PDB-3cb4: The Crystal Structure of LepA

ID or keywords:

Entry

Database: PDB / ID: 3cb4

Title

The Crystal Structure of LepA

Components

GTP-binding protein lepA

Keywords

TRANSLATION /

GTPAse / OB-fold / GTP-binding /

Membrane / Nucleotide-binding

Function / homology

Function and homology information

: / response to pH /

guanosine tetraphosphate binding /

ribosomal large subunit binding /

ribosomal small subunit binding /

translation elongation factor activity / response to salt stress / response to cold / positive regulation of translation /

ribosomal small subunit biogenesis ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 2.8 Å

Authors

Evans, R.N. / Blaha, G. / Bailey, S. / Steitz, T.A.

Citation

Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: The structure of LepA, the ribosomal back translocase.
Authors: Evans, R.N. / Blaha, G. / Bailey, S. / Steitz, T.A.

History

Deposition	Feb 21, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 18, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3cb4.cif.gz	575.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3cb4.ent.gz	490.8 KB	Display	PDB format
PDBx/mmJSON format	3cb4.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/cb/3cb4 ftp://data.pdbj.org/pub/pdb/validation_reports/cb/3cb4	HTTPS FTP

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Related structure data

Similar structure data	4fsh-d 2ywf-d 4p1l-d 2ywe-d 3t7g-d 6qf7-1 3u92-d 3u93-d 6iwb-d 1qs8-3 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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#81 - Sep 2006 Elongation Factors similarity (10) #121 - Jan 2010 70S Ribosomes similarity (10) #245 - May 2020 Spliceosomes similarity (8) #104 - Aug 2008 Selenocysteine Synthase similarity (5) #157 - Jan 2013 Transfer-Messenger RNA similarity (7)

Deposited unit

D: GTP-binding protein lepA

A: GTP-binding protein lepA

B: GTP-binding protein lepA

C: GTP-binding protein lepA

E: GTP-binding protein lepA

F: GTP-binding protein lepA

400 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: GTP-binding protein lepA

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

2

B: GTP-binding protein lepA

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

3

C: GTP-binding protein lepA

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

4

D: GTP-binding protein lepA

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

5

E: GTP-binding protein lepA

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

6

F: GTP-binding protein lepA

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

Unit cell

Length a, b, c (Å)	97.960, 146.243, 139.317
Angle α, β, γ (deg.)	90.00, 100.60, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Details

The biological unit is a monomer. There are 6 biological units in the asymmetric unit (chains A, B, C, D, E, and F). The 6 biological units are arranged as a trimer of dimers.

#1: Protein	GTP-binding protein lepA Mass: 66652.094 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: lepA / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P60785
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

GTP-binding protein lepA

Mass: 66652.094 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: K12 / Gene: lepA / Plasmid: pET28a / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P60785

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 49.85 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM Tris-HCl pH 8.0 10% Peg 2000MME, 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
1,2		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	NSLS	X25	1	0.979
SYNCHROTRON	ALS	8.2.2	2	0.979

Detector

Type	ID	Detector	Date
ADSC QUANTUM 315	1	CCD	Sep 28, 2007
ADSC QUANTUM 315	2	CCD

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Si(111)	SINGLE WAVELENGTH	M	x-ray	1
2	Si(111)	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.8→50 Å / Num. all: 92895 / Num. obs: 88629 / % possible obs: 94.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / R_merge(I) obs: 0.117 / R_sym value: 0.088 / Net I/σ(I): 9.8

Reflection shell

Resolution: 2.8→2.9 Å / Redundancy: 2.4 % / R_merge(I) obs: 0.588 / Mean I/σ(I) obs: 1.4 / Num. unique all: 6070 / R_sym value: 0.494 / % possible all: 64.9

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
CBASS		data collection
HKL-2000		data reduction
SCALEPACK		data scaling
SOLVE		phasing

Refinement

Method to determine structure:

SIRAS / Resolution: 2.8→50 Å / Cor.coef. F_o:F_c: 0.905 / Cor.coef. F_o:F_c free: 0.855 / SU B: 46.615 / SU ML: 0.396 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.46 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29455	4590	5.2 %	RANDOM
R_work	0.24644	-	-	-
obs	0.24896	84039	95.38 %	-

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: 54.18 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.53 Å²	0 Å²	0.42 Å²
2-	-	1.64 Å²	0 Å²
3-	-	-	-3.02 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24492	0	0	3	24495

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	24909
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.088	1.975	33762
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.567	5	3132
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.681	24.392	1134
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.304	15	4344
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.504	15	180
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	3900
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	18726
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.196	0.2	10787
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.301	0.2	16785
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.122	0.2	678
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	0.239	0.2	82
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.239	0.2	7
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	0.206	1.5	16049
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.371	2	25320
X-RAY DIFFRACTION	r_scbond_it	0.466	3	9790
X-RAY DIFFRACTION	r_scangle_it	0.812	4.5	8442
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.8→2.873 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.43	163	-
R_work	0.401	3062	-
obs	-	-	64.46 %

