PDB-4n8j: F60M mutant, RipA structure

ID or keywords:

Entry

Database: PDB / ID: 4n8j

Title

F60M mutant, RipA structure

Components

Putative 4-hydroxybutyrate coenzyme A transferase

Keywords

TRANSFERASE / Coenzyme A transferase

Function / homology

Function and homology information

acetate CoA-transferase activity / acetate metabolic process
Similarity search - Function

Biological species

Yersinia pestis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.01 Å

Authors

Torres, R. / Goulding, C.W.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural snapshots along the reaction pathway of Yersinia pestis RipA, a putative butyryl-CoA transferase.
Authors: Torres, R. / Lan, B. / Latif, Y. / Chim, N. / Goulding, C.W.

History

Deposition	Oct 17, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 9, 2014	Provider: repository / Type: Initial release
Revision 1.1	Apr 16, 2014	Group: Database references
Revision 1.2	Oct 9, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4n8j.cif.gz	1012.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4n8j.ent.gz	860.4 KB	Display	PDB format
PDBx/mmJSON format	4n8j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4n8j_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4n8j_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4n8j_validation.xml.gz	82.4 KB	Display
Data in CIF	4n8j_validation.cif.gz	116.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n8/4n8j ftp://data.pdbj.org/pub/pdb/validation_reports/n8/4n8j	HTTPS FTP

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Related structure data

Related structure data	4n8hC 4n8iC 4n8kC 4n8lC C: citing same article (ref.)
Similar structure data	5z2c-3 4n8h-2 5u4p-d 3km0-1 5z2c-2 5z2c-8 5z2c-4 3uxj-2 3pgd-2 5zsk-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) 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

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	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: Putative 4-hydroxybutyrate coenzyme A transferase

B: Putative 4-hydroxybutyrate coenzyme A transferase

C: Putative 4-hydroxybutyrate coenzyme A transferase

D: Putative 4-hydroxybutyrate coenzyme A transferase

hetero molecules

212 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative 4-hydroxybutyrate coenzyme A transferase

hetero molecules

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

2

B: Putative 4-hydroxybutyrate coenzyme A transferase

hetero molecules

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

3

C: Putative 4-hydroxybutyrate coenzyme A transferase

hetero molecules

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

4

D: Putative 4-hydroxybutyrate coenzyme A transferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	197.307, 197.307, 59.931
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	144
Space group name H-M	P3₁

#1: Protein	Putative 4-hydroxybutyrate coenzyme A transferase / Putative Coenzyme A transferase / Similar to 4-hydroxybutyrate CoA transferase Mass: 52268.371 Da / Num. of mol.: 4 / Mutation: F60M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: aCH1, y2385, YPO1926, YP_1668 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZC36
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1350 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.22 Å³/Da / Density % sol: 61.82 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 25% PEG 3350, 0.4 M ammonium phosphate monobasic and 1 mM butyryl CoA, pH 7.4, VAPOR DIFFUSION, HANGING 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 315 / Detector: CCD / Date: Oct 19, 2011

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: 2→50 Å / Num. obs: 173491 / % possible obs: 97.9 % / Redundancy: 5 % / B_iso Wilson estimate: 27.61 Å² / R_merge(I) obs: 0.082 / Net I/σ(I): 17.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Diffraction-ID	% possible all
2-2.07	3.5	0.396	14120	1	79.5
2.07-2.15	4	0.294	17685	1	100
2.15-2.25	4.6	0.226	17651	1	100
2.25-2.37	4.9	0.166	17730	1	100
2.37-2.52	5	0.126	17773	1	100
2.52-2.71	5.1	0.098	17705	1	100
2.71-2.99	5.3	0.078	17689	1	100
2.99-3.42	5.5	0.072	17699	1	100
3.42-4.31	5.7	0.082	17733	1	100
4.31-50	5.7	0.059	17706	1	99.9

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Processing

Software

Name	Version	Classification
PHENIX	1.8.3_1479	refinement
PDB_EXTRACT	3.11	data extraction
BOS		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Resolution: 2.01→41.286 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.9063 / SU ML: 0.16 / σ(F): 0.09 / Phase error: 16.71 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1737	1944	1.15 %
R_work	0.14	166617	-
obs	0.1404	168561	97.01 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 257.64 Å² / B_iso mean: 44.1625 Å² / B_iso min: 14.99 Å²

