PDB-3fn8: Crystal Structure of MerB complexed with mercury

ID or keywords:

Entry

Database: PDB / ID: 3fn8

Title

Crystal Structure of MerB complexed with mercury

Components

Alkylmercury lyase

Keywords

LYASE / Winged-helix / Mercuric resistance / Mercury

Function / homology

Function and homology information

alkylmercury lyase / alkylmercury lyase activity / : / response to mercury ion
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.88 Å

Authors

Momany, C. / Summers, A. / Cagle, C. / Teske, J.

Citation

Journal: TO BE PUBLISHED
Title: Crystal Structure of MerB complexed with mercury
Authors: Momany, C. / Summers, A. / Cagle, C. / Teske, J.

History

Deposition	Dec 23, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 3, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3fn8.cif.gz	98.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3fn8.ent.gz	77 KB	Display	PDB format
PDBx/mmJSON format	3fn8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3fn8_validation.pdf.gz	420.1 KB	Display	wwPDB validaton report
Full document	3fn8_full_validation.pdf.gz	421.9 KB	Display
Data in XML	3fn8_validation.xml.gz	10.5 KB	Display
Data in CIF	3fn8_validation.cif.gz	16.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fn/3fn8 ftp://data.pdbj.org/pub/pdb/validation_reports/fn/3fn8	HTTPS FTP

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Related structure data

Related structure data	1s6l 3f0p
Similar structure data	5u7c-1 5dsf-1 5u7a-2 5u83-1 5u88-2 5u7c-2 5u82-1 5u82-2 5c0t-1 3f2g-1 5u79-1 5u7b-2 5u79-2 5c0t-2 3f0p-1 5c0u-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

1s6l

3f0p

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#147 - Mar 2012 Rhodopsin similarity (1) #100 - Apr 2008 Adrenergic Receptors similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #224 - Aug 2018 Legumain similarity (1) #225 - Sep 2018 Phytase similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #27 - Mar 2002 Bacteriorhodopsin similarity (1) #49 - Jan 2004 Carbonic Anhydrase similarity (1) #58 - Oct 2004 G Proteins similarity (1) #66 - Jun 2005 Carotenoid Oxygenase similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#147 - Mar 2012
Rhodopsin
similarity (1)
#100 - Apr 2008
Adrenergic Receptors
similarity (1)
#156 - Dec 2012
ABO Blood Type Glycosyltransferases
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#196 - Apr 2016
Lead Poisoning
similarity (1)
#224 - Aug 2018
Legumain
similarity (1)
#225 - Sep 2018
Phytase
similarity (1)
#238 - Oct 2019
Ribonucleotide Reductase
similarity (1)
#27 - Mar 2002
Bacteriorhodopsin
similarity (1)
#49 - Jan 2004
Carbonic Anhydrase
similarity (1)
#58 - Oct 2004
G Proteins
similarity (1)
#66 - Jun 2005
Carotenoid Oxygenase
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Alkylmercury lyase

B: Alkylmercury lyase

hetero molecules

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

1

A: Alkylmercury lyase

hetero molecules

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

2

B: Alkylmercury lyase

hetero molecules

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

Unit cell

Length a, b, c (Å)	38.638, 88.972, 54.680
Angle α, β, γ (deg.)	90.000, 97.160, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Alkylmercury lyase / Organomercurial lyase Mass: 24129.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: merB / Plasmid: pQZB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P77072, alkylmercury lyase
#2: Chemical	ChemComp-HG / MERCURY (II) ION Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 283 / 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: 1.93 Å³/Da / Density % sol: 36.35 %
Crystal grow	Temperature: 283 K / pH: 7 Details: 2 microliter protein (in 20 mM tris pH 8, 0.5 mM EDTA, 5% v/v glycerol) mixed with 2 microliter precipitant (40% w/v PEG 550 monomethylether, 100 mM Magnesium chloride, 100 mM 2-[N- ...Details: 2 microliter protein (in 20 mM tris pH 8, 0.5 mM EDTA, 5% v/v glycerol) mixed with 2 microliter precipitant (40% w/v PEG 550 monomethylether, 100 mM Magnesium chloride, 100 mM 2-[N-morpholino]ethanesulfonic acid monohydrate) over 1ml well of 40% w/v PEG 550 monomethylether, VAPOR DIFFUSION, HANGING DROP, temperature 283K

