PDB-2nwc: A 3.02 angstrom crystal structure of wild-type apo GroEL in a mon...

ID or keywords:

Entry

Database: PDB / ID: 2nwc

Title

A 3.02 angstrom crystal structure of wild-type apo GroEL in a monoclinic space group

Components

60 kDa chaperonin

Keywords

CHAPERONE / chaperonin / HSP60

Function / homology

Function and homology information

GroEL-GroES complex / chaperonin ATPase / virion assembly / : / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.02 Å

Authors

Kiser, P.D. / Lodowski, D.T. / Palczewski, K.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Purification, crystallization and structure determination of native GroEL from Escherichia coli lacking bound potassium ions
Authors: Kiser, P.D. / Lodowski, D.T. / Palczewski, K.

History

Deposition	Nov 14, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 22, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Aug 30, 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 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.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2nwc.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb2nwc.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	2nwc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2nwc_validation.pdf.gz	500.5 KB	Display	wwPDB validaton report
Full document	2nwc_full_validation.pdf.gz	569.5 KB	Display
Data in XML	2nwc_validation.xml.gz	130.3 KB	Display
Data in CIF	2nwc_validation.cif.gz	198.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nw/2nwc ftp://data.pdbj.org/pub/pdb/validation_reports/nw/2nwc	HTTPS FTP

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Related structure data

Related structure data	1kp8S S: Starting model for refinement
Similar structure data	4hel-d 1xck-d 1ss8-1 1oel-1 2ynj-d 6kfv-d 4wsc-d 5w0s-d 5opw-d 4v43-2 4wgl-d 1sx3-d 1kp8-d 2yey-d 4v43-1 3e76-d 3407 3c9v-d 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 (11)

