PDB-6muy: Fluoroacetate dehalogenase, room temperature structure solved by ...

ID or keywords:

Entry

Database: PDB / ID: 6muy

Title

Fluoroacetate dehalogenase, room temperature structure solved by serial 3 degree oscillation crystallography

Components

Fluoroacetate dehalogenase

Keywords

HYDROLASE / Dehalogenase / defluorinase

Function / homology

Function and homology information

haloacetate dehalogenase / haloacetate dehalogenase activity
Similarity search - Function

Biological species

Rhodopseudomonas palustris (phototrophic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Finke, A.D. / Wierman, J.L. / Pare-Labrosse, O. / Sarrachini, A. / Besaw, J. / Mehrabi, P. / Gruner, S.M. / Miller, R.J.D.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM-103485	United States
National Science Foundation (NSF, United States)	DMR-1332208	United States

Citation

Journal: IUCrJ / Year: 2019
Title: Fixed-target serial oscillation crystallography at room temperature.
Authors: Wierman, J.L. / Pare-Labrosse, O. / Sarracini, A. / Besaw, J.E. / Cook, M.J. / Oghbaey, S. / Daoud, H. / Mehrabi, P. / Kriksunov, I. / Kuo, A. / Schuller, D.J. / Smith, S. / Ernst, O.P. / ...

History

Deposition	Oct 24, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 27, 2019	Provider: repository / Type: Initial release
Revision 1.1	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Oct 11, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6muy.cif.gz	255.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6muy.ent.gz	204.9 KB	Display	PDB format
PDBx/mmJSON format	6muy.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6muy_validation.pdf.gz	434.7 KB	Display	wwPDB validaton report
Full document	6muy_full_validation.pdf.gz	440.1 KB	Display
Data in XML	6muy_validation.xml.gz	24.4 KB	Display
Data in CIF	6muy_validation.cif.gz	34.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mu/6muy ftp://data.pdbj.org/pub/pdb/validation_reports/mu/6muy	HTTPS FTP

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Related structure data

Related structure data	6muhC 6muzC 6mv0C 6mzzC 6n00C 6n02C 6n03C 6fsxS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6n00-d 6mzz-d 7a42-d 6gxt-d 6gxf-d 6qhz-d 6qhw-d 5nyv-d 5tni-1 6qhu-d 5k3e-d 6qn5-2 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	#220 - Apr 2018 Dehalogenases similarity (4) #165 - Sep 2013 Designed Protein Cages similarity (3) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: Fluoroacetate dehalogenase

B: Fluoroacetate dehalogenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	41.600, 79.100, 83.800
Angle α, β, γ (deg.)	90.00, 103.00, 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 (strain ATCC BAA-98 / CGA009) (phototrophic) Strain: ATCC BAA-98 / CGA009 / Gene: RPA1163 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 217 / 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: 1.97 Å³/Da / Density % sol: 37.61 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.5 mM defluorinase with a mother liquor of 16-20% PEG 3350, 100mM Tris-Cl pH 8.5, and 200mM CaCl2

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Data collection

Diffraction	Mean temperature: 298 K / Serial crystal experiment: Y
Diffraction source	Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1.2155 Å
Detector	Type: DECTRIS EIGER X 1M / Detector: PIXEL / Date: Mar 2, 2018 / Details: Be compound refractive lens
Radiation	Monochromator: W/B4C multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.2155 Å / Relative weight: 1
Reflection	Resolution: 1.8→39.55 Å / Num. obs: 48608 / % possible obs: 99.02 % / Redundancy: 12.6 % / CC_1/2: 0.992 / R_rim(I) all: 0.2694 / Net I/σ(I): 6.65
Reflection shell	Resolution: 1.8→1.864 Å / Num. unique obs: 4676 / CC_1/2: 0.106
Serial crystallography sample delivery	Description: fixed target on Si microchips / Method: fixed target
Serial crystallography sample delivery fixed target	Details: 3 degree oscillation per sample / Motion control: Geobrick LV-IMS-II / Sample holding: Si microchip / Support base: goniometer
Serial crystallography data reduction	Frame hits: 48690 / Frames indexed: 34800 / Frames total: 201165 / Lattices indexed: 2320

