PDB-3e3x: The C-terminal part of BipA protein from Vibrio parahaemolyticus ...

ID or keywords:

Entry

Database: PDB / ID: 3e3x

Title

The C-terminal part of BipA protein from Vibrio parahaemolyticus RIMD 2210633

Components

BipA

Keywords

HYDROLASE / BipA protein / MCSG / PSI2 / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics / GTP-binding / Nucleotide-binding

Function / homology

Function and homology information

guanosine tetraphosphate binding / ribosome binding / ribosomal large subunit assembly / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / tRNA binding / rRNA binding / GTPase activity / GTP binding / cytoplasm
Similarity search - Function

Biological species

Vibrio parahaemolyticus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.95 Å

Authors

Nocek, B. / Mulligan, R. / Duggan, E. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The C-terminal part of BipA protein from Vibrio parahaemolyticus RIMD 2210633
Authors: Nocek, B. / Mulligan, R. / Duggan, E. / Clancy, S. / Joachimiak, A.

History

Deposition	Aug 8, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 30, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3e3x.cif.gz	74.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3e3x.ent.gz	62.2 KB	Display	PDB format
PDBx/mmJSON format	3e3x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3e3x_validation.pdf.gz	446.4 KB	Display	wwPDB validaton report
Full document	3e3x_full_validation.pdf.gz	453.9 KB	Display
Data in XML	3e3x_validation.xml.gz	15.9 KB	Display
Data in CIF	3e3x_validation.cif.gz	22.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e3/3e3x ftp://data.pdbj.org/pub/pdb/validation_reports/e3/3e3x	HTTPS FTP

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Related structure data

Similar structure data	6mi6-d 5usf-2 6laz-d 6lax-d 3zby-3 5jq2-d 5e8j-d 6l1a-d 4b91-d 6yn0-d 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
Other databases	TargetDB: apc91207.1

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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

A: BipA

hetero molecules

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

1

A: BipA

hetero molecules

A: BipA

hetero molecules

defined by software
75.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	90.600, 104.571, 74.348
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-1172- HOH

Details

authors state that the biological assembly is unknown

#1: Protein	BipA Mass: 37423.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: bipA, VP0122 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9L5X8
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.35 Å³/Da / Density % sol: 47.72 %
Crystal grow	Temperature: 277 K / pH: 7.5 Details: 0.1 M Hepes, 20 % PEG 4k 10% Isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2008 / Details: MIRRORS
Radiation	Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.95→40 Å / Num. obs: 25871 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / R_merge(I) obs: 0.09 / Net I/σ(I): 29.8
Reflection shell	Resolution: 1.95→1.98 Å / Redundancy: 7.2 % / R_merge(I) obs: 0.56 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELX		phasing
ARP		model building
Coot		model building
MLPHARE		phasing
CCP4		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.95→40 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.941 / SU B: 6.06 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.223	1314	5.1 %	RANDOM
R_work	0.172	-	-	-
obs	0.174	24524	99.6 %	-
all	-	25838	-	-

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: 17.25 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.62 Å²	0 Å²	0 Å²
2-	-	-0.85 Å²	0 Å²
3-	-	-	0.24 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2261	0	13	203	2477

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.022	2308
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1593
X-RAY DIFFRACTION	r_angle_refined_deg	1.845	1.992	3110
X-RAY DIFFRACTION	r_angle_other_deg	0.989	3	3878
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.465	5	288
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.381	24.144	111
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.358	15	387
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.382	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	349
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2577
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	455
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	405
X-RAY DIFFRACTION	r_nbd_other	0.216	0.2	1779
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	1100
X-RAY DIFFRACTION	r_nbtor_other	0.091	0.2	1290
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.182	0.2	143
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	0.175	0.2	11
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.306	0.2	33
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.55	0.2	11
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	1.39	1.5	1697
X-RAY DIFFRACTION	r_mcbond_other	0.312	1.5	589
X-RAY DIFFRACTION	r_mcangle_it	1.597	2	2293
X-RAY DIFFRACTION	r_scbond_it	3.065	3	940
X-RAY DIFFRACTION	r_scangle_it	4.618	4.5	815
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.95→2 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.229	94	-
R_work	0.182	1734	-
obs	-	-	97.34 %