Deposited unit

A: 60 kDa chaperonin

B: 60 kDa chaperonin

C: 60 kDa chaperonin

D: 60 kDa chaperonin

E: 60 kDa chaperonin

F: 60 kDa chaperonin

G: 60 kDa chaperonin

H: 60 kDa chaperonin

I: 60 kDa chaperonin

J: 60 kDa chaperonin

K: 60 kDa chaperonin

L: 60 kDa chaperonin

M: 60 kDa chaperonin

N: 60 kDa chaperonin

802 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	136.423, 262.254, 147.074
Angle α, β, γ (deg.)	90.00, 99.83, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-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	1	ALA	ALA	VAL	VAL	1	D	D	2 - 39	1 - 38
2	1	1	ALA	ALA	VAL	VAL	1	A	A	2 - 39	1 - 38
3	1	1	ALA	ALA	VAL	VAL	1	B	B	2 - 39	1 - 38
4	1	1	ALA	ALA	VAL	VAL	1	C	C	2 - 39	1 - 38
5	1	1	ALA	ALA	VAL	VAL	1	E	E	2 - 39	1 - 38
6	1	1	ALA	ALA	VAL	VAL	1	F	F	2 - 39	1 - 38
7	1	1	ALA	ALA	VAL	VAL	1	G	G	2 - 39	1 - 38
8	2	1	LEU	LEU	ALA	ALA	6	D	D	40 - 46	39 - 45
9	2	1	LEU	LEU	ALA	ALA	6	A	A	40 - 46	39 - 45
10	2	1	LEU	LEU	ALA	ALA	6	B	B	40 - 46	39 - 45
11	2	1	LEU	LEU	ALA	ALA	6	C	C	40 - 46	39 - 45
12	2	1	LEU	LEU	ALA	ALA	6	E	E	40 - 46	39 - 45
13	2	1	LEU	LEU	ALA	ALA	6	F	F	40 - 46	39 - 45
14	2	1	LEU	LEU	ALA	ALA	6	G	G	40 - 46	39 - 45
15	3	1	PRO	PRO	PHE	PHE	1	D	D	47 - 195	46 - 194
16	3	1	PRO	PRO	PHE	PHE	1	A	A	47 - 195	46 - 194
17	3	1	PRO	PRO	PHE	PHE	1	B	B	47 - 195	46 - 194
18	3	1	PRO	PRO	PHE	PHE	1	C	C	47 - 195	46 - 194
19	3	1	PRO	PRO	PHE	PHE	1	E	E	47 - 195	46 - 194
20	3	1	PRO	PRO	PHE	PHE	1	F	F	47 - 195	46 - 194
21	3	1	PRO	PRO	PHE	PHE	1	G	G	47 - 195	46 - 194
22	4	1	ASP	ASP	ASP	ASP	6	D	D	196 - 224	195 - 223
23	4	1	ASP	ASP	ASP	ASP	6	A	A	196 - 224	195 - 223
24	4	1	ASP	ASP	ASP	ASP	6	B	B	196 - 224	195 - 223
25	4	1	ASP	ASP	ASP	ASP	6	C	C	196 - 224	195 - 223
26	4	1	ASP	ASP	ASP	ASP	6	E	E	196 - 224	195 - 223
27	4	1	ASP	ASP	ASP	ASP	6	F	F	196 - 224	195 - 223
28	4	1	ASP	ASP	ASP	ASP	6	G	G	196 - 224	195 - 223
29	5	1	LYS	LYS	ASP	ASP	6	D	D	225 - 473	224 - 472
30	5	1	LYS	LYS	ASP	ASP	6	A	A	225 - 473	224 - 472
31	5	1	LYS	LYS	ASP	ASP	6	B	B	225 - 473	224 - 472
32	5	1	LYS	LYS	ASP	ASP	6	C	C	225 - 473	224 - 472
33	5	1	LYS	LYS	ASP	ASP	6	E	E	225 - 473	224 - 472
34	5	1	LYS	LYS	ASP	ASP	6	F	F	225 - 473	224 - 472
35	5	1	LYS	LYS	ASP	ASP	6	G	G	225 - 473	224 - 472
36	6	1	ILE	ILE	PRO	PRO	1	D	D	489 - 525	488 - 524
37	6	1	ILE	ILE	PRO	PRO	1	A	A	489 - 525	488 - 524
38	6	1	ILE	ILE	PRO	PRO	1	B	B	489 - 525	488 - 524
39	6	1	ILE	ILE	PRO	PRO	1	C	C	489 - 525	488 - 524
40	6	1	ILE	ILE	PRO	PRO	1	E	E	489 - 525	488 - 524
41	6	1	ILE	ILE	PRO	PRO	1	F	F	489 - 525	488 - 524
42	6	1	ILE	ILE	PRO	PRO	1	G	G	489 - 525	488 - 524
1	1	2	ALA	ALA	VAL	VAL	1	H	H	2 - 39	1 - 38
2	1	2	ALA	ALA	VAL	VAL	1	N	N	2 - 39	1 - 38
3	1	2	ALA	ALA	VAL	VAL	1	I	I	2 - 39	1 - 38
4	1	2	ALA	ALA	VAL	VAL	1	J	J	2 - 39	1 - 38
5	1	2	ALA	ALA	VAL	VAL	1	L	L	2 - 39	1 - 38
6	1	2	ALA	ALA	VAL	VAL	1	M	M	2 - 39	1 - 38
7	1	2	ALA	ALA	VAL	VAL	1	K	K	2 - 39	1 - 38
8	2	2	LEU	LEU	ALA	ALA	6	H	H	40 - 46	39 - 45
9	2	2	LEU	LEU	ALA	ALA	6	N	N	40 - 46	39 - 45
10	2	2	LEU	LEU	ALA	ALA	6	I	I	40 - 46	39 - 45
11	2	2	LEU	LEU	ALA	ALA	6	J	J	40 - 46	39 - 45
12	2	2	LEU	LEU	ALA	ALA	6	L	L	40 - 46	39 - 45
13	2	2	LEU	LEU	ALA	ALA	6	M	M	40 - 46	39 - 45
14	2	2	LEU	LEU	ALA	ALA	6	K	K	40 - 46	39 - 45
15	3	2	PRO	PRO	PHE	PHE	1	H	H	47 - 195	46 - 194
16	3	2	PRO	PRO	PHE	PHE	1	N	N	47 - 195	46 - 194
17	3	2	PRO	PRO	PHE	PHE	1	I	I	47 - 195	46 - 194
18	3	2	PRO	PRO	PHE	PHE	1	J	J	47 - 195	46 - 194
19	3	2	PRO	PRO	PHE	PHE	1	L	L	47 - 195	46 - 194
20	3	2	PRO	PRO	PHE	PHE	1	M	M	47 - 195	46 - 194
21	3	2	PRO	PRO	PHE	PHE	1	K	K	47 - 195	46 - 194
22	4	2	ASP	ASP	ASP	ASP	6	H	H	196 - 224	195 - 223
23	4	2	ASP	ASP	ASP	ASP	6	N	N	196 - 224	195 - 223
24	4	2	ASP	ASP	ASP	ASP	6	I	I	196 - 224	195 - 223
25	4	2	ASP	ASP	ASP	ASP	6	J	J	196 - 224	195 - 223
26	4	2	ASP	ASP	ASP	ASP	6	L	L	196 - 224	195 - 223
27	4	2	ASP	ASP	ASP	ASP	6	M	M	196 - 224	195 - 223
28	4	2	ASP	ASP	ASP	ASP	6	K	K	196 - 224	195 - 223
29	5	2	LYS	LYS	ASP	ASP	6	H	H	225 - 473	224 - 472
30	5	2	LYS	LYS	ASP	ASP	6	N	N	225 - 473	224 - 472
31	5	2	LYS	LYS	ASP	ASP	6	I	I	225 - 473	224 - 472
32	5	2	LYS	LYS	ASP	ASP	6	J	J	225 - 473	224 - 472
33	5	2	LYS	LYS	ASP	ASP	6	L	L	225 - 473	224 - 472
34	5	2	LYS	LYS	ASP	ASP	6	M	M	225 - 473	224 - 472
35	5	2	LYS	LYS	ASP	ASP	6	K	K	225 - 473	224 - 472
36	6	2	ILE	ILE	PRO	PRO	1	H	H	489 - 525	488 - 524
37	6	2	ILE	ILE	PRO	PRO	1	N	N	489 - 525	488 - 524
38	6	2	ILE	ILE	PRO	PRO	1	I	I	489 - 525	488 - 524
39	6	2	ILE	ILE	PRO	PRO	1	J	J	489 - 525	488 - 524
40	6	2	ILE	ILE	PRO	PRO	1	L	L	489 - 525	488 - 524
41	6	2	ILE	ILE	PRO	PRO	1	M	M	489 - 525	488 - 524
42	6	2	ILE	ILE	PRO	PRO	1	K	K	489 - 525	488 - 524

