PDB-8sdd: Crystal structure of fluoroacetate dehalogenase Daro3835 H274N mu...

ID or keywords:

Entry

Database: PDB / ID: 8sdd

Title

Crystal structure of fluoroacetate dehalogenase Daro3835 H274N mutant with D107-glycolyl intermediate

Components

Alpha/beta hydrolase fold protein

Keywords

HYDROLASE / FLUOROACETATE / DEHALOGENASE / ALPHA/BETA HYDROLASE

Function / homology

alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Alpha/beta hydrolase fold protein

Function and homology information

Biological species

Dechloromonas aromatica RCB (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Stogios, P.J. / Skarina, T. / Khusnutdinova, A. / Iakounine, A. / Savchenko, A.

Funding support

1items

Citation

Journal: Febs J. / Year: 2023
Title: Structural insights into hydrolytic defluorination of difluoroacetate by microbial fluoroacetate dehalogenases.
Authors: Khusnutdinova, A.N. / Batyrova, K.A. / Brown, G. / Fedorchuk, T. / Chai, Y.S. / Skarina, T. / Flick, R. / Petit, A.P. / Savchenko, A. / Stogios, P. / Yakunin, A.F.

History

Deposition	Apr 6, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 14, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8sdd.cif.gz	289.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8sdd.ent.gz	208.6 KB	Display	PDB format
PDBx/mmJSON format	8sdd.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/sd/8sdd ftp://data.pdbj.org/pub/pdb/validation_reports/sd/8sdd	HTTPS FTP

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Related structure data

Related structure data	8sdcC C: citing same article (ref.)
Similar structure data	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 (3) #165 - Sep 2013 Designed Protein Cages similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: Alpha/beta hydrolase fold protein

B: Alpha/beta hydrolase fold protein

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

1

A: Alpha/beta hydrolase fold protein

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

2

B: Alpha/beta hydrolase fold protein

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

Unit cell

Length a, b, c (Å)	42.937, 58.485, 138.188
Angle α, β, γ (deg.)	90.000, 93.023, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Alpha/beta hydrolase fold protein Mass: 33069.520 Da / Num. of mol.: 2 / Mutation: H274N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dechloromonas aromatica RCB (bacteria) / Gene: Daro_3835 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q479B8
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 660 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.62 Å³/Da / Density % sol: 53.05 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 25% (W/V) PEG3350, 0.2 M MGCL2, 0.1 M BIS-TRIS (PH 5.5)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 28, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2→46 Å / Num. obs: 43884 / % possible obs: 94.6 % / Redundancy: 4.8 % / B_iso Wilson estimate: 21.37 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.049 / R_pim(I) all: 0.025 / Net I/σ(I): 23.3
Reflection shell	Resolution: 2→2.05 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.098 / Mean I/σ(I) obs: 11.3 / Num. unique obs: 2917 / CC_1/2: 0.986 / R_pim(I) all: 0.075 / % possible all: 85.5

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Processing

Software

Name	Version	Classification
PHENIX	1.15_3448	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→30.4 Å / SU ML: 0.247 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 24.148
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2623	1995	4.55 %	RANDOM
R_work	0.2189	41852	-	-
obs	0.2209	43847	94.28 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 32.89 Å²

Refinement step

Cycle: LAST / Resolution: 2→30.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4640	0	0	660	5300

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0052	4770
X-RAY DIFFRACTION	f_angle_d	0.7355	6482
X-RAY DIFFRACTION	f_chiral_restr	0.0484	695
X-RAY DIFFRACTION	f_plane_restr	0.0052	857
X-RAY DIFFRACTION	f_dihedral_angle_d	20.8118	1738

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 (%)
2-2.05	0.3077	128	0.2441	2676	X-RAY DIFFRACTION	84.82
2.05-2.11	0.2832	137	0.2358	2912	X-RAY DIFFRACTION	93.56
2.11-2.17	0.2511	142	0.2295	2907	X-RAY DIFFRACTION	91.26
2.17-2.24	0.2685	144	0.224	2937	X-RAY DIFFRACTION	94.08
2.24-2.32	0.2554	141	0.2271	2913	X-RAY DIFFRACTION	92.83
2.32-2.41	0.2689	136	0.2298	3012	X-RAY DIFFRACTION	94.39
2.41-2.52	0.3184	145	0.2349	2976	X-RAY DIFFRACTION	93.89
2.52-2.65	0.2726	134	0.2332	2980	X-RAY DIFFRACTION	94.88
2.65-2.82	0.2783	139	0.2365	3037	X-RAY DIFFRACTION	95.63
2.82-3.04	0.271	155	0.2356	3019	X-RAY DIFFRACTION	95.78
3.04-3.34	0.2797	146	0.2194	3048	X-RAY DIFFRACTION	95.92
3.34-3.82	0.2472	147	0.2076	3115	X-RAY DIFFRACTION	97.87
3.82-4.81	0.2421	151	0.1861	3118	X-RAY DIFFRACTION	96.95
4.81-30.4	0.236	150	0.2164	3202	X-RAY DIFFRACTION	98.04