Crystal

Density Matthews: 1.93 Å³/Da / Density % sol: 36.35 %

Crystal grow

Temperature: 283 K / pH: 7
Details: 2 microliter protein (in 20 mM tris pH 8, 0.5 mM EDTA, 5% v/v glycerol) mixed with 2 microliter precipitant (40% w/v PEG 550 monomethylether, 100 mM Magnesium chloride, 100 mM 2-[N- ...

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
1,2		1

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
SYNCHROTRON	APS	19-BM		1	1.0073
ROTATING ANODE			ENRAF-NONIUS FR591	2	1.54184

Detector

Type	ID	Detector	Date	Details
MARRESEARCH	1	CCD	Nov 15, 2003	mirrors
Nonius Kappa CCD	2	CCD	Oct 15, 2003	monochromator

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID	Monochromator
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	1	GRAPHITE

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.0073	1
2	1.54184	1

Reflection

Resolution: 1.87→50 Å / Num. all: 20330 / Num. obs: 20330 / % possible obs: 65.9 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 7.7 % / R_merge(I) obs: 0.071 / R_sym value: 0.071 / Net I/σ(I): 29.67

Reflection shell

Resolution: 1.87→1.94 Å / Redundancy: 1.7 % / R_merge(I) obs: 0 / Mean I/σ(I) obs: 2.1 / % possible all: 3.8

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Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
1	2 wavelength	1	1.0073	10.91	-14.96
1	2 wavelength	2	1.5418	10.89	-4.16

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Hg	41.807	0.683	0.478	0.379	0.762
2	Hg	53.628	0.148	0.96	0.238	0.893

Phasing dm

FOM : 0.58 / FOM acentric: 0.58 / FOM centric: 0.6 / Reflection: 18937 / Reflection acentric: 18344 / Reflection centric: 593

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
5.7-35.208	0.92	0.93	0.86	1092	996	96
3.6-5.7	0.92	0.92	0.83	3307	3158	149
2.9-3.6	0.8	0.81	0.62	4131	3998	133
2.5-2.9	0.47	0.47	0.38	4123	4015	108
2.1-2.5	0.3	0.3	0.29	4822	4734	88
2-2.1	0.16	0.16	0.11	1462	1443	19

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.05	phasing
RESOLVE	2.06	phasing
REFMAC		refinement
PDB_EXTRACT	3.006	data extraction
HKL-2000		data collection

Refinement

Method to determine structure:

MAD / Resolution: 1.88→46.32 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.922 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 8.674 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 22 group TLS refinement defined by TLS Motion Determination (TLSMD) http://skuld.bmsc.washington.edu/~tlsmd/

	R_factor	Num. reflection	% reflection
R_free	0.248	1021	5 %
R_work	0.184	-	-
obs	0.187	20230	67.4 %
all	-	20230	-

Solvent computation

Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 39.61 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.87 Å²	0 Å²	1.43 Å²
2-	-	-2.26 Å²	0 Å²
3-	-	-	-1.25 Å²

Refinement step

Cycle: LAST / Resolution: 1.88→46.32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3190	0	14	283	3487

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	3294
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.063	1.966	4497
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.163	5	426
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.284	23.284	134
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.694	15	524
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.131	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	532
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	2478
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.183	0.2	1567
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.293	0.2	2268
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.106	0.2	252
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.156	0.2	72
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.105	0.2	27
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.42	2	2166
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.738	3	3394
X-RAY DIFFRACTION	r_scbond_it	1.922	6	1279
X-RAY DIFFRACTION	r_scangle_it	3.013	10	1100
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.88→1.93 Å

