PDB-4fcw: Crystal structure of the C-terminal domain of ClpB

ID or keywords:

Entry

Database: PDB / ID: 4fcw

Title

Crystal structure of the C-terminal domain of ClpB

Components

Chaperone protein ClpB

Keywords

CHAPERONE / AAA domain

Function / homology

Function and homology information

response to heat / protein refolding /

ATP hydrolysis activity /

ATP binding / identical protein binding /

cytoplasm
Similarity search - Function

Biological species

Thermus thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Biter, A.B. / Lee, S. / Sung, N. / Tsai, F.T.F.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis for intersubunit signaling in a protein disaggregating machine.
Authors: Biter, A.B. / Lee, S. / Sung, N. / Tsai, F.T.

History

Deposition	May 25, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 18, 2012	Provider: repository / Type: Initial release
Revision 1.1	Aug 22, 2012	Group: Database references
Revision 1.2	Apr 18, 2018	Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4fcw.cif.gz	361.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4fcw.ent.gz	308.7 KB	Display	PDB format
PDBx/mmJSON format	4fcw.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/fc/4fcw ftp://data.pdbj.org/pub/pdb/validation_reports/fc/4fcw	HTTPS FTP

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Related structure data

Related structure data	4fctC 4fcvC 4fd2C C: citing same article (ref.)
Similar structure data	4fcv-2 6pfv-1 4fcv-1 1mhp-2 3p5n-d 1mfp-d 3pjd-d 2w45-1 4jqc-d 2p68-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

4fctC

4fcvC

4fd2C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (4) #176 - Aug 2014 Dynein similarity (4) #150 - Jun 2012 Sliding Clamps similarity (1)

Deposited unit

A: Chaperone protein ClpB

C: Chaperone protein ClpB

F: Chaperone protein ClpB

hetero molecules

108 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Chaperone protein ClpB

hetero molecules

defined by author&software
36 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Chaperone protein ClpB

hetero molecules

defined by author&software
36 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

F: Chaperone protein ClpB

hetero molecules

defined by author&software
36 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	129.238, 129.238, 122.972
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	170
Space group name H-M	P6₅

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	C
3	1	F
1	2	A
2	2	C
3	2	F
1	3	A
2	3	C
3	3	F

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	6	A	545 - 635
2	1	1	6	C	545 - 635
3	1	1	6	F	545 - 635
1	1	2	6	A	651 - 756
2	1	2	6	C	651 - 756
3	1	2	6	F	651 - 756
1	1	3	6	A	757 - 852
2	1	3	6	C	757 - 852
3	1	3	6	F	757 - 852

NCS ensembles :

ID
1
2
3

#1: Protein	Chaperone protein ClpB / Mass: 35615.008 Da / Num. of mol.: 3 / Fragment: UNP resisdues 544-852 / Mutation: E668A, I683M, L706M, L770M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: clpB, TTHA1487 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL CodonPlus / References: UniProt: Q9RA63
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.77 Å³/Da / Density % sol: 55.67 %
Crystal grow	Temperature: 294 K / Method: hanging drop / pH: 5.5 Details: sodium citrate, isopropanol, pH 5.5, hanging drop, temperature 294K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X25

Detector

Type: ADSC QUANTUM 315 / Detector: CCD

Radiation

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

Radiation wavelength

Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.334
1	1	-H-K, K, -L	2	0.666

Reflection

Resolution: 2.35→50 Å / Num. obs: 48173

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Processing

Software

Name	Version	Classification	NB
REFMAC	5.5.0109	refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.35→44.55 Å / Cor.coef. F_o:F_c: 0.927 / Cor.coef. F_o:F_c free: 0.906 / Occupancy max: 1 / Occupancy min: 1 / SU B: 31.557 / SU ML: 0.287 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2915	2120	4.4 %	RANDOM
R_work	0.2524	-	-	-
obs	0.2541	48173	99.42 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 95.85 Å² / B_iso mean: 19.8005 Å² / B_iso min: 2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.15 Å²	0 Å²	0 Å²
2-	-	6.15 Å²	0 Å²
3-	-	-	-12.3 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→44.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7368	0	81	23	7472

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	7575
X-RAY DIFFRACTION	r_angle_refined_deg	1.283	2.002	10235
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.112	5	918
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.427	22.652	362
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.305	15	1386
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.008	15	96
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	1153
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	5674
X-RAY DIFFRACTION	r_mcbond_it	2.238	1.5	4593
X-RAY DIFFRACTION	r_mcangle_it	3.509	2	7415
X-RAY DIFFRACTION	r_scbond_it	5.427	3	2982
X-RAY DIFFRACTION	r_scangle_it	7.991	4.5	2820
X-RAY DIFFRACTION	r_rigid_bond_restr	3.863	3	7575