Refinement step

Cycle: LAST / Resolution: 2.01→41.286 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13692	0	177	1350	15219

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	14115
X-RAY DIFFRACTION	f_angle_d	1.287	19160
X-RAY DIFFRACTION	f_chiral_restr	0.052	2168
X-RAY DIFFRACTION	f_plane_restr	0.007	2496
X-RAY DIFFRACTION	f_dihedral_angle_d	13.731	5257

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.0097-2.06	0.2537	128	0.2022	10832	10960	88
2.06-2.1157	0.2096	116	0.1755	11203	11319	92
2.1157-2.1779	0.2127	137	0.1547	11559	11696	94
2.1779-2.2482	0.1957	136	0.1503	11648	11784	95
2.2482-2.3285	0.1798	129	0.1395	11822	11951	96
2.3285-2.4218	0.2089	139	0.1419	12008	12147	98
2.4218-2.532	0.1757	143	0.1468	12015	12158	98
2.532-2.6654	0.1824	144	0.1482	12126	12270	99
2.6654-2.8324	0.2004	148	0.1491	12176	12324	99
2.8324-3.051	0.1745	148	0.1556	12197	12345	100
3.051-3.3579	0.1983	144	0.1493	12275	12419	100
3.3579-3.8435	0.1846	142	0.1338	12254	12396	100
3.8435-4.8413	0.1307	148	0.1086	12260	12408	100
4.8413-41.295	0.1401	142	0.1336	12242	12384	100

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	1.6821	-0.0224	-0.5135	1.5058	0.2084	1.2318	-0.12	-0.1986	-0.1359	0.1808	0.0502	0.1003	0.0664	0.0233	0.0523	0.1914	0.0641	0.0354	0.2646	0.0542	0.1357	23.9476	-44.5492	13.7328
2	0.7292	0.1054	0.3125	2.4778	-0.0609	0.2979	-0.0083	0.1271	0.0329	-0.2596	-0.0268	0.2528	-0.0682	-0.0561	0.0401	0.2258	0.0632	-0.0046	0.263	0.0029	0.162	22.5654	-35.2904	-9.0556
3	4.1171	-1.4288	0.4549	2.8771	-0.4053	0.852	-0.04	-0.2531	0.0946	-0.1064	0.0433	0.3205	-0.0016	-0.1271	0.0253	0.2566	0.0383	-0.0403	0.2472	0.0161	0.2304	16.0546	-14.5411	-9.5288
4	0.1594	-0.1868	0.3956	3.0774	-1.6475	1.4715	-0.1455	0.4113	-0.1763	0.1839	-0.0705	0.8567	-0.3276	-0.4959	0.3045	0.2152	0.0667	-0.0799	0.4748	-0.2162	0.4618	27.8812	-57.9799	-27.566
5	1.7385	-0.0983	-0.6977	1.8691	0.2051	2.3306	-0.0044	0.4136	-0.1989	-0.3331	-0.1083	0.098	0.0533	-0.1005	0.1021	0.2327	0.0875	-0.0247	0.3351	-0.0838	0.174	50.8688	-62.033	-31.9624
6	4.6892	-0.484	-1.7857	3.4417	0.1431	2.9794	-0.0181	0.0635	-0.187	0.0276	0.1237	-0.3731	0.0604	0.2328	-0.0846	0.1789	0.0776	-0.0141	0.2915	-0.0858	0.2254	62.1326	-63.8653	-27.4168
7	2.7403	0.1277	-0.2685	1.5622	-0.1987	0.4778	0.126	0.286	0.0093	-0.1829	-0.1605	-0.1575	-0.0889	0.0679	0.0382	0.2545	0.0619	-0.0047	0.2876	-0.0068	0.1296	57.1629	-51.9931	-26.8583
8	4.4136	0.721	-0.7302	3.0398	0.448	2.3622	-0.0027	0.2151	-0.0174	-0.107	-0.0529	0.1922	0.0116	-0.1373	0.051	0.1626	0.0514	-0.0185	0.2256	-0.0498	0.1321	40.2721	-54.747	-20.8629
9	2.3312	-0.7211	0.7901	2.7554	1.1527	1.676	-0.0772	0.0434	-0.0802	-0.0063	-0.1085	0.2579	0.021	-0.203	0.1729	0.182	0.0219	0.0308	0.3211	-0.0593	0.2121	37.7743	-58.1581	-18.1409
10	5.9322	1.6726	3.7086	0.6815	0.9199	2.3931	0.3445	-0.0114	-0.8809	0.0973	-0.0599	-0.4124	0.193	0.2124	-0.2993	0.2488	0.0327	-0.0053	0.3698	0.0838	0.3636	60.9218	-64.5366	-2.4089
11	2.0758	0.5925	-0.1876	1.8444	-0.264	1.654	0.0379	-0.338	-0.0489	0.2817	-0.0535	0.0148	-0.002	0.105	0.0078	0.1594	0.0387	0.0046	0.2817	-0.009	0.1153	51.9792	-52.882	-1.0302
12	1.8776	0.679	2.7727	0.788	0.4206	4.7173	-0.1354	0.6812	-0.0969	-0.6843	0.2378	0.0812	0.0274	0.1271	-0.1044	0.4412	0.0346	-0.0689	0.4641	-0.0156	0.4462	74.2619	-53.911	-14.49
13	3.8241	-0.8022	0.4759	2.2756	-0.1723	0.6824	0.1477	-0.0338	-0.2452	-0.1225	-0.151	-0.2674	0.1142	0.0656	0.03	0.205	0.0193	-0.0338	0.2852	0.0273	0.237	78.0135	-50.3359	-2.7883
14	1.728	-0.4227	-0.0867	1.6055	-0.0216	0.8336	0.0417	0.1103	0.3587	-0.1722	-0.0741	-0.1164	-0.0527	-0.0132	0.0249	0.225	0.0362	-0.0267	0.1749	0.0643	0.3089	35.4747	5.6308	-12.0627
15	1.2205	0.5207	-0.3723	1.396	-0.5793	1.16	0.037	-0.1533	0.2543	0.1705	-0.0828	-0.2034	-0.133	0.0646	0.0672	0.228	0.0536	-0.0472	0.2348	-0.0054	0.3325	47.3464	-5.3679	2.8588
16	2.307	-0.057	-1.0103	2.9317	0.3447	2.5115	0.0136	-0.2262	0.2977	0.3982	-0.0824	0.3004	-0.2173	-0.2438	0.0961	0.3046	0.0711	0.0052	0.3048	-0.0551	0.2119	27.7896	-13.8152	18.734
17	1.8642	-0.1712	0.0989	1.3797	0.1885	0.9222	-0.0055	-0.2186	0.2691	0.0794	-0.0273	-0.2567	-0.0227	0.0553	0.0199	0.1549	-0.0076	-0.0628	0.2413	-0.0087	0.3104	85.7826	-23.4218	-0.2471
18	0.9416	0.3536	0.3698	1.7078	0.6555	1.1523	-0.0576	0.1202	0.2944	-0.2249	0.0052	-0.1093	-0.131	0.0647	0.0695	0.1894	0.024	-0.0182	0.2777	0.0458	0.3365	70.3403	-18.639	-15.1849
19	3.8437	0.1846	-1.926	2.6905	0.5171	3.5381	-0.197	0.0092	0.0255	-0.1592	0.0868	-0.3554	0.1137	0.466	0.1284	0.1925	0.0209	0.0048	0.3265	0.0208	0.1837	72.081	-35.9969	-26.272
20	3.3057	1.6788	-1.1776	2.8762	-0.557	2.9382	-0.0362	0.5576	-0.4038	-0.4964	-0.0903	-0.5623	0.067	0.1671	0.1321	0.348	0.0266	0.0977	0.4609	-0.0196	0.2635	73.6614	-44.4261	-36.8577

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -6 through 189 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 190 through 346 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 347 through 440 )	A
4	X-RAY DIFFRACTION	4	chain 'B' and (resid -6 through 17 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 18 through 59 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 60 through 99 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 100 through 133 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 134 through 165 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 166 through 189 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 190 through 216 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 217 through 322 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 323 through 346 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 347 through 440 )	B
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 1 through 133 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 134 through 346 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 347 through 440 )	C
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1 through 133 )	D
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 134 through 346 )	D
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 347 through 399 )	D
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 400 through 440 )	D

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