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

ID or keywords:

Entry

Database: PDB / ID: 5nyv

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
Similarity search - Function

Biological species

Rhodopseudomonas palustris ATCC 17001 (phototrophic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 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: J.Appl.Crystallogr. / Year: 2017
Title: Protein crystals IR laser ablated from aqueous solution at high speed retain their diffractive properties: applications in high-speed serial crystallography.
Authors: Schulz, E.C. / Kaub, J. / Busse, F. / Mehrabi, P. / Muller-Werkmeister, H.M. / Pai, E.F. / Robertson, W.D. / Miller, R.J.D.

History

Deposition	May 11, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 21, 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: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5nyv.cif.gz	344 KB	Display	PDBx/mmCIF format
PDB format	pdb5nyv.ent.gz	287.8 KB	Display	PDB format
PDBx/mmJSON format	5nyv.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/ny/5nyv ftp://data.pdbj.org/pub/pdb/validation_reports/ny/5nyv	HTTPS FTP

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Related structure data

Similar structure data	5o2g-d 6gxf-d 5k3e-d 5k3b-d 6gxt-d 6mzz-d 3r41-d 6qhz-d 6qi0-d 6gxl-d 3r3u-2 7a42-d 6n00-d 3r3z-1 5tng-1 6qkt-d 5tni-1 5tnr-1 6muh-d 6qhu-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)	42.535, 80.889, 85.633
Angle α, β, γ (deg.)	90.00, 102.72, 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 ATCC 17001 (phototrophic) Gene: RPA1163 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.11 Å³/Da / Density % sol: 41.67 %
Crystal grow	Temperature: 293 K / Method: batch mode / pH: 8.5 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: 0.976 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 12, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 1.6→83.7 Å / Num. obs: 4516925 / % possible obs: 99.7 % / Redundancy: 59.4 % / Net I/σ(I): 4.2

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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: 1.6→83.534 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.08

	R_factor	Num. reflection	% reflection
R_free	0.2193	1995	2.68 %
R_work	0.1926	-	-
obs	0.1933	74331	99.66 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.6→83.534 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4687	0	0	389	5076

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	4877
X-RAY DIFFRACTION	f_angle_d	0.833	6647
X-RAY DIFFRACTION	f_dihedral_angle_d	22.982	2871
X-RAY DIFFRACTION	f_chiral_restr	0.046	682
X-RAY DIFFRACTION	f_plane_restr	0.005	872