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6FSX

6fsx

Resolution: 1.8→39.55 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.42

	R_factor	Num. reflection	% reflection
R_free	0.1985	2422	4.99 %
R_work	0.1631	-	-
obs	0.1649	48560	99.03 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→39.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4704	0	1	217	4922

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4914
X-RAY DIFFRACTION	f_angle_d	0.966	6698
X-RAY DIFFRACTION	f_dihedral_angle_d	16.095	3964
X-RAY DIFFRACTION	f_chiral_restr	0.05	684
X-RAY DIFFRACTION	f_plane_restr	0.006	879

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 (%)
1.8001-1.8368	0.5241	138	0.5046	2562	X-RAY DIFFRACTION	95
1.8368-1.8768	0.4802	141	0.3997	2670	X-RAY DIFFRACTION	98
1.8768-1.9204	0.3687	144	0.3644	2707	X-RAY DIFFRACTION	99
1.9204-1.9685	0.3378	141	0.2942	2715	X-RAY DIFFRACTION	99
1.9685-2.0217	0.3098	142	0.2642	2667	X-RAY DIFFRACTION	99
2.0217-2.0812	0.3003	146	0.2469	2764	X-RAY DIFFRACTION	99
2.0812-2.1483	0.3104	134	0.2336	2658	X-RAY DIFFRACTION	99
2.1483-2.2251	0.2588	142	0.2106	2717	X-RAY DIFFRACTION	99
2.2251-2.3142	0.242	144	0.1866	2754	X-RAY DIFFRACTION	100
2.3142-2.4195	0.2028	144	0.1645	2717	X-RAY DIFFRACTION	99
2.4195-2.547	0.1876	141	0.1595	2699	X-RAY DIFFRACTION	99
2.547-2.7066	0.2337	142	0.1566	2727	X-RAY DIFFRACTION	100
2.7066-2.9155	0.2179	143	0.1586	2731	X-RAY DIFFRACTION	100
2.9155-3.2088	0.182	146	0.1501	2773	X-RAY DIFFRACTION	100
3.2088-3.6729	0.1771	144	0.1271	2717	X-RAY DIFFRACTION	100
3.6729-4.6264	0.1223	144	0.1099	2789	X-RAY DIFFRACTION	100
4.6264-40.8366	0.1637	146	0.1414	2771	X-RAY DIFFRACTION	99

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	2.0732	0.0222	-0.0031	1.7706	1.0248	1.4185	-0.0876	-0.368	0.01	0.3331	-0.0732	0.0305	0.5789	-0.2078	0.1063	0.4182	0.0236	0.0159	0.376	0.0635	0.2758	-18.0297	-73.4325	103.464
2	0.2431	0.1764	-0.7696	1.0998	0.3455	3.1554	-0.1703	-0.2648	-0.0439	0.1019	0.1023	-0.0463	0.3464	0.4872	0.0166	0.3427	0.1315	-0.0128	0.3821	0.0257	0.2952	-9.1825	-72.0373	101.702
3	1.4178	0.2123	-0.5245	1.1788	0.1147	3.0325	0.0252	-0.0609	0.0808	0.0045	-0.0089	0.1265	0.0383	-0.3816	-0.0009	0.2021	0.0263	0.0043	0.2551	-0.0091	0.2759	-23.1781	-64.158	95.1316
4	1.3661	0.1355	0.4537	1.0476	0.2773	1.3807	0.0171	-0.2522	0.229	0.1146	0.1481	-0.1116	-0.1202	0.023	-0.1535	0.2376	0.0381	0.0006	0.243	-0.0198	0.2611	-11.6761	-58.283	96.6174
5	0.4089	-0.289	-0.5057	1.2814	0.1516	1.7396	-0.0053	0.1181	0.0342	-0.0771	0.1865	-0.0603	-0.1399	0.2929	-0.193	0.267	0.0003	-0.0013	0.2204	-0.0129	0.2605	-8.7148	-59.9932	77.6024
6	1.7458	-0.9375	0.2149	1.182	-0.2994	2.2901	-0.156	0.015	-0.3185	0.1371	0.188	-0.1416	0.5415	0.3032	-0.0605	0.3463	0.0683	0.0069	0.2168	0.0055	0.3228	-8.8719	-77.5674	83.7083
7	1.109	0.0335	-0.0172	2.1971	0.8139	1.6836	0.0047	0.0881	0.1919	0.1009	-0.0372	0.1454	-0.1996	-0.1521	0.0218	0.271	0.0269	-0.0021	0.2206	0.0149	0.2762	-18.4028	-60.0749	83.6428
8	1.7744	-0.6973	-0.3461	2.0649	0.1737	1.1809	0.2371	-0.1075	-0.1218	-0.3819	-0.0433	-0.1492	-0.2593	0.5628	-0.1683	0.323	0.0256	-0.0074	0.4013	-0.0845	0.3777	-2.7625	-55.4738	93.0666
9	1.8436	-0.074	-0.0452	1.758	0.8052	2.0812	-0.0926	-0.4018	0.0813	0.2724	0.3179	-0.4694	0.0796	0.7873	-0.182	0.2851	0.0662	-0.0463	0.558	-0.0651	0.3634	-0.1461	-61.1984	98.0956
10	2.989	-0.0586	-1.262	1.818	-0.0936	3.187	0.0371	0.3524	-0.1767	-0.1208	-0.0748	0.0424	0.3698	-0.2878	0.0206	0.3397	-0.0327	-0.0051	0.3461	-0.0551	0.288	-8.6097	-69.6914	44.9126
11	1.8875	0.2059	0.2694	0.8024	-0.2736	1.9799	0.1032	0.3066	0.2141	-0.0775	-0.0705	-0.04	-0.1546	0.1141	-0.0148	0.2636	0.0064	0.0099	0.2778	0.0092	0.2602	-0.8236	-60.6108	46.7293
12	1.332	-0.1919	-0.9729	0.4544	0.2377	1.9503	0.1238	0.0255	0.1857	-0.1143	0.0643	0.0235	-0.3047	-0.0046	-0.1787	0.3425	-0.0033	-0.0013	0.2987	-0.0073	0.3066	-7.2269	-59.2185	67.9131
13	3.4611	-2.0561	1.8547	2.0692	-1.2371	2.6475	0.0017	-0.2617	-0.1425	-0.0078	0.228	0.2823	0.2691	-0.4031	-0.1997	0.3116	-0.0098	0.003	0.3594	0.0221	0.3093	-16.2727	-72.0964	64.9834
14	3.5606	-0.2371	0.0521	0.754	0.1252	2.9508	0.1052	0.3573	-0.1734	-0.2402	-0.062	-0.0117	0.3226	-0.4517	-0.0311	0.3164	-0.0847	0.0167	0.3569	-0.0627	0.3254	-22.0131	-70.4349	54.3352
15	2.1619	0.8598	-0.6601	2.0371	-1.4732	1.4774	0.0373	-0.2424	0.0493	0.1863	-0.0878	-0.1584	-0.1113	0.1405	0.075	0.2878	0.0053	-0	0.3138	-0.0466	0.249	0.1212	-65.3911	61.2324
16	5.3636	1.334	0.3049	1.0251	-0.5368	0.5586	0.3582	-0.5788	0.4606	0.2079	-0.1928	0.2163	-0.6447	-0.1061	-0.1898	0.4517	-0.0263	0.0594	0.3601	0.0028	0.4615	-7.6829	-49.4065	53.8742
17	1.8546	0.2252	-1.1482	1.8077	0.2251	2.0974	0.1286	0.4544	0.5881	-0.1065	0.079	0.2105	-0.5228	-0.4943	-0.1697	0.3949	0.0696	0.0207	0.3744	0.0934	0.3834	-13.071	-51.1461	48.4718

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 37 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 38 through 63 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 64 through 104 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 105 through 137 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 138 through 164 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 165 through 208 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 209 through 235 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 236 through 259 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 260 through 300 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 3 through 84 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 85 through 137 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 138 through 164 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 165 through 185 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 186 through 208 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 209 through 235 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 236 through 259 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 260 through 300 )

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