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

ID or keywords:

Entry

Database: PDB / ID: 6muh

Title

Fluoroacetate dehalogenase, room temperature structure solved by serial 1 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 23, 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 / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6muh.cif.gz	253.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6muh.ent.gz	204.1 KB	Display	PDB format
PDBx/mmJSON format	6muh.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6muh_validation.pdf.gz	428.2 KB	Display	wwPDB validaton report
Full document	6muh_full_validation.pdf.gz	431.6 KB	Display
Data in XML	6muh_validation.xml.gz	23.6 KB	Display
Data in CIF	6muh_validation.cif.gz	33.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mu/6muh ftp://data.pdbj.org/pub/pdb/validation_reports/mu/6muh	HTTPS FTP

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Related structure data

Related structure data	6muyC 6muzC 6mv0C 6mzzC 6n00C 6n02C 6n03C 6fsxS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6qi1-d 7a42-d 6qhu-d 6qhs-d 5k3e-d 6gxt-d 6qhz-d 6n00-d 6mzz-d 6qi0-d 3r3z-1 5k3b-d 6gxf-d 5nyv-d 6qhw-d 5o2i-d 5o2g-d 6qi3-d 4yx9-2 3r3v-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	#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

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

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 BL21(DE3) (bacteria) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H₂O

#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 BL21(DE3) (bacteria) / References: UniProt: Q6NAM1, haloacetate dehalogenase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 211 / 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: F3 / Wavelength: 1.2155 Å
Detector	Type: DECTRIS EIGER X 1M / Detector: PIXEL / Date: Mar 4, 2018
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→40.826 Å / Num. obs: 48288 / % possible obs: 98.42 % / Redundancy: 6.3 % / CC_1/2: 0.993 / R_rim(I) all: 0.188 / Net I/σ(I): 9.33
Reflection shell	Resolution: 1.8→1.864 Å / Num. unique obs: 4597 / CC_1/2: 0.176 / R_rim(I) all: 0.03651
Serial crystallography sample delivery	Description: fixed target Si microchips / Method: fixed target
Serial crystallography sample delivery fixed target	Description: Si wafers / Details: oscillation 1 degree per crystal / Motion control: Geobrick LV-IMS-II / Sample dehydration prevention: mylar windows / Sample holding: wells on silicon wafers / Sample unit size: 50 µm / Support base: piezoelectric translation stage on goniometer
Serial crystallography data reduction	Frames indexed: 2269 / Frames total: 67055

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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→40.826 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.98

	R_factor	Num. reflection	% reflection
R_free	0.1813	2413	5 %
R_work	0.1518	-	-
obs	0.1533	48271	98.43 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→40.826 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4712	0	0	211	4923

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4924
X-RAY DIFFRACTION	f_angle_d	0.96	6713
X-RAY DIFFRACTION	f_dihedral_angle_d	16.005	3978
X-RAY DIFFRACTION	f_chiral_restr	0.051	688
X-RAY DIFFRACTION	f_plane_restr	0.006	884