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 (%)
1.6-1.64	0.339	140	0.3249	4995	X-RAY DIFFRACTION	96
1.64-1.6844	0.3254	136	0.2917	5114	X-RAY DIFFRACTION	100
1.6844-1.7339	0.274	137	0.253	5144	X-RAY DIFFRACTION	100
1.7339-1.7899	0.2538	141	0.2314	5162	X-RAY DIFFRACTION	100
1.7899-1.8539	0.2599	139	0.2117	5211	X-RAY DIFFRACTION	100
1.8539-1.9281	0.2187	156	0.1891	5127	X-RAY DIFFRACTION	100
1.9281-2.0159	0.2171	139	0.1849	5192	X-RAY DIFFRACTION	100
2.0159-2.1222	0.2486	144	0.2298	5167	X-RAY DIFFRACTION	100
2.1222-2.2551	0.2108	144	0.1929	5169	X-RAY DIFFRACTION	100
2.2551-2.4293	0.2112	138	0.1723	5166	X-RAY DIFFRACTION	100
2.4293-2.6737	0.1913	144	0.1654	5202	X-RAY DIFFRACTION	100
2.6737-3.0607	0.1702	141	0.1605	5198	X-RAY DIFFRACTION	100
3.0607-3.8561	0.1753	147	0.1422	5199	X-RAY DIFFRACTION	100
3.8561-83.6475	0.1642	149	0.1335	5290	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	0.4349	-0.19	-0.5956	1.2923	0.2152	0.8174	0.0106	-0.0081	-0.0078	0.0519	0.011	-0.0032	0.073	-0.0292	-0.0245	0.1362	0.0071	-0.0075	0.1141	0.0709	0.0929	20.0512	-79.3858	147.4798
2	2.5841	-1.0858	0.158	2.4966	-0.9344	1.8544	-0.0271	-0.0907	-0.183	0.0498	0.0231	0.1252	0.0887	-0.0172	-0.011	0.0436	-0.0119	0.0238	0.1371	-0.0043	0.0806	6.0627	-68.7352	144.2735
3	0.1048	0.0061	-0.0143	0.2618	0.0741	0.1505	0.0119	-0.0552	-0.0274	0.0709	0.0129	-0.0253	0.0571	0.0035	0.0215	0.0319	0.0095	-0.0102	0.0445	0.0278	0.0229	20.7876	-69.5734	144.2761
4	1.2785	-0.9596	-0.5943	1.6872	0.8415	2.9473	-0.001	-0.0521	0.0183	0.0984	0.0433	-0.1489	0.0541	0.2192	-0.0382	0.1187	0.0104	-0.0482	0.1591	0.0127	0.0636	27.8058	-69.727	152.5756
5	1.168	0.2686	0.7842	0.3257	0.3027	1.1632	0.0098	-0.056	-0.0754	0.018	-0.0106	0.0082	0.0544	-0.0428	-0.0238	0.0107	0.0035	0.0109	0.0364	0.0135	0.0263	12.8802	-69.7153	139.2634
6	2.8213	-0.5395	-0.2652	2.2935	-0.9638	4.1179	-0.0039	0.1618	0.1239	-0.2136	0.0389	0.3266	-0.0735	-0.3134	-0.0258	0.0494	0.0294	-0.0318	0.0943	0.0074	0.0961	4.7616	-58.9836	126.7137
7	0.0392	-0.0255	0.032	0.0434	-0.0169	0.6615	-0.0062	-0.0851	0.0071	0.0592	0.0134	0.0447	-0.0118	-0.0676	0.0129	0.0366	0.0206	0.017	0.083	-0.0054	0.0395	10.4449	-59.2037	143.8299
8	0.311	-0.0985	0.0052	0.3857	-0.001	0.6	0.0008	-0.0301	0.0578	0.02	0.0075	-0.0091	-0.0628	0.0066	-0.0154	0.0108	-0.001	0.0052	0.0075	-0.0089	0.0221	22.4369	-54.9576	137.6741
9	1.4081	0.934	-0.7995	2.9932	0.2091	4.7509	0.0401	-0.0543	0.0716	0.062	-0.0382	0.0662	-0.1183	-0.0471	0.0114	0.0728	-0.0445	0.0224	0.1038	-0.0358	0.0672	30.9357	-56.8492	118.7645
10	0.3012	0.1293	0.0452	0.4064	0.0484	0.178	-0.0035	0.0127	-0.0201	-0.025	0.0117	0.0153	0.0127	-0.0057	0.0138	0.023	-0.0054	-0.0064	0.0024	-0.0033	0.0303	17.888	-64.931	118.6044