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	4.6113	0.7041	0.2571	2.1642	0.3879	3.117	-0.0714	0.1603	-0.0429	-0.3432	0.2163	-0.3424	0.1329	0.4409	-0.1449	-0.1413	-0.043	-0.0037	-0.1347	0.0547	-0.2324	30.9432	110.7694	146.8033
2	3.1426	-1.1721	-0.0711	4.6356	-0.4762	3.3763	-0.0455	0.0342	0.0731	0.4412	-0.0883	0.4243	-0.2745	-0.3411	0.1338	-0.0987	-0.1322	-0.1259	-0.0322	-0.0285	-0.2399	79.2723	92.2992	139.7363
3	5.4656	-0.6874	1.1829	1.4714	-0.5949	4.7835	-0.0837	0.6489	0.9801	-0.1725	0.0703	0.5348	-0.7853	-0.3321	0.0134	0.018	-0.0695	-0.062	-0.0132	0.0234	0.1421	45.6948	59.0578	101.229
4	4.3446	-0.2547	1.0283	1.9799	0.407	3.1762	-0.2213	-0.3681	0.1357	0.3612	0.1385	-0.0681	-0.0873	0.2432	0.0828	0.0286	0.0087	0.1033	-0.0968	0.1535	-0.1436	58.2667	58.6721	40.8229
5	2.0164	-0.2639	-0.2712	4.4482	0.7298	3.2075	-0.0181	0.3155	-0.4878	-0.3387	0.0546	0.148	0.7179	-0.1688	-0.0365	0.1266	0.009	0.0961	0.054	-0.0127	0.0603	95.0224	89.9618	64.3688
6	3.3244	1.1028	-0.5845	2.7382	0.16	2.5385	0.0794	-0.41	-0.4372	0.085	-0.1017	-0.0145	0.4266	-0.307	0.0223	-0.0517	0.0088	0.0531	0.1776	-0.0262	-0.136	40.379	108.9992	84.8798
7	0.4344	-0.7454	-0.772	4.1571	-0.9737	4.4062	-0.0067	0.2022	0.2027	0.2566	0.0116	-0.0206	-0.1337	0.2208	-0.0049	-0.3348	0.0106	0.0164	-0.1497	-0.0114	-0.0854	24.2869	76.4601	139.7182
8	3.3402	1.4979	0.2126	0.737	0.4275	4.7637	-0.1477	0.1534	0.0367	-0.0057	0.0504	-0.1306	-0.3858	0.2584	0.0973	-0.1518	-0.0091	0.0304	-0.1939	-0.0047	-0.1557	61.6395	61.9864	142.1917
9	2.0402	1.8435	-1.0745	2.7777	1.0645	4.2921	0.1027	-0.1422	0.2012	0.162	-0.202	0.2236	-0.1684	-0.2049	0.0992	-0.247	0.0568	0.0025	-0.1757	0.006	-0.2052	79.5935	69.4796	103.1206
10	1.7503	1.081	-0.692	3.7911	-0.663	2.5807	-0.008	-0.0996	-0.1779	0.0901	-0.0586	-0.0931	0.2092	0.2511	0.0667	-0.193	0.0425	-0.0433	-0.0761	0.0101	-0.2231	39.8759	89.0049	43.3086
11	4.3764	-0.068	-1.0717	0.0886	-0.3966	5.0332	-0.1703	-0.2972	-0.4509	0.0757	0.053	0.0176	0.2907	-0.0576	0.1173	-0.1521	-0.0385	0.0038	-0.2765	-0.0346	-0.1745	69.8235	113.8651	53.8436
12	3.0148	-1.467	-0.4594	1.206	-0.1866	3.4539	-0.0089	0.2664	-0.0172	-0.1373	-0.0206	0.0163	0.0727	-0.2102	0.0295	-0.1103	-0.0821	-0.0069	-0.1908	-0.0228	-0.1695	73.9336	109.0541	97.2294
13	0.0111	-0.1072	-0.014	3.682	-0.9861	0.4923	0.1596	0.2455	0.0639	-0.2855	-0.1564	-0.2942	-0.078	0.1069	-0.0032	-0.0174	0.0196	0.0745	0.1271	0.0248	-0.0745	33.9428	78.8115	124.015
14	2.522	1.9717	0.9294	1.6703	1.0262	1.0393	-0.0611	-0.3172	0.3139	0.0154	0.0038	0.3684	-0.292	-0.0629	0.0574	-0.0328	0.0671	0.0695	-0.0114	-0.0238	-0.1085	54.748	68.3139	158.1526
15	1.2642	1.7251	0.5937	2.4974	0.3523	1.7407	-0.12	0.1133	0.4489	-0.2298	0.1605	0.2654	-0.0252	-0.3806	-0.0406	0.049	0.0126	0.0595	-0.0975	0.038	-0.1032	78.0721	73.6712	85.0655
16	0.0307	-0.2621	0.138	3.6304	-0.7954	0.7261	-0.0248	-0.2059	0.058	0.2206	0.0117	-0.2628	0.1427	0.1492	0.0131	0.009	-0.0637	0.0009	0.2016	0.0229	-0.1233	43.6615	88.8023	61.3062
17	3.6999	-0.5874	-0.3819	0.0932	0.0616	1.1166	-0.0792	0.16	-0.4725	0.0621	0.0611	0.1932	0.3509	0.0594	0.0181	0.0061	-0.0464	0.0407	-0.0538	-0.0796	-0.1464	71.6691	107.269	36.8421
18	4.6705	-1.7081	-0.2836	0.7234	-0.1563	0.702	0.0027	-0.1555	-0.4259	0.1527	0.0649	0.0884	0.1279	-0.2167	-0.0676	0.0347	-0.0528	0.0348	-0.0756	0.0124	-0.1753	66.9436	102.9943	113.2461
19	3.2353	0.4595	0.6202	5.1698	-0.3958	5.1086	-0.0281	-0.1443	0.0758	-0.0438	0.0341	0.4726	0.0898	-0.2053	-0.006	-0.4537	-0.0144	-0.0679	-0.3257	-0.0061	-0.2584	8.0346	99.8679	150.6475
20	4.7078	0.2051	1.6098	3.2031	0.6538	5.1298	-0.0911	0.1089	-0.3118	0.0911	-0.0374	-0.5998	0.4882	0.3724	0.1286	-0.2108	-0.0896	-0.0426	-0.1663	0.0757	-0.1648	90.0621	69.8009	133.7751
21	3.815	0.9735	-0.1031	4.598	0.5305	4.1139	-0.0332	-0.2351	-0.5594	0.0795	0.0459	-0.0487	0.5004	0.2807	-0.0127	-0.2318	0.0186	0.0424	-0.2003	-0.0131	-0.2366	63.4658	45.9242	114.2713
22	4.1437	0.4183	-1.2601	4.5515	-1.8427	3.7119	0.0705	0.0628	-0.2777	-0.2819	-0.0613	0.2087	0.1543	-0.5282	-0.0092	-0.2478	-0.1009	0.0326	-0.1691	0.0171	-0.1639	36.2402	62.3153	28.3368
23	4.9493	-0.0361	-0.2885	2.2317	0.0112	3.7989	0.0871	-0.1787	0.6089	0.1662	0.1019	-0.458	-0.4717	0.1561	-0.189	-0.1221	-0.0181	0.0292	-0.2213	0.0082	-0.0953	94.2005	114.2484	72.398
24	5.2113	-0.1236	-1.3154	3.842	1.6808	4.4939	0.1179	0.2044	0.6194	-0.0871	-0.1057	-0.0101	-0.5397	0.0652	-0.0123	-0.1167	0.0401	0.0241	-0.167	0.0129	-0.1945	57.0704	127.8242	79.8477