	R_factor	Num. reflection	% reflection
R_free	0.476	5	-
R_work	0.364	102	-
obs	-	-	4.81 %

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	27.956	-3.2148	-2.5297	1.1615	4.7588	25.44	-0.2617	0.2487	1.9273	-0.496	0.6066	-0.3974	-1.6654	0.5893	-0.3449	-0.0662	-0.0476	0.0459	-0.0365	0.0158	-0.0715	26.573	49.306	54.035
2	13.0841	3.0847	-2.3594	34.4326	2.0945	2.574	0.3635	1.5173	-0.6255	-0.0721	-0.1941	1.0267	0.1705	-0.974	-0.1694	-0.0249	-0.0579	0.0995	0.1619	-0.1545	0.0268	19.837	35.776	51.134
3	5.2104	2.3515	-0.756	10.2991	1.7277	4.6015	0.1103	-0.178	-0.2832	0.4269	-0.3506	-0.6486	0.2877	0.024	0.2403	-0.0838	0.0012	-0.0049	-0.1093	0.0111	-0.1262	30.011	23.678	42.763
4	10.0918	-6.2701	-0.2972	21.4403	-3.9592	7.0138	0.2389	-0.2449	0.0203	0.7267	-0.2408	0.8521	0.2238	-0.4332	0.0019	-0.0312	-0.1196	0.0451	-0.0328	-0.1927	-0.1393	20.073	21.358	46.778
5	11.0162	2.8925	4.5356	8.4519	1.3377	4.9194	0.2482	-0.1998	0.1445	-0.5639	-0.2161	0.0274	0.1138	-0.2491	-0.0321	-0.073	0.0434	0.0169	-0.1155	0.0031	-0.1076	25.315	27.666	35.013
6	3.9813	0.5968	-3.1212	6.467	1.9594	7.5381	0.0399	-0.1044	-0.2579	-0.5373	0.1031	-0.6506	0.2099	0.4006	-0.143	-0.1105	-0.0148	0.0403	-0.0787	0.025	-0.043	36.217	35.662	38.072
7	2.8025	1.3409	-1.0531	4.4417	-1.5596	5.3114	-0.0983	-0.311	-0.2591	-0.3378	-0.1275	-1.0932	0.1025	0.7041	0.2257	-0.2064	-0.0125	0.0612	-0.0298	0.0408	0.0397	42.209	41.571	41.485
8	33.4764	6.7316	-6.7472	6.521	1.1607	6.5687	-0.4578	0.295	0.8097	-0.3479	0.2093	-0.3178	-0.1946	0.031	0.2485	-0.1098	-0.0817	-0.0695	-0.0529	0.0665	-0.141	34.763	50.125	43.172
9	23.9622	5.6292	-10.5	2.0185	-9.2868	71.4222	0.3154	0.2158	0.0637	0.2302	-0.2076	0.512	-0.6022	-3.0913	-0.1078	0.0179	-0.0644	-0.0395	0.2132	-0.1163	0.0684	18.565	41.582	41.028
10	1.1538	-0.651	0.3758	6.6968	-2.4001	3.8317	-0.0195	-0.2846	0.0626	0.0756	0.0288	-0.0387	-0.438	-0.0496	-0.0093	-0.1052	-0.0096	-0.0171	-0.0154	-0.0242	-0.1367	31.045	49.662	44.921
11	52.8148	12.8932	7.2098	28.7866	-3.8079	32.5075	-0.1684	0.5342	-3.0455	0.2207	1.4527	0.4391	4.0008	-0.521	-1.2843	0.1939	0.0845	0.0765	0.0463	0.215	0.1557	27.131	29.285	59.403