NCS ensembles :

ID
1
2

Details

Biological assembly is identical to that of deposited coordinates.

#1: Protein	60 kDa chaperonin / Protein Cpn60 / groEL protein Mass: 57260.504 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: groL, groEL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta 2(DE3)pLysS References: UniProt: Q1R3B6, UniProt: P0A6F5*PLUS, EC: 3.6.4.9

#1: Protein

60 kDa chaperonin / Protein Cpn60 / groEL protein

Mass: 57260.504 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Gene: groL, groEL / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta 2(DE3)pLysS
References: UniProt: Q1R3B6, UniProt: P0A6F5*PLUS, EC: 3.6.4.9

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.23 Å³/Da / Density % sol: 61.95 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion / pH: 8 Details: 0.1 M imidazole, 35% MPD, 0.2 M MgCl2, pH 8.0, VAPOR DIFFUSION, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 3.02→50 Å / Num. all: 202060 / Num. obs: 202060 / % possible obs: 99.7 % / Redundancy: 3.8 % / R_sym value: 0.087 / Net I/σ(I): 9.8
Reflection shell	Resolution: 3.02→3.13 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.02 / Num. unique all: 20078 / R_sym value: 0.757 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1kp8

1kp8

Resolution: 3.02→30 Å / Cor.coef. F_o:F_c: 0.93 / Cor.coef. F_o:F_c free: 0.904 / SU B: 44.905 / SU ML: 0.358 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.433 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26269	10042	5.1 %	RANDOM
R_work	0.2266	-	-	-
obs	0.22841	188012	99.72 %	-
all	-	198054	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 70.399 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.46 Å²	0 Å²	2.6 Å²
2-	-	-3.3 Å²	0 Å²
3-	-	-	5.65 Å²