11	2.9964	0.2285	2.1899	0.4372	0.3727	2.1694	0.0204	0.021	-0.0779	-0.0147	0.0148	-0.0316	0.065	0.032	-0.0261	0.0681	-0	0.0004	0.031	0.0053	0.0583	22.3247	-76.3342	122.532
12	0.8368	-0.1795	-0.4084	1.4755	-0.7627	1.0858	0.0063	-0.0268	0.0023	-0.0158	-0.0319	-0.1159	0.0214	0.0767	0.0558	0.0699	0.0465	-0.0197	0.074	-0.0071	0.1301	31.9134	-76.0892	132.1385
13	0.4384	0.231	0.2019	0.4173	0.0909	0.372	0.0256	-0.0053	-0.0788	-0.0135	0.0016	0.0144	0.0589	-0.0059	-0.023	0.0499	-0.0124	-0.0069	0.0082	0.0028	0.0542	15.4074	-77.3711	130.2857
14	0.142	0.1545	0.0681	0.532	0.1479	0.1406	-0.0184	-0.0125	0.029	0.0034	-0.0016	0.0135	-0.0337	-0.0083	-0.0119	0.0327	0.0225	-0.0101	-0.0129	-0.0071	0.0391	15.0092	-57.0033	126.9897
15	0.4623	-0.7201	1.0635	1.1224	-1.6586	2.4528	-0.027	-0.0017	0.0358	0.0234	-0.004	-0.0254	-0.0532	0.0046	0.0203	0.1017	0.009	-0.0164	0.028	-0.0134	0.0906	23.2711	-44.8029	139.9635
16	1.3297	-0.4822	-0.054	0.4463	0.005	0.0032	0.0184	0.1161	0.0017	-0.0376	-0.0153	-0.0615	0.0122	0.0754	-0.0069	0.0297	0.0062	0.0076	0.1003	-0.0283	0.1074	34.9906	-59.2588	134.261
17	2.0314	-0.5657	-0.8239	1.204	-0.1652	1.7196	-0.0053	0.1027	0.0018	-0.1294	0.0201	-0.2205	-0.0698	0.2043	-0.0187	0.0895	-0.0411	-0.0041	0.1258	-0.0411	0.1436	33.8955	-50.6748	134.0885
18	0.5253	-0.5432	0.0689	1.1541	0.3183	0.315	-0.0313	-0.0697	0.1044	0.0693	0.0178	-0.1439	-0.0183	0.0416	-0.0093	0.0346	-0.0064	-0.0059	0.0941	-0.0374	0.1141	33.2804	-53.9882	139.2624
19	0.5104	0.1472	-0.0509	0.6435	0.7045	0.8932	-0.0071	-0.0537	-0.0247	0.055	0.0055	-0.0933	0.0375	0.0895	0.0005	0.0515	0.0399	-0.0331	0.1092	0.0009	0.1258	33.878	-69.4975	140.8477
20	1.4123	0.6881	0.0938	2.6824	0.4908	4.4213	-0.0082	-0.0868	-0.0314	0.1164	0.0261	-0.1387	0.1058	0.1729	-0.0183	0.1129	0.0002	-0.0526	0.1566	-0.0175	0.0738	32.109	-60.7942	151.3058
21	3.0919	-0.5559	-0.3273	0.3857	-0.0408	4.9276	-0.0614	-0.1164	-0.1668	-0.052	0.0296	0.0807	0.3132	-0.2839	0.0277	0.1838	-0.0333	-0.0341	0.2216	-0.073	0.1153	14.3864	-72.8606	83.1074
22	5.0173	0.6517	2.1025	2.7789	-0.0832	3.4525	0.0428	0.1028	-0.1385	-0.0905	-0.0156	0.0645	0.1414	-0.0624	-0.0316	0.1766	0.0188	0.0577	0.1332	-0.0319	0.1138	32.5859	-74.519	85.1754
23	0.1184	-0.0106	-0.0983	0.2427	-0.0322	0.1488	-0.0069	0.0806	-0.0079	-0.0817	-0.0016	0.014	0.0201	-0.0389	0.003	0.0712	-0.0374	0.0039	0.1371	-0.0167	0.0329	21.8386	-64.6481	86.6303
24	1.8993	0.7167	-1.3056	1.1018	-0.5381	3.4467	0.0184	0.1223	0.1335	0.0297	0.0471	0.1035	-0.176	-0.2429	-0.0665	0.1244	-0.0008	-0.0091	0.1692	0.0195	0.0386	17.2945	-58.3096	79.1136
25	0.2125	-0.2771	0.2388	0.7841	-0.2921	1.1881	0.0174	0.0332	-0.0413	-0.0218	-0.0154	0.0386	0.0897	-0.0232	-0.0154	0.0993	-0.0339	0.0158	0.0795	-0.0338	0.0506	27.0634	-71.3965	91.567
26	4.7208	1.5023	2.7214	6.1708	4.3221	9.2225	0.0634	0.0058	-0.2457	0.2648	0.1391	-0.5065	0.2325	0.3183	-0.2008	0.1386	0.0233	0.0168	0.1327	0.0142	0.1378	40.2798	-72.6902	103.99