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	A	718	LOOSE POSITIONAL	0.57	5
1	2	C	718	LOOSE POSITIONAL	0.51	5
1	3	F	718	LOOSE POSITIONAL	0.48	5
1	1	A	718	LOOSE THERMAL	2.69	10
1	2	C	718	LOOSE THERMAL	2.59	10
1	3	F	718	LOOSE THERMAL	2.1	10
2	1	A	880	LOOSE POSITIONAL	0.9	5
2	2	C	880	LOOSE POSITIONAL	0.93	5
2	3	F	880	LOOSE POSITIONAL	1.09	5
2	1	A	880	LOOSE THERMAL	2.67	10
2	2	C	880	LOOSE THERMAL	2.37	10
2	3	F	880	LOOSE THERMAL	1.68	10
3	1	A	760	LOOSE POSITIONAL	0.6	5
3	2	C	760	LOOSE POSITIONAL	0.46	5
3	3	F	760	LOOSE POSITIONAL	0.73	5
3	1	A	760	LOOSE THERMAL	2.21	10
3	2	C	760	LOOSE THERMAL	2.64	10
3	3	F	760	LOOSE THERMAL	2.54	10

LS refinement shell

Resolution: 2.35→2.412 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.345	161	-
R_work	0.258	3278	-
all	-	3439	-
obs	-	-	96.55 %

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	14.0083	-13.8762	-8.7246	12.1931	3.189	45.5927	-0.2858	-0.6223	0.8438	0.3864	0.3671	-0.8816	0.0182	0.8175	-0.0814	0.3864	0.0249	0.1311	0.1259	0.0566	0.7842	-27.3383	2.2434	50.5156
2	3.9122	1.0491	-0.2063	2.0185	0.1951	2.2221	-0.0761	0.1099	-0.0793	-0.2321	-0.064	-0.1384	0.2288	0.0698	0.1401	0.387	-0.0014	0.0726	0.2747	0.0336	0.546	-40.0215	9.4011	44.6993
3	3.0119	-0.3037	0.1557	3.6147	0.315	4.7777	0.1095	-0.1626	0.5538	0.0791	-0.1481	0.2458	-0.5248	-0.3265	0.0387	0.3529	-0.0294	0.0603	0.2633	-0.021	0.5951	-46.5948	26.178	52.7896
4	-0.2362	-0.1598	-0.0243	-0.6676	0.134	-0.2072	-0.0243	0.0152	-0.216	-0.0417	0.1	-0.01	-0.0397	0.1376	-0.0757	0.9525	-0.0404	0.0413	0.8964	-0.1066	1.0982	-50.068	13.1869	25.6041
5	3.2434	1.8231	-1.3278	6.8879	-1.5932	1.9419	-0.1012	0.3556	0.0444	-0.9815	0.0128	0.087	0.0572	-0.0903	0.0885	0.4234	-0.014	-0.0124	0.3369	0.0011	0.4224	-49.3459	11.9783	38.2361
6	3.6232	0.9067	-0.5153	5.0103	-1.1612	4.8508	-0.2044	-0.0024	0.0005	-0.0029	-0.0544	0.2445	0.1667	-0.0338	0.2587	0.19	-0.0286	0.0756	0.3077	-0.1323	0.6123	-63.366	-8.547	52.6216
7	13.0869	-8.0986	4.7556	7.6687	-1.443	12.9455	0.3616	-0.8969	-0.8847	-0.8831	0.2807	1.4142	1.5088	-0.099	-0.6424	0.5842	-0.1727	-0.0363	0.5693	-0.2124	0.7657	-68.5956	-19.6845	50.3952
8	17.028	-9.439	10.5602	1.518	-1.1022	-3.2968	-1.6692	-0.0614	1.6089	1.7679	0.6352	0.2694	-0.732	0.3517	1.034	1.9417	0.5139	0.6019	1.5656	0.4371	1.5256	-15.4453	54.2808	31.5274
9	1.4955	-0.4399	-0.5362	2.5799	0.2494	2.6575	-0.0541	-0.1076	0.0074	0.0087	-0.057	-0.0199	0.1008	0.2226	0.1111	0.49	0.1088	0.0181	0.3885	0.086	0.6395	-33.0763	44.0942	26.4902
10	27.9376	9.5353	-25.5379	0.6471	-6.9607	17.9435	-0.0573	1.8269	0.3256	-0.0102	0.4506	-0.0441	0.3174	-1.3599	-0.3934	0.8232	0.0891	0.2259	1.0014	0.0427	0.7547	-57.3581	46.7962	44.2808
11	3.3134	-1.0974	-0.8284	3.8904	-0.0228	2.894	-0.1231	-0.1077	0.0341	0.0576	0.0533	0.3808	0.137	-0.0942	0.0698	0.4113	0.1169	0.0443	0.3327	0.111	0.628	-43.6899	48.5687	29.941
12	2.1781	0.7422	-2.1533	0.2073	-0.4644	0.521	0.465	-0.1428	0.2338	-0.0476	-0.1949	-0.2886	-0.3241	0.1553	-0.2701	0.9392	0.0014	0.1265	0.7875	0.0896	0.9775	-35.1834	38.5484	4.7179
13	1.4527	-1.4093	0.2756	4.1002	-1.6822	1.0376	0.1385	0.1751	-0.1516	-0.4239	-0.3036	-0.0315	0.1597	0.1142	0.1651	0.4069	0.0892	0.0924	0.2729	0.0466	0.536	-28.6163	23.9494	26.2977
14	23.4943	-1.4925	1.0335	6.9641	1.1498	9.6782	0.8889	0.3673	-0.8438	0.3021	-0.2211	-0.4168	0.217	1.2731	-0.6678	0.5861	0.2142	0.2354	0.2507	0.0922	0.6864	-17.5091	6.0917	28.8951
15	1.6832	0.597	0.1318	1.0714	-0.2044	1.8472	-0.0736	-0.0448	-0.0317	-0.0939	0.034	0.0706	-0.0107	0.1649	0.0397	0.3882	0.0403	0.045	0.4496	0.033	0.6224	9.7498	-31.9752	34.3414
16	-1.5554	3.0025	-3.4522	-5.5287	-1.9199	5.1295	0.5637	-0.7213	-0.0216	0.1174	-0.1204	-0.0114	-1.306	1.5169	-0.4434	1.4257	-0.1467	-0.1828	0.926	-0.1399	0.9545	-3.0779	-12.4905	15.8465
17	4.392	0.5572	0.1279	2.3326	-0.4717	2.2839	-0.0163	0.1303	0.2988	0.1145	0.0843	0.2239	-0.0852	-0.0412	-0.068	0.2944	0.0475	0.0297	0.3458	0.0549	0.5916	0.7101	-24.21	31.2112
18	2.3414	1.3152	-0.2402	-0.3002	0.1212	-0.6305	0.2556	-0.8018	-0.1873	0.2864	-0.1897	-0.1225	0.123	0.0004	-0.0659	1.05	-0.0225	-0.1142	0.999	0.074	0.875	13.0124	-26.2795	56.3785
19	4.9366	0.1288	-1.6616	1.6328	-0.2712	2.5545	-0.1243	-0.7785	0.0011	0.2926	0.0765	0.0203	-0.0492	0.1778	0.0477	0.3374	0.0183	0.0065	0.4428	0.024	0.477	13.9563	-26.0894	43.6327
20	4.8641	0.6569	-1.4468	1.8781	-0.062	3.9664	0.0146	-0.3396	0.0521	0.0212	-0.163	-0.086	0.2186	0.1851	0.1484	0.3381	-0.0419	-0.0566	0.4173	0.1102	0.6122	38.8122	-24.0288	29.3517
21	13.3953	-4.9696	-1.9131	15.3604	3.0467	10.4096	-0.2278	-0.4579	-0.2846	0.1328	0.6085	-0.2968	0.6396	1.0432	-0.3807	0.2053	-0.0396	-0.0832	0.6864	0.2169	0.526	50.0254	-26.0639	31.8101