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	1.95941892135	0.54492872949	0.198596549058	6.96290229034	-1.98164336226	2.85500755261	-0.0810301187652	0.456184565078	0.000343892725814	-0.652049766224	0.19836285996	0.5754697669	0.101806986852	-0.431350734542	-0.101592559012	0.160681637279	-0.0110644716624	-0.0584883719143	0.254704579615	-0.00198659617196	0.211612900509	39.7202580376	-1.66839486499	136.496120562
2	1.68301694738	-0.0244390948918	-0.384023368294	0.40452178464	0.0461251786342	1.4681282487	-0.041594450096	-0.280262604708	0.000643352071824	-0.0252822998277	0.0176783400594	-0.0103884783623	0.0233673307065	-0.0622809951423	0.0123585210066	0.136579373758	0.00080242416486	-0.0365727203586	0.0798448955211	-0.0114201021867	0.143277874512	47.1261080625	-3.73256241444	152.825850525
3	4.17676669861	-1.92484108927	-0.793888713736	4.35103072294	2.24632228031	2.86372221929	0.00713711433689	-0.747335263802	0.528637763007	0.257949793808	0.181086728705	-0.141164915468	-0.037505018936	0.226140269372	-0.178401256956	0.13565960673	-0.0564486463415	-0.007524953309	0.227273318404	-0.0361675037266	0.222520909336	61.5621209917	5.44507550577	154.900643245
4	3.43040783978	1.09073568569	-1.54387884573	1.46267974309	-1.37481364376	1.93894486852	0.240535974357	-0.264324002935	0.35895641176	-0.145512678385	-0.0834675126027	-0.0535408283233	-0.418420035433	0.0800265549733	-0.071864928183	0.244898946927	-0.0323261121028	-0.0197836005704	0.0802019801159	-0.0118253013722	0.237319449282	53.9285676073	11.2536301346	146.056657548
5	2.02023910648	-0.50050368454	-0.612395837779	7.04696891623	-0.884761564706	2.5340084154	-0.328663817522	-0.514776765228	-0.566081409224	0.265645426807	0.232851160352	0.706244555574	-0.0079427401145	-0.214991556415	0.121340155615	0.236891091576	-0.0111303114823	0.0445429470387	0.938550051701	-0.0869569913831	0.59039514503	33.5048398658	-5.71263097596	204.399428582
6	0.844345105987	0.570235399035	0.995023700414	1.03322120072	1.18045322056	1.58142318587	0.0180699661161	-0.524429964101	-0.22946141994	0.52801082584	0.183376596487	0.0615468873407	0.276044423703	-0.249604996246	-0.0517005774187	0.37050922047	0.205970359403	0.0365510686699	0.936871455074	0.053055246483	0.122383322312	40.1960413052	-8.38195404854	207.860937476
7	0.791677553225	0.541582208383	-0.128364492728	0.764046314006	-0.170243625659	2.01768325606	-0.27823131335	-0.522076236012	0.0376135815267	0.233539521623	0.228797904285	0.0596460092703	0.309882248002	0.129829603095	0.0599587842596	0.304130409451	0.122787667114	0.0901585748647	0.790869561119	-0.0224620136881	0.225329090881	41.4831984267	-4.20080374316	197.481443978
8	0.50108320628	0.504359711278	-0.481848075062	0.537785469172	-0.613947517093	1.00367477695	0.0479226204341	-0.400142930514	0.0474996796048	0.0350291442113	0.0401646372262	-0.0717656491718	-0.211925242452	0.0664693640575	-0.0830584733603	0.326680889948	0.163155175402	0.0854300443623	1.04648939516	-0.00135279629764	0.108144010273	51.4298975084	-4.25471146276	200.03146762
9	0.123016509948	0.237797857615	0.423897143564	0.870321172536	0.684728078877	1.56283639532	-0.123669855778	-0.333582822981	0.00680809627866	0.18061052977	0.117279735951	-0.0817093016439	0.16746503904	0.454426293677	0.00640885152291	0.236788461384	0.0234376749823	0.00644623335673	0.509526842563	0.0398363536339	0.156426816035	50.8185183759	-4.20931601358	177.138044583
10	2.25573971684	-0.615476600105	-0.628827260239	1.6121246136	0.468207580749	2.47416104769	-0.164181551152	-0.422266371527	-0.177509061931	0.113046489116	0.0279099059008	0.146693798626	0.186551295933	0.0191225498591	0.144211493141	0.206022398832	0.0141592111389	0.0516633736245	0.476052802588	0.0474721538007	0.174615941807	39.3552226787	-6.31423441906	183.82437723
11	1.01568006126	0.458240941383	0.346671037798	0.865554338531	0.243021442372	1.29191953919	-0.152126006339	-0.298910195566	-0.127957547896	0.11911505891	0.168472067682	-0.0880093567692	0.407932657899	0.751450557669	-0.0396666062725	0.444244976487	0.205974324162	0.0574999475584	0.944863726207	0.0999893501829	0.276560765187	57.9337860992	-12.321627759	191.807832284
12	1.82473657273	1.03332310054	0.597429885128	2.81901357171	-1.61856142772	2.58818321241	-0.0250105324939	-0.41172115411	-0.106199288613	0.69988678979	-0.225037818528	-0.219355487026	-0.328691622624	0.502574209449	0.222427184875	0.808113631797	0.332467497099	0.163146527956	0.939435720998	0.264956405805	0.388401287517	53.7620361951	-19.1666054497	204.148713843

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 29 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 30 through 236 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 237 through 270 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 271 through 296 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 16 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 17 through 34 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 35 through 95 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 96 through 134 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 135 through 161 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 162 through 228 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 229 through 280 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 281 through 296 )

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