27	0.1673	-0.0142	0.1582	0.1327	-0.1298	1.4613	0.021	0.0646	0.0043	-0.0556	-0.0106	-0.0143	0.0616	0.0374	-0.0003	0.0795	-0.0063	0.0217	0.0987	-0.0148	0.033	36.2268	-64.7971	89.0288
28	0.4911	-0.0297	-0.0568	0.2681	0.0049	0.6218	0.0119	0.0619	0.0382	-0.0314	-0.006	-0.0235	-0.0531	0.0228	-0.0118	0.0602	-0.0293	0.0115	0.0712	-0.0094	0.0258	30.6216	-54.8695	92.7885
29	1.7	-0.0397	0.2216	2.5963	0.1457	2.7359	0.003	-0.0456	0.1908	0.0478	0.005	0.0769	-0.2166	-0.0579	0.0028	0.1328	0.0045	-0.0019	0.0677	-0.0356	0.0783	29.3333	-51.0797	109.2537
30	0.7954	0.5075	-0.0339	3.264	1.5845	1.5309	-0.0214	0.0703	0.095	-0.1621	0.0122	0.0762	-0.1111	-0.0501	0.0181	0.1131	0.0006	0.0185	0.0334	0.0036	0.0506	20.8718	-54.548	113.8669
31	0.4889	-0.0442	0.1232	1.022	0.0013	0.3709	-0.0031	-0.0375	-0.0762	0.0534	0.0304	0.0259	0.0638	-0.0035	-0.0109	0.06	0.007	0.0053	0.0414	-0.001	0.0347	26.1715	-69.105	112.1445
32	2.1239	-1.3366	0.841	3.4221	-1.9268	2.4841	-0.0012	-0.0424	-0.0954	0.0363	0.0221	0.0861	0.0736	-0.0531	-0.0234	0.0809	-0.0358	0.0038	0.0892	0.0253	0.0669	13.5909	-70.2276	106.6352
33	1.5997	-0.3311	-0.1897	1.8323	1.2033	2.0597	0.0298	0.0084	0.0075	-0.0284	-0.0096	0.0442	-0.053	-0.0872	0.0074	0.0636	-0.0249	-0.0151	0.1186	0.0028	0.0591	9.3793	-64.8339	97.6751
34	0.6631	0.0426	0.3881	1.8474	0.1798	2.3783	0.0518	0.0162	-0.1782	-0.0295	-0.0126	0.0655	0.1534	-0.0508	-0.0242	0.1317	-0.0479	0.0258	0.0638	-0.0287	0.0889	20.8222	-76.7	100.8808
35	0.4414	0.3067	-0.0998	0.7155	-0.2397	0.4519	-0.0074	-0.0224	0.0377	0.0437	-0.0082	-0.0293	-0.0658	0.0397	-0.0058	0.0581	-0.0334	0.0002	0.0603	-0.0325	0.0441	35.5323	-59.84	104.5931
36	1.7248	-0.0627	-0.3076	0.6196	-0.0257	0.691	0.0124	-0.0758	0.0224	0.0462	-0.0248	-0.0122	-0.0393	0.0248	0.0074	0.1367	-0.0046	0.0344	0.0922	0.0173	0.1087	26.1402	-47.7994	94.2927
37	0.8792	0.2956	0.7738	1.5668	0.9388	1.0265	0.0574	-0.3274	-0.0869	0.3193	-0.0532	0.0718	0.0537	-0.0517	-0.0052	0.2654	-0.0011	0.0175	0.2661	0.0101	0.2614	20.9039	-46.4609	104.1629
38	2.0554	0.16	0.0679	0.2976	-0.1196	0.2317	0.0019	-0.0005	0.2468	0.0138	0.0213	0.0472	-0.1469	-0.0547	-0.0036	0.1702	-0.0461	0.0416	0.113	0.0272	0.1514	26.9374	-43.4739	95.1467
39	1.7945	0.3982	0.6829	1.2424	-0.0393	3.0414	-0.0014	0.015	0.1222	-0.0404	-0.0141	0.1284	-0.1359	-0.1622	0.0095	0.0411	0.0176	0.0124	0.1365	0.0258	0.1046	12.1489	-55.5034	94.1406
40	1.7941	1.0509	-0.4047	1.9635	-0.7724	2.9104	0.025	0.1155	0.1692	-0.033	0.0413	0.1344	-0.1214	-0.1643	-0.0635	0.1994	0.0367	-0.0397	0.2146	0.0617	0.1047	18.1666	-49.8009	83.4832

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)
14	X-RAY DIFFRACTION	14	(chain A and resid 212:233)
15	X-RAY DIFFRACTION	15	(chain A and resid 234:244)
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