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	B	1 - 185	1 - 185
2	X-RAY DIFFRACTION	2	B	C	1 - 185	1 - 185
3	X-RAY DIFFRACTION	3	C	D	1 - 185	1 - 185
4	X-RAY DIFFRACTION	4	D	A	1 - 185	1 - 185
5	X-RAY DIFFRACTION	5	E	E	1 - 185	1 - 185
6	X-RAY DIFFRACTION	6	F	F	1 - 185	1 - 185
7	X-RAY DIFFRACTION	7	A	B	290 - 375	290 - 375
8	X-RAY DIFFRACTION	8	B	C	290 - 375	290 - 375
9	X-RAY DIFFRACTION	9	C	D	290 - 375	290 - 375
10	X-RAY DIFFRACTION	10	D	A	290 - 375	290 - 375
11	X-RAY DIFFRACTION	11	E	E	290 - 375	290 - 375
12	X-RAY DIFFRACTION	12	F	F	290 - 375	290 - 375
13	X-RAY DIFFRACTION	13	A	B	376 - 555	376 - 555
14	X-RAY DIFFRACTION	14	B	C	376 - 555	376 - 555
15	X-RAY DIFFRACTION	15	C	D	376 - 555	376 - 555
16	X-RAY DIFFRACTION	16	D	A	376 - 555	376 - 555
17	X-RAY DIFFRACTION	17	E	E	376 - 555	376 - 555
18	X-RAY DIFFRACTION	18	F	F	376 - 555	376 - 555
19	X-RAY DIFFRACTION	19	A	B	186 - 289	186 - 289
20	X-RAY DIFFRACTION	20	B	C	186 - 289	186 - 289
21	X-RAY DIFFRACTION	21	C	D	186 - 289	186 - 289
22	X-RAY DIFFRACTION	22	D	A	186 - 289	186 - 289
23	X-RAY DIFFRACTION	23	E	E	186 - 289	186 - 289
24	X-RAY DIFFRACTION	24	F	F	186 - 289	186 - 289

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi