PDB-5o2g: Crystal structure determination from picosecond infrared laser ab...

ID or keywords:

Entry

Database: PDB / ID: 5o2g

Title

Crystal structure determination from picosecond infrared laser ablated protein crystals by serial synchrotron crystallography

Components

Fluoroacetate dehalogenase

Keywords

HYDROLASE / SSX / PIRL / serial crystallography / fixed target

Function / homology

Function and homology information

haloacetate dehalogenase / haloacetate dehalogenase activity / epoxide hydrolase activity
Similarity search - Function

Biological species

Rhodopseudomonas palustris (phototrophic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Schulz, E.C. / Kaub, J. / Busse, F. / Mehrabi, P. / Mueller-Werkmeiser, H. / Pai, E.F. / Robertson, W.D. / Miller, R.J.D.

Citation

Journal: To Be Published
Title: Crystal structure determination from picosecond infrared laser ablated protein crystals by serial synchrotron crystallography
Authors: Schulz, E.C. / Mehrabi, P. / Pai, E.F. / Miller, R.J.D.

History

Deposition	May 20, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 30, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2019	Group: Data collection / Category: reflns_shell
Revision 1.2	May 8, 2024	Group: Advisory / Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5o2g.cif.gz	255 KB	Display	PDBx/mmCIF format
PDB format	pdb5o2g.ent.gz	207.6 KB	Display	PDB format
PDBx/mmJSON format	5o2g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5o2g_validation.pdf.gz	437.4 KB	Display	wwPDB validaton report
Full document	5o2g_full_validation.pdf.gz	446.6 KB	Display
Data in XML	5o2g_validation.xml.gz	28.2 KB	Display
Data in CIF	5o2g_validation.cif.gz	41.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o2/5o2g ftp://data.pdbj.org/pub/pdb/validation_reports/o2/5o2g	HTTPS FTP

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Related structure data

Similar structure data	5nyv-d 6qi0-d 6gxl-d 5k3e-d 6gxf-d 5k3b-d 3r3u-2 6qkt-d 6gxt-d 3r41-d 5t4t-d 7a42-d 3r3x-d 6qhx-d 3r3z-1 5tnn-1 6mzz-d 6qhu-d 6kxr-1 6n00-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	#165 - Sep 2013 Designed Protein Cages similarity (3) #220 - Apr 2018 Dehalogenases similarity (3) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: Fluoroacetate dehalogenase

B: Fluoroacetate dehalogenase

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	42.413, 80.349, 85.648
Angle α, β, γ (deg.)	90.00, 102.96, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Fluoroacetate dehalogenase Mass: 34073.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Gene: RPA1163 / Production host: Escherichia coli (E. coli) References: UniProt: Q6NAM1, UniProt: A0A2R4GQN1*PLUS, haloacetate dehalogenase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.09 Å³/Da / Density % sol: 41.06 %
Crystal grow	Temperature: 293 K / Method: batch mode Details: 18-20 % (w/v) PEG3350, 200 mM CaCl2, and 100 mM Tris-HCl pH 8.5

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Data collection

Diffraction	Mean temperature: 293 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97627 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97627 Å / Relative weight: 1
Reflection	Resolution: 2.1→83.5 Å / Num. obs: 32773 / % possible obs: 99.9 % / Redundancy: 9.1 % / Net I/σ(I): 3

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2666: ???)	refinement
cctbx.xfel		data reduction
cctbx.prime		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→83.467 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.65 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.27	1626	4.97 %
R_work	0.2223	-	-
obs	0.2247	32749	99.84 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1→83.467 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4676	0	0	445	5121

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	4857
X-RAY DIFFRACTION	f_angle_d	0.8	6617
X-RAY DIFFRACTION	f_dihedral_angle_d	15.055	3931
X-RAY DIFFRACTION	f_chiral_restr	0.047	679
X-RAY DIFFRACTION	f_plane_restr	0.005	867

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.1-2.1618	0.3557	130	0.3163	2576	X-RAY DIFFRACTION	99
2.1618-2.2316	0.3338	139	0.282	2591	X-RAY DIFFRACTION	100
2.2316-2.3114	0.2789	138	0.2563	2545	X-RAY DIFFRACTION	100
2.3114-2.4039	0.3107	137	0.2568	2581	X-RAY DIFFRACTION	100
2.4039-2.5133	0.2965	138	0.2522	2603	X-RAY DIFFRACTION	100
2.5133-2.6459	0.2807	140	0.2387	2572	X-RAY DIFFRACTION	100
2.6459-2.8116	0.2787	128	0.2306	2591	X-RAY DIFFRACTION	100
2.8116-3.0287	0.2832	135	0.2256	2610	X-RAY DIFFRACTION	100
3.0287-3.3335	0.2548	136	0.2184	2572	X-RAY DIFFRACTION	100
3.3335-3.8159	0.2258	136	0.1889	2611	X-RAY DIFFRACTION	100
3.8159-4.8076	0.2246	135	0.1606	2610	X-RAY DIFFRACTION	100
4.8076-83.5331	0.255	134	0.1949	2661	X-RAY DIFFRACTION	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	0.2126	0.0785	-0.1279	0.0565	0.0203	0.2631	-0.0025	0.0866	-0.0165	-0.0497	-0.0303	-0.0533	0.1295	-0.0265	-0.0102	0.4958	0.0225	0.0413	0.3088	0.156	0.1513	19.0172	-79.6064	147.1884
2	3.901	-1.8396	-1.8792	3.3376	-0.4233	3.1329	-0.245	-0.2576	-0.3311	0.0901	-0.0276	0.274	0.2985	0.0697	0.0777	0.0616	-0.0983	0.0527	0.2293	-0.0804	0.2289	5.0382	-69.005	143.9693
3	0.9577	-0.1162	-1.0222	0.4431	0.2821	1.3866	-0.0523	-0.317	-0.0909	0.016	0.0572	-0.0805	0.1762	0.3383	0.1113	0.0929	0.0098	0.0183	0.1297	0.1007	0.1054	19.9115	-69.8029	144.1769
4	0.0658	-0.1437	-0.0006	0.3953	0.0256	0.7117	-0.0351	-0.0833	-0.0106	0.1331	0.0181	-0.1313	0.0911	0.132	0.0548	0.2251	0.132	-0.0477	0.3916	0.1151	0.0842	26.9236	-70.045	152.5913
5	1.4523	0.5119	0.973	0.5325	0.1603	2.451	-0.0185	-0.0533	-0.1066	0.0695	0.017	0.0457	0.2402	-0.1288	-0.0143	0.1634	-0.0217	-0.024	0.192	-0.0155	0.0536	12.0805	-69.8647	139.0753
6	2.1287	0.054	-1.0846	1.3125	-0.8884	2.1629	0.0303	0.1058	0.1075	-0.0033	0.1253	0.1716	-0.0717	-0.2289	0.1082	0.1788	0.0425	0.1321	0.3225	0.0252	0.2346	4.0245	-59.0637	126.5746
7	0.4365	0.0733	-0.2883	0.3298	0.0724	1.489	-0.0054	-0.0882	-0.0675	0.0716	0.0659	0.1121	-0.0308	-0.0952	-0.0999	0.0755	0.0285	0.1155	0.1251	0.0448	0.0112	9.8297	-59.3698	143.6537
8	0.4625	-0.0961	0.1105	0.155	-0.0212	0.3851	0.0552	-0.1198	0.0163	-0.009	-0.0094	-0.0468	0.0612	-0.0083	0.4206	0.0379	0.055	-0.076	0.2219	0.0078	0.0043	21.6921	-55.1575	137.6606
9	0.4361	0.5653	0.4581	1.8029	0.6911	2.5423	0.0445	-0.172	0.1707	0.1625	-0.1075	0.0048	-0.2062	-0.0493	0.1194	0.1981	-0.1237	-0.0353	0.2105	-0.1149	0.1642	30.3492	-56.8529	118.4634
10	0.1476	-0.0489	0.0736	0.1914	0.1616	0.2496	-0.016	0.1084	0.1028	-0.0682	0.1165	-0.0011	-0.0469	-0.0764	0.0215	0.1395	-0.0415	0.019	0.0978	0.0441	0.0779	17.1571	-65.1252	118.4864
11	2.8185	0.2755	1.2554	0.0615	-0.1288	2.4251	-0.0032	0.065	-0.1629	0.041	0.068	-0.0978	0.152	0.0413	-0.0523	0.1233	0.1396	0.019	0.1127	-0.0689	0.1592	21.6124	-76.4115	122.4509
12	2.2128	0.0428	-0.7653	2.0401	-1.1405	2.2202	0.0442	-0.0027	0.0779	0.0114	-0.0932	-0.263	0.0279	0.2493	0.1079	0.1743	0.0886	-0.0495	0.1897	0.0419	0.2753	31.1416	-76.2868	132.0881
13	0.5799	0.6067	0.2604	0.6816	0.2908	2.0676	0.0206	-0.184	-0.1984	0.0227	-0.0354	0.0582	0.3799	-0.0942	-0.0443	0.1501	0.0339	0.0557	0.2404	0.0725	0.1453	14.7038	-77.4824	130.0262
14	0.6659	0.2492	-0.1006	2.4307	0.7606	0.7011	0.0772	0.1868	0.1497	-0.0234	-0.0918	-0.2166	-0.1652	0.016	-0.0565	0.0927	0.0207	-0.0272	0.0622	0.0063	0.0617	14.3614	-57.1287	126.9026
15	0.0102	-0.0063	0.0417	0.0175	-0.0616	0.2812	-0.0482	-0.0329	0.0442	0.0247	0.0001	0.0538	-0.0502	-0.0046	-0.1181	0.2039	0.053	0.019	0.1419	-0.1467	0.1229	22.5292	-45.0133	139.9644
16	2.3314	-0.8095	0.4101	2.9601	1.1891	0.7346	0.0778	0.3101	0.0557	-0.5007	-0.0997	0.0567	-0.2293	0.1956	-0.0308	0.261	0.0744	-0.0691	0.3007	-0.063	0.1531	34.2829	-59.5229	134.3396
17	3.2788	-0.409	-0.6194	2.1449	-0.2851	0.1787	0.1072	0.2684	0.0182	-0.0877	0.053	-0.5052	0.0679	0.2249	-0.0919	0.1031	0.0511	0.0093	0.3937	-0.0294	0.2538	33.368	-50.9914	134.1289
18	0.9204	-0.5837	-0.2064	2.3594	0.9426	0.9074	-0.0584	-0.2806	0.1222	0.1513	0.23	-0.3014	-0.141	0.4443	-0.1387	0.2278	-0.0226	0.0546	0.3596	-0.0532	0.1332	32.557	-54.2487	139.3899
19	2.034	0.7975	1.398	1.592	1.1159	3.9295	-0.0541	-0.3579	-0.0227	0.2517	0.1959	-0.2979	0.1319	0.2998	-0.0704	0.1475	0.1167	-0.0083	0.2963	-0.0412	0.122	33.0573	-69.8315	140.9502
20	0.0805	0.07	0.1358	0.2674	-0.115	0.4862	-0.0037	-0.1452	-0.0671	0.1762	0.0729	-0.2356	0.1034	0.1997	0.0812	0.0823	0.0582	-0.0921	0.2164	0.0359	0.1345	31.2536	-61.2039	151.0992
21	3.725	0.1636	-0.6754	2.1229	0.1719	5.8226	-0.0984	0.0116	-0.3001	0.0163	0.058	0.143	0.5886	-0.4718	0.0225	0.3628	-0.0648	0.0593	0.409	-0.007	0.1729	13.8567	-73.0196	83.1439
22	2.6938	1.9273	2.3462	2.9483	0.919	2.8128	0.1331	0.1983	-0.2292	-0.0798	-0.0591	-0.0634	0.1849	-0.1449	-0.0307	0.2559	0.0386	0.0194	0.1758	0.0101	0.2204	32.0504	-74.7788	85.0777
23	0.3566	0.2533	-0.4046	0.575	-0.5004	0.8095	-0.0333	0.2134	-0.0964	-0.1006	0.1467	0.0855	0.237	-0.347	-0.048	0.1298	-0.025	0.0152	0.1819	-0.0104	0.08	21.2748	-64.8671	86.444
24	1.7191	0.9591	-1.9062	1.6584	-0.0527	3.0124	-0.0244	0.4646	0.2187	-0.2354	0.0522	0.1545	-0.1698	-0.4563	-0.0909	0.1852	-0.0424	0.0139	0.2648	0.0642	0.1202	16.7213	-58.6465	78.8265
25	0.2398	0.1451	0.0743	0.3381	-0.3593	0.6951	-0.0179	-0.0402	-0.1793	-0.0351	0.0215	-0.0453	0.1671	-0.0786	0.0651	0.0636	-0.1094	0.0889	0.0763	-0.0221	0.1504	26.4327	-71.6046	91.4233
26	4.691	4.8995	2.3287	5.9053	3.4049	3.4735	0.0211	-0.5092	-0.0426	0.1915	0.0643	-0.5948	0.0339	0.3314	-0.0795	0.0689	-0.0021	-0.0187	0.4802	0.0077	0.3812	39.4669	-72.6307	103.8595
27	0.1128	0.0728	-0.0342	0.2337	0.1059	0.5176	0.0176	0.1172	-0.0708	0.2215	0.0081	-0.0286	0.1932	-0.0017	0.1067	0.1917	-0.0244	0.0307	0.083	0.0589	-0.1533	35.6427	-65.0509	88.9783
28	1.0693	-0.0636	-0.4797	0.6795	-0.1165	1.5473	0.0539	-0.0861	0.07	-0.0852	0.0649	-0.0734	0.0721	0.1383	-0.1149	0.1265	-0.0249	-0.024	0.1392	0.0062	0.0724	30.0267	-55.0486	92.617