Refinement step

Cycle: LAST / Resolution: 3.02→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	53970	0	0	0	53970

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	54362
X-RAY DIFFRACTION	r_angle_refined_deg	0.971	1.988	73402
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.479	5	7322
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.52	26.067	2100
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.461	15	10080
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.941	15	308
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	8932
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	39494
X-RAY DIFFRACTION	r_nbd_refined	0.184	0.2	25139
X-RAY DIFFRACTION	r_nbtor_refined	0.288	0.2	38349
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.111	0.2	1284
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.213	0.2	24
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.195	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	0.194	1.5	37177
X-RAY DIFFRACTION	r_mcangle_it	0.326	2	57876
X-RAY DIFFRACTION	r_scbond_it	0.411	3	18651
X-RAY DIFFRACTION	r_scangle_it	0.733	4.5	15526

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	D	1619	tight positional	0.01	0.05
1	2	A	1619	tight positional	0.02	0.05
1	3	B	1619	tight positional	0.01	0.05
1	4	C	1619	tight positional	0.01	0.05
1	5	E	1619	tight positional	0.01	0.05
1	6	F	1619	tight positional	0.01	0.05
1	7	G	1619	tight positional	0.03	0.05
2	1	H	1619	tight positional	0.01	0.05
2	2	N	1619	tight positional	0.01	0.05
2	3	I	1619	tight positional	0.01	0.05
2	4	J	1619	tight positional	0.01	0.05
2	5	L	1619	tight positional	0.01	0.05
2	6	M	1619	tight positional	0.01	0.05
2	7	K	1619	tight positional	0.01	0.05
1	1	D	2121	loose positional	0.47	5
1	2	A	2121	loose positional	1.37	5
1	3	B	2121	loose positional	1.26	5
1	4	C	2121	loose positional	0.76	5
1	5	E	2121	loose positional	0.78	5
1	6	F	2121	loose positional	0.54	5
1	7	G	2121	loose positional	0.54	5
2	1	H	2121	loose positional	0.62	5
2	2	N	2121	loose positional	0.47	5
2	3	I	2121	loose positional	0.64	5
2	4	J	2121	loose positional	0.6	5
2	5	L	2121	loose positional	0.91	5
2	6	M	2121	loose positional	0.81	5
2	7	K	2121	loose positional	0.64	5
1	1	D	1619	tight thermal	0.02	0.5
1	2	A	1619	tight thermal	0.02	0.5
1	3	B	1619	tight thermal	0.02	0.5
1	4	C	1619	tight thermal	0.02	0.5
1	5	E	1619	tight thermal	0.02	0.5
1	6	F	1619	tight thermal	0.02	0.5
1	7	G	1619	tight thermal	0.02	0.5
2	1	H	1619	tight thermal	0.02	0.5
2	2	N	1619	tight thermal	0.02	0.5
2	3	I	1619	tight thermal	0.02	0.5
2	4	J	1619	tight thermal	0.02	0.5
2	5	L	1619	tight thermal	0.02	0.5
2	6	M	1619	tight thermal	0.02	0.5
2	7	K	1619	tight thermal	0.02	0.5
1	1	D	2121	loose thermal	0.82	10
1	2	A	2121	loose thermal	0.7	10
1	3	B	2121	loose thermal	0.67	10
1	4	C	2121	loose thermal	0.65	10
1	5	E	2121	loose thermal	0.61	10
1	6	F	2121	loose thermal	0.71	10
1	7	G	2121	loose thermal	0.73	10
2	1	H	2121	loose thermal	0.61	10
2	2	N	2121	loose thermal	0.84	10
2	3	I	2121	loose thermal	0.64	10
2	4	J	2121	loose thermal	0.66	10
2	5	L	2121	loose thermal	0.64	10
2	6	M	2121	loose thermal	0.59	10
2	7	K	2121	loose thermal	0.65	10

LS refinement shell

Resolution: 3.02→3.098 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.369	758	-
R_work	0.348	13658	-
obs	-	-	98.92 %

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