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 (%)
1.8-1.8368	0.4176	133	0.385	2520	X-RAY DIFFRACTION	93
1.8368-1.8767	0.3231	138	0.3221	2629	X-RAY DIFFRACTION	97
1.8767-1.9204	0.3006	140	0.276	2678	X-RAY DIFFRACTION	97
1.9204-1.9684	0.3138	141	0.2469	2682	X-RAY DIFFRACTION	98
1.9684-2.0216	0.2693	140	0.2343	2660	X-RAY DIFFRACTION	98
2.0216-2.0811	0.2607	144	0.2224	2740	X-RAY DIFFRACTION	99
2.0811-2.1483	0.2665	140	0.1977	2653	X-RAY DIFFRACTION	99
2.1483-2.225	0.1951	142	0.1714	2699	X-RAY DIFFRACTION	99
2.225-2.3141	0.2174	144	0.1665	2736	X-RAY DIFFRACTION	99
2.3141-2.4194	0.186	143	0.1513	2715	X-RAY DIFFRACTION	99
2.4194-2.547	0.2041	142	0.1556	2697	X-RAY DIFFRACTION	99
2.547-2.7065	0.203	143	0.1499	2714	X-RAY DIFFRACTION	99
2.7065-2.9154	0.2043	143	0.1525	2725	X-RAY DIFFRACTION	99
2.9154-3.2087	0.1455	146	0.1388	2767	X-RAY DIFFRACTION	100
3.2087-3.6728	0.1579	143	0.1165	2706	X-RAY DIFFRACTION	99
3.6728-4.6263	0.1095	146	0.1043	2775	X-RAY DIFFRACTION	99
4.6263-40.8366	0.1491	145	0.1261	2762	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	1.8434	-0.1826	-0.2157	3.2586	0.7752	4.3817	-0.0293	-0.3939	-0.1214	0.3097	0.0491	-0.0787	0.4238	0.1151	-0.0383	0.2204	0.0275	0.0028	0.2315	0.0514	0.1913	-13.9274	-72.7836	102.8325
2	1.5945	0.1229	-0.1507	2.3043	0.6494	7.3975	0.0464	-0.1315	0.0192	0.0187	-0.0233	0.1539	-0.0777	-0.4254	-0.0246	0.1178	0.0167	0.01	0.2126	-0.0102	0.2446	-23.1513	-64.05	95.0776
3	2.4776	-0.0167	0.1383	3.5391	0.5443	5.5206	0.0303	-0.262	0.2283	0.1902	-0.0201	-0.0977	-0.1634	0.0143	-0.0096	0.1545	0.0008	0.0028	0.1841	-0.0156	0.1941	-11.6208	-58.2942	96.5973
4	0.9795	-0.4059	-0.7732	0.8265	1.1566	3.971	0.0421	0.0596	0.1281	-0.0279	0.1732	-0.1073	-0.099	0.4213	-0.2167	0.2326	0.0016	0.0014	0.1995	0.013	0.2461	-8.6484	-59.9483	77.5797
5	4.0493	-1.4615	2.437	2.2147	-0.9387	4.5958	0.0178	0.1869	-0.1468	-0.0583	0.0429	-0.1612	0.4376	0.2954	-0.093	0.24	0.0313	0.0258	0.1596	-0.0041	0.2683	-9.2901	-77.956	83.6558
6	1.6968	1.0003	0.6343	2.4532	1.3997	2.1216	-0.0237	0.0247	0.1853	-0.0603	-0.0301	0.1428	-0.213	-0.0704	0.0421	0.1811	0.0388	0.0055	0.1598	0.0105	0.201	-18.6251	-60.6111	83.643
7	6.384	-4.292	-1.3346	7.6337	0.5255	3.3641	0.109	-0.0124	0.2608	-0.2144	-0.0681	-0.4332	-0.2357	0.5725	-0.0815	0.2436	-0.0621	-0.0077	0.3089	-0.0416	0.3244	-1.9522	-54.1966	94.0968
8	2.8708	-1.7054	-1.2936	5.1445	2.1769	2.5261	-0.0175	-0.4427	-0.0314	0.5647	0.2887	-0.4947	0.3025	0.7275	-0.2376	0.2025	0.0415	-0.0494	0.4264	0.0053	0.3033	0.1993	-67.5644	99.9673
9	3.6058	0.21	-1.3566	1.4856	-0.3194	4.731	0.0233	0.59	-0.133	-0.2759	-0.0222	0.0964	0.2701	-0.4742	-0.0142	0.2772	-0.0386	-0.0097	0.3525	-0.0503	0.1957	-11.367	-67.8732	41.0846
10	2.6831	1.3459	-1.1067	3.1491	-1.8312	8.3339	0.0325	0.0163	-0.2042	0.0458	-0.1161	-0.0963	0.4655	0.4177	0.0935	0.1986	0.0438	0.0298	0.2233	-0.0284	0.2312	1.0327	-69.6794	48.8844
11	6.2753	0.354	-1.9289	1.8038	-0.1966	4.3914	0.0685	0.3084	0.3663	-0.0561	0.0446	-0.0321	-0.3062	-0.0462	-0.1175	0.234	-0.0246	0.0068	0.2163	0.0017	0.2014	-2.9848	-57.2613	49.3631
12	2.8508	0.035	-2.2092	0.2197	0.7312	4.3118	0.1115	0.1511	0.2341	0.034	0.1289	0.0289	-0.3891	-0.0164	-0.2509	0.2262	-0.0092	-0.0113	0.1827	-0.0025	0.1719	-6.9441	-59.6563	67.9584
13	8.4093	-2.4649	4.1368	1.6077	-1.4106	5.5623	-0.117	-0.12	-0.2489	0.0262	0.2445	0.1269	0.2547	-0.4183	-0.1543	0.2615	-0.0814	0.0358	0.2504	0.0046	0.2327	-19.2692	-71.2294	59.3535
14	2.2595	0.5688	-0.4827	2.2511	-1.6746	2.626	-0.0062	-0.1845	0.1257	0.0342	-0.0574	-0.1893	-0.1995	0.1617	0.0907	0.2428	-0.0113	0.0301	0.2211	-0.0697	0.1803	-0.8668	-60.2617	57.4374
15	6.94	3.3319	0.2615	5.1093	1.2963	2.0429	0.2339	-0.012	0.5981	-0.0547	-0.1974	0.323	-0.4138	-0.3891	-0.0228	0.3394	0.0728	0.0395	0.3301	0.0528	0.3231	-13.2532	-50.9653	50.4122

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 63 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 64 through 104 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 105 through 137 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 138 through 164 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 165 through 208 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 209 through 235 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 236 through 276 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 277 through 300 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 4 through 63 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 64 through 104 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 105 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 208 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 209 through 249 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 250 through 300 )

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