29	2.87	-1.2666	0.3916	5.0141	0.9017	1.8631	0.1262	-0.1482	0.3511	0.2394	0.1774	0.2316	-0.369	-0.1739	-0.2311	0.2261	-0.0097	0.0453	0.2433	-0.0209	0.2167	28.7266	-51.3026	109.0245
30	0.9505	1.3171	1.1183	3.6747	1.9272	2.3871	-0.0708	0.2276	0.0525	-0.278	0.1414	-0.0354	-0.3405	-0.011	-0.0837	0.234	0.0995	0.0959	0.285	-0.0001	0.0211	20.3207	-54.5706	113.8746
31	1.147	-0.6234	0.4559	1.1476	-0.0454	1.3288	0.1096	-0.0147	-0.0343	-0.0013	0.0129	0.1882	0.1254	0.1797	-0.0857	0.115	-0.0098	0.0017	0.1245	0.0447	0.0772	25.5442	-69.2385	112.0511
32	3.9896	-2.1966	0.1671	4.6337	-2.1517	4.331	0.0435	-0.0916	-0.2317	-0.0264	0.0839	0.0942	0.3503	-0.1669	-0.0891	0.1513	-0.0174	-0.0096	0.1304	-0.0132	0.0976	13.0015	-70.4085	106.5081
33	0.7153	-0.2005	0.1011	1.0473	0.4534	0.2821	-0.007	-0.0822	0.0358	-0.1496	-0.0046	0.2776	-0.0256	-0.1505	0.084	0.0829	-0.0378	-0.0615	0.3098	-0.0406	0.1477	8.7438	-65.0661	97.3215
34	0.4072	0.6394	1.091	1.7965	0.6882	4.2227	0.0635	0.1443	-0.2934	-0.007	-0.0929	0.1025	0.3698	-0.1771	-0.0179	0.2043	-0.0621	0.0418	0.1831	-0.0861	0.1687	20.1355	-76.9084	100.7927
35	1.8657	0.6985	-0.3884	2.6694	-0.4385	1.3519	-0.0327	0.0009	-0.0335	0.2738	0.0679	-0.1636	-0.2535	0.2265	-0.0371	0.1358	-0.0168	0.003	0.1419	-0.0298	0.068	35.2366	-59.6823	104.3467
36	2.5651	-0.6026	0.047	0.7925	0.4289	0.3245	0.1055	-0.1833	-0.1483	-0.0019	0.065	-0.1317	-0.1108	-0.052	-0.0732	0.3418	0.0513	-0.0101	0.0162	0.0751	0.1649	25.5211	-47.9729	94.0553
37	3.9749	1.5413	-3.7828	0.8148	-1.4374	3.6039	0.0913	-0.3847	-0.2813	0.4006	-0.1869	0.4284	0.3103	-0.2976	0.1123	0.2312	-0.0733	0.0729	0.6419	0.1786	0.4028	20.1476	-46.143	102.982
38	0.4714	0.0772	0.2468	0.8902	0.5551	1.4986	0.059	0.0008	0.1881	-0.1587	0.016	0.0537	-0.3905	-0.0784	0.1348	0.2349	-0.0081	0.0844	0.0904	-0.0639	0.2372	26.4189	-43.5797	94.9004
39	2.4151	1.3216	1.4788	3.2961	-0.4432	4.0881	-0.1217	0.0881	0.3084	-0.2202	0.0125	0.4371	-0.4172	-0.5551	-0.0125	0.2383	0.0762	-0.0044	0.2742	0.0098	0.116	11.5726	-55.6486	93.933
40	6.1845	2.8128	-3.2875	4.1324	-1.5463	6.2018	0.1861	0.4258	0.2391	-0.1844	0.1199	0.288	-0.2531	-0.4376	-0.2725	0.2872	0.1256	-0.0023	0.2366	0.0379	0.1813	17.5517	-49.9848	83.3172

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 4:13)
2	X-RAY DIFFRACTION	2	(chain A and resid 14:23)
3	X-RAY DIFFRACTION	3	(chain A and resid 24:48)
4	X-RAY DIFFRACTION	4	(chain A and resid 49:59)
5	X-RAY DIFFRACTION	5	(chain A and resid 60:74)
6	X-RAY DIFFRACTION	6	(chain A and resid 75:81)
7	X-RAY DIFFRACTION	7	(chain A and resid 82:103)
8	X-RAY DIFFRACTION	8	(chain A and resid 104:144)
9	X-RAY DIFFRACTION	9	(chain A and resid 145:152)
10	X-RAY DIFFRACTION	10	(chain A and resid 153:169)
11	X-RAY DIFFRACTION	11	(chain A and resid 170:182)
12	X-RAY DIFFRACTION	12	(chain A and resid 183:199)
13	X-RAY DIFFRACTION	13	(chain A and resid 200:211)
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