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	35.8683	-10.1374	4.3224	8.3907	0.332	9.4398	0.2553	0.2199	-1.0146	-0.2296	0.3359	0.8684	0.0151	-0.5998	-0.5912	0.0501	-0.0354	-0.0295	0.0706	0.0958	0.2702	35.7079	24.3392	-10.5653
2	2.2144	0.2615	0.2668	4.0408	-0.51	2.7881	-0.0093	0.0157	-0.0281	0.2097	-0.0652	-0.0896	0.2825	0.2559	0.0745	0.1532	0.0373	0.018	0.0836	-0.0015	0.0818	47.059	8.1474	1.9697
3	6.6023	-3.1306	4.4966	9.1942	-3.8206	4.3966	0.1193	0.0713	-0.0668	-0.464	0.0941	0.6455	0.1661	-0.134	-0.2134	0.1402	-0.0064	-0.0372	0.0728	0.0047	0.1524	35.4485	6.6318	-5.861
4	16.0327	-0.1582	-3.1225	10.7141	-1.8431	8.9108	0.108	0.4749	0.1266	-1.3517	0.2532	2.0972	0.1968	-0.3214	-0.3612	0.0555	-0.0438	-0.2873	-0.0246	0.0971	0.2961	32.2731	15.3977	-11.7151
5	11.8373	-12.3515	-0.9003	24.5836	-1.1631	3.25	0.2871	0.4228	0.231	-0.9871	-0.1346	0.3087	0.1763	0.1803	-0.1525	0.125	-0.0307	-0.0594	0.0914	0.0165	0.0159	41.4554	15.0474	-10.8354
6	6.0965	-3.5159	-4.0886	21.941	-7.6243	9.1105	-0.0971	-0.0527	0.336	0.8824	0.4475	0.1148	-0.4995	-0.6272	-0.3504	0.1128	0.0498	0.0238	0.0799	0.0076	0.1834	34.2534	19.7671	0.1455
7	3.9297	1.2235	-0.8369	3.653	-4.1982	4.9168	0.1621	-0.057	0.3091	0.2418	-0.0606	0.358	-0.2102	0.0667	-0.1015	0.1682	0.0253	0.0293	0.0825	-0.0269	0.1455	40.0046	13.087	1.6655
8	4.2152	2.6574	-3.0543	12.2573	-18.2615	30.5344	-0.2528	0.3786	-0.1889	-0.4326	0.4214	0.0705	0.5212	-0.5892	-0.1686	0.0753	-0.0145	-0.0128	0.0942	-0.028	0.1485	39.6902	31.7153	-18.1183
9	2.8243	-0.4184	-1.245	1.6255	1.5964	5.4296	-0.1586	-0.1895	0.0554	0.2957	-0.1631	0.1215	-0.093	-0.2087	0.3217	0.1418	0.0175	-0.0058	0.0439	-0.0125	0.133	33.7741	41.9942	0.2785
10	9.7541	-1.8984	-1.1924	4.1419	3.128	5.4972	0.0353	-0.0482	0.4743	0.0398	0.0808	-0.2804	-0.2419	0.2465	-0.1161	0.127	-0.0263	0.0111	0.0044	-0.0201	0.1456	37.114	45.8401	-1.2316
11	2.1435	-1.0634	-0.9052	1.8852	1.2785	3.5539	-0.1191	-0.2933	0.0662	0.4074	-0.0149	0.0223	0.1527	-0.1873	0.134	0.1587	-0.0119	0.034	0.1095	-0.0668	0.146	29.8553	44.2819	2.4988
12	7.7004	-0.6453	-3.7072	14.0221	8.1007	38.7385	-0.2658	-0.4087	0.0738	0.5106	-0.1948	-0.3855	0.9983	1.0138	0.4606	0.1749	0.0719	-0.0084	0.0051	0.0177	0.1087	39.0681	36.4589	5.9491