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	542 - 548
2	X-RAY DIFFRACTION	2	A	549 - 615
3	X-RAY DIFFRACTION	3	A	616 - 715
4	X-RAY DIFFRACTION	4	A	716 - 735
5	X-RAY DIFFRACTION	5	A	736 - 769
6	X-RAY DIFFRACTION	5	A	770
7	X-RAY DIFFRACTION	6	A	771 - 837
8	X-RAY DIFFRACTION	7	A	838 - 852
9	X-RAY DIFFRACTION	8	C	542 - 546
10	X-RAY DIFFRACTION	9	C	547 - 637
11	X-RAY DIFFRACTION	10	C	638 - 648
12	X-RAY DIFFRACTION	11	C	649 - 715
13	X-RAY DIFFRACTION	12	C	716 - 734
14	X-RAY DIFFRACTION	13	C	735 - 835
15	X-RAY DIFFRACTION	14	C	836 - 852
16	X-RAY DIFFRACTION	15	F	542 - 638
17	X-RAY DIFFRACTION	16	F	639 - 649
18	X-RAY DIFFRACTION	17	F	650 - 715
19	X-RAY DIFFRACTION	18	F	716 - 734
20	X-RAY DIFFRACTION	19	F	735 - 769
21	X-RAY DIFFRACTION	19	F	770
22	X-RAY DIFFRACTION	20	F	771 - 835
23	X-RAY DIFFRACTION	21	F	836 - 852

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