	0.0279	0.0743	-0.2372	0.0602	-0.056	0.1902	0.0454	0.2051	-0.0279	-0.2122	0.4143	0.1622	0.23	-1.6159	-70.6337	48.1109
4	0.9835	-0.0767	0.5151	2.0468	-0.339	1.015	-0.0744	-0.1402	0.2341	0.2349	0.1364	-0.2538	-0.0117	-0.2327	-0.0485	0.2199	-0.0558	0.027	0.2385	-0.0447	0.246	16.3689	-61.3859	93.3823
5	0.503	0.8017	0.1413	1.7549	-0.201	0.8029	-0.0883	-0.075	0.246	0.0282	-0.2613	0.7351	0.1408	-0.4871	0.0869	0.0359	0.199	-0.0783	-0.0008	0.1389	0.0604	5.5834	-44.1553	76.0353
6	0.5798	-0.2605	-1.3286	0.7726	1.4054	3.5376	0.2806	0.1405	0.1389	-0.1409	0.0485	-0.1207	-0.0935	0.0135	-0.1356	0.396	-0.0467	-0.2754	0.3067	0.1082	0.2891	3.3959	-44.4894	42.8569
7	0.6782	0.7969	-0.2504	1.0094	-0.7436	1.9517	0.0508	-0.0435	-0.1459	0.1128	-0.2273	-0.1874	-0.1457	-0.0014	0.1196	-0.0115	0.0058	0.0378	0.0954	-0.084	0.1738	29.9337	-24.0819	79.6462
8	1.458	0.469	0.686	1.0664	0.4451	1.9947	0.4179	0.4478	0.0152	-0.328	-0.1339	0.0939	-0.264	0.5434	-0.1756	0.3122	0.1623	-0.0577	0.1118	0.0045	0.0776	26.8888	-15.0593	54.6755
9	0.7246	0.6641	0.2267	1.5324	0.7739	0.2117	0.1345	-0.1358	0.0007	-0.1169	0.1144	-0.2087	-0.3199	0.0937	-0.1137	0.3879	-0.1033	-0.1957	0.5317	0.0208	0.0803	20.1349	-30.6731	26.0996
10	1.5932	-0.4206	-0.4055	0.2414	0.4921	1.8352	0.0098	-0.089	0.1411	-0.2163	-0.0667	0.1413	-0.331	0.2265	0.0166	0.3324	-0.0429	0.133	0.244	0.0192	0.5047	58.2624	-11.2402	51.5436
11	0.9017	-0.233	-0.2917	0.9213	0.2555	0.6873	0.0097	0.2423	-0.0114	-0.199	0.2704	0.1354	-0.2043	-0.2055	-0.0515	0.5949	-0.1781	0.032	0.4347	-0.036	0.3954	56.5577	-16.087	25.321
12	0.2111	0.4376	0.0406	3.3985	1.1514	0.2008	-0.051	-0.2594	0.1578	-0.4607	0.1801	-0.2255	-0.1707	-0.3414	-0.0948	0.5535	-0.2043	-0.0986	0.6028	0.0308	0.1958	38.7201	-38.1286	7.9259
13	0.7233	-0.3354	0.3183	1.5443	0.8856	1.4437	-0.0155	-0.0904	0.0294	0.1191	0.0712	0.0711	0.1992	0.1874	-0.012	0.102	0.0189	0.0297	0.13	0.0784	0.1643	84.5433	-31.0989	25.5851
14	1.0421	0.2123	0.3585	0.4844	-0.1828	0.8186	-0.1102	0.282	-0.0312	-0.1926	0.2638	0.0683	0.2393	-0.4179	-0.0657	0.1552	-0.155	0.0071	0.1789	0.0614	0.0652	76.8603	-46.6503	5.2533
15	0.7399	0.5993	-0.4856	0.9693	-0.4308	0.2118	0.1186	-0.2834	-0.0945	0.087	-0.203	-0.146	-0.0543	-0.012	0.0583	0.2659	-0.1197	-0.1883	0.3853	0.0102	0.1958	48.0447	-61.831	-1.4626
16	1.0828	0.4764	0.0927	1.8813	0.0459	1.4084	-0.0786	0.2741	0.0453	0.2599	0.1284	-0.1307	0.3178	0.1296	0.0195	0.2173	0.0616	0.0151	0.2263	0.0733	0.2108	93.2171	-71.0658	16.6958
17	0.7964	-0.1225	0.5883	2.0386	-0.9506	0.8895	0.1745	0.1725	0.0024	-0.7121	-0.0677	0.0764	0.1836	0.2486	-0.1517	0.1913	-0.0826	-0.0505	0.1064	-0.1412	0.0866	75.9076	-88.2965	5.8476
18	2.6283	-0.9687	-0.4524	0.7327	0.0381	0.0793	-0.2464	0.0815	-0.1363	0.1021	0.0848	0.0867	0.1641	-0.0846	0.1448	0.2692	-0.075	-0.2387	0.3404	0.033	0.4247	42.7351	-87.9701	3.5647
19	2.1416	0.6939	-0.0212	1.2614	-0.9269	0.7191	0.1079	-0.0802	-0.1134	0.1578	-0.1625	-0.0383	-0.1161	-0.0762	0.0671	0.2421	0.0644	0.0717	0.1576	-0.0101	0.0661	79.4362	-108.3681	30.2224
20	1.8203	-0.8821	1.3479	1.0616	-0.4897	0.9897	-0.0027	-0.5673	-0.5161	-0.29	-0.0583	0.3508	0.1253	-0.4436	0.0904	0.1009	-0.0177	-0.0191	0.0073	-0.1715	0.2131	54.4767	-117.39	27.0994