13	3.3471	-0.1632	-1.558	0.4799	1.3961	8.3077	0.0057	-0.024	0.0239	0.2346	-0.064	-0.0087	0.0052	-0.2078	0.0582	0.138	0.0336	0.006	-0.0509	-0.0016	0.1643	34.659	37.2686	-3.6881
14	19.1175	-21.1033	10.416	23.2953	-11.498	5.6751	1.0199	0.7038	-0.0348	-0.7965	-0.2111	-1.4368	-0.9167	-0.6131	-0.8089	0.8333	0.1077	-0.2235	0.3785	0.1005	0.4932	52.1778	33.4876	0.7094
15	2.1751	-0.3932	-1.5024	4.983	2.5795	4.497	-0.0588	-0.3879	0.1171	0.6022	0.2488	-0.3764	0.3035	0.7519	-0.1901	0.1127	0.0423	-0.124	0.202	-0.0198	0.1061	61.2746	18.9803	15.8728
16	1.8283	-0.896	0.8004	7.0962	-0.5404	9.3196	0.0062	-0.5224	0.2345	0.3449	-0.1136	-0.0023	-0.2239	0.3903	0.1074	0.1179	0.0089	-0.0585	0.1679	-0.0267	0.06	56.6722	23.4696	16.386
17	2.9891	-0.4031	-0.0939	2.0041	0.6401	3.7441	-0.0441	-0.1142	0.2146	0.2515	0.0506	-0.2716	-0.2055	0.4015	-0.0065	0.0954	0.0079	-0.0724	0.1433	0.0034	0.1311	59.6041	21.5182	8.6163
18	1.9418	-0.2058	1.5786	0.1939	0.4753	3.6828	0.0117	-0.1477	-0.2092	0.1104	-0.0284	-0.0835	-0.1274	0.2792	0.0166	0.154	-0.0496	-0.0089	0.3067	-0.013	0.1123	52.3867	23.0408	18.3738
19	12.3614	-3.6883	-5.1853	9.3314	4.6111	10.7953	-0.0831	0.1105	0.6372	-0.0757	-0.1396	0.3914	-0.5721	-0.1373	0.2228	0.105	0.0163	-0.0672	0.0393	0.0225	0.162	47.7703	25.0052	1.0909
20	8.2007	1.9692	-1.6736	2.2327	-0.1392	2.567	-0.0091	0.1375	0.108	0.065	0.0319	-0.1044	0.1073	0.3227	-0.0228	0.1123	0.0353	-0.04	0.1277	0.0114	0.0799	55.1798	15.9601	0.845

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	27 - 33
2	X-RAY DIFFRACTION	2	A	34 - 48
3	X-RAY DIFFRACTION	3	A	49 - 63
4	X-RAY DIFFRACTION	4	A	64 - 74
5	X-RAY DIFFRACTION	5	A	75 - 86
6	X-RAY DIFFRACTION	6	A	87 - 96
7	X-RAY DIFFRACTION	7	A	97 - 108
8	X-RAY DIFFRACTION	8	A	109 - 119
9	X-RAY DIFFRACTION	9	A	120 - 138
10	X-RAY DIFFRACTION	10	A	139 - 153
11	X-RAY DIFFRACTION	11	A	154 - 171
12	X-RAY DIFFRACTION	12	A	172 - 182
13	X-RAY DIFFRACTION	13	A	183 - 203
14	X-RAY DIFFRACTION	14	A	204 - 210
15	X-RAY DIFFRACTION	15	A	211 - 229
16	X-RAY DIFFRACTION	16	A	230 - 239
17	X-RAY DIFFRACTION	17	A	240 - 261
18	X-RAY DIFFRACTION	18	A	262 - 289
19	X-RAY DIFFRACTION	19	A	290 - 300
20	X-RAY DIFFRACTION	20	A	301 - 325

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