21	0.3621	-0.8883	0.1565	1.603	-0.5703	0.5738	-0.2194	-0.0126	-0.2552	0.1188	0.109	0.2382	0.0618	0.2511	-0.0183	0.1123	-0.0654	-0.2147	0.4902	0.1462	0.3293	25.9225	-101.7739	20.2555
22	1.8503	-0.4198	-0.0182	0.5755	0.6227	1.5693	0.1131	-0.1039	-0.2086	0.0124	-0.0033	0.2999	0.1244	0.1216	-0.1185	0.529	-0.0049	0.1692	0.2366	0.0362	0.2725	51.297	-121.2115	58.5123
23	0.8027	-0.7244	0.0237	1.5236	0.2471	1.2094	-0.4076	0.1977	-0.0323	-0.0077	0.1616	0.3265	-0.0305	-0.0477	0.0273	0.4025	0.0056	0.1127	0.4248	0.1816	0.5194	25.0815	-116.3557	56.7259
24	0.111	-1.0183	0.0572	3.6627	-0.8723	0.4681	-0.0791	0.2861	-0.1791	0.2244	0.007	0.2313	0.0487	0.4467	0.1098	0.232	-0.0027	-0.0703	0.6117	0.2143	0.5133	7.7462	-94.3211	38.8232

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 7:141 or resid 400:519)	A	7 - 141
2	X-RAY DIFFRACTION	1	chain A and (resid 7:141 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 7:141 or resid 400:519)	B	7 - 141
7	X-RAY DIFFRACTION	4	chain B and (resid 7:141 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 7:141 or resid 400:519)	C	7 - 141
12	X-RAY DIFFRACTION	7	chain C and (resid 7:141 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 7:141 or resid 400:519)	D	7 - 141
17	X-RAY DIFFRACTION	10	chain D and (resid 7:141 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
19	X-RAY DIFFRACTION	11	chain D and (resid 362:399 or resid 142:210)	D	142 - 210
20	X-RAY DIFFRACTION	12	chain D and resid 211:361	D	211 - 361
21	X-RAY DIFFRACTION	13	chain E and (resid 7:141 or resid 400:519)	E	7 - 141
22	X-RAY DIFFRACTION	13	chain E and (resid 7:141 or resid 400:519)	E	400 - 519
23	X-RAY DIFFRACTION	14	chain E and (resid 362:399 or resid 142:210)	E	362 - 399
24	X-RAY DIFFRACTION	14	chain E and (resid 362:399 or resid 142:210)	E	142 - 210
25	X-RAY DIFFRACTION	15	chain E and resid 211:361	E	211 - 361
26	X-RAY DIFFRACTION	16	chain F and (resid 7:141 or resid 400:519)	F	7 - 141
27	X-RAY DIFFRACTION	16	chain F and (resid 7:141 or resid 400:519)	F	400 - 519
28	X-RAY DIFFRACTION	17	chain F and (resid 362:399 or resid 142:210)	F	362 - 399
29	X-RAY DIFFRACTION	17	chain F and (resid 362:399 or resid 142:210)	F	142 - 210
30	X-RAY DIFFRACTION	18	chain F and resid 211:361	F	211 - 361
31	X-RAY DIFFRACTION	19	chain G and (resid 7:141 or resid 400:519)	G	7 - 141
32	X-RAY DIFFRACTION	19	chain G and (resid 7:141 or resid 400:519)	G	400 - 519
33	X-RAY DIFFRACTION	20	chain G and (resid 362:399 or resid 142:210)	G	362 - 399
34	X-RAY DIFFRACTION	20	chain G and (resid 362:399 or resid 142:210)	G	142 - 210
35	X-RAY DIFFRACTION	21	chain G and resid 211:361	G	211 - 361
36	X-RAY DIFFRACTION	22	chain H and (resid 7:141 or resid 400:519)	H	7 - 141
37	X-RAY DIFFRACTION	22	chain H and (resid 7:141 or resid 400:519)	H	400 - 519
38	X-RAY DIFFRACTION	23	chain H and (resid 362:399 or resid 142:210)	H	362 - 399
39	X-RAY DIFFRACTION	23	chain H and (resid 362:399 or resid 142:210)	H	142 - 210
40	X-RAY DIFFRACTION	24	chain H and resid 211:361	H	211 - 361

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