12	12.5667	6.4327	-4.0506	26.4256	-5.5369	12.4337	0.1938	0.1053	0.4156	0.4068	0.0425	0.0462	-0.295	0.3575	-0.2363	-0.1763	-0.018	0.0403	-0.0356	0.0157	-0.1988	29.089	46.217	8.798
13	8.562	8.4094	-2.416	8.2594	-2.3729	0.6817	0.0602	0.3779	-0.7805	-0.8866	-0.3175	-1.0874	1.0213	0.0007	0.2574	0.2065	0.0214	0.1362	-0.0042	-0.0238	0.0828	24.388	30.959	11.129
14	3.9083	-4.1686	-6.3486	17.0009	1.7347	12.3333	-0.2569	0.1292	-0.175	-0.0402	0.2447	1.0461	0.8864	-0.93	0.0122	0.047	-0.1662	-0.088	-0.0781	0.0002	-0.0783	12.003	28.49	20.317
15	18.8253	6.1572	5.5533	9.2682	1.712	15.0626	0.5525	0.1256	-0.3765	-0.4866	-0.4777	-0.3411	2.2059	0.2526	-0.0749	0.3647	-0.0015	0.1511	-0.2538	-0.0012	-0.1276	19.989	21.38	14.555
16	4.4047	-2.9154	1.0182	10.2236	-3.3034	4.0108	0.1978	0.2231	0.1082	-0.2746	-0.0813	-0.2505	0.3069	0.0031	-0.1166	-0.0133	-0.0069	-0.0271	-0.13	-0.0253	-0.1018	19.874	29.582	25.604
17	12.1982	1.1386	3.5736	9.81	0.1542	13.152	-0.1017	-0.3909	-0.4309	0.5014	0.0754	0.5954	0.391	-1.0185	0.0263	-0.0091	-0.0069	0.0576	-0.0522	-0.0493	-0.0959	10.77	41.671	27.033
18	2.8448	-1.1206	0.6874	3.0662	0.0623	1.9469	-0.0148	-0.0279	-0.2618	-0.1852	0.1088	0.1699	-0.0048	-0.211	-0.094	-0.0477	-0.0059	-0.0018	-0.0877	0.0208	-0.0719	13.598	42.435	19.013
19	3.6895	-0.766	0.7475	1.7129	-0.5082	2.5383	0.0686	0.1172	0.0999	0.1275	-0.0665	-0.0183	-0.3208	-0.1047	-0.0021	-0.0273	-0.0066	-0.0104	-0.1279	0.0163	-0.0758	16.598	52.86	20.937
20	4.436	2.4909	0.0047	1.8539	-1.5118	5.0382	-0.176	0.2181	-0.463	0.3862	-0.286	-0.2679	0.4032	0.6104	0.462	-0.0252	-0.0219	-0.0144	-0.0065	0.0142	-0.0504	27.358	46.97	22.251
21	1.8737	0.0214	1.6615	1.3178	1.021	4.504	-0.1608	0.4326	0.2337	-0.0593	0.0247	-0.0578	-0.1967	0.6145	0.1361	-0.0542	-0.0438	0.028	-0.0087	0.0354	-0.0708	25.752	52.769	16.166
22	6.1834	15.3255	14.99	46.1507	35.6134	36.6299	0.3842	1.0876	-0.6378	0.7408	2.108	-1.1876	2.5931	-0.0979	-2.4922	0.4686	0.0261	0.1126	0.3542	-0.0815	0.1123	18.767	34.069	3.23

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 8
2	X-RAY DIFFRACTION	2	A	9 - 20
3	X-RAY DIFFRACTION	3	A	21 - 41
4	X-RAY DIFFRACTION	4	A	42 - 60
5	X-RAY DIFFRACTION	5	A	61 - 78
6	X-RAY DIFFRACTION	6	A	79 - 105
7	X-RAY DIFFRACTION	7	A	106 - 136
8	X-RAY DIFFRACTION	8	A	137 - 148
9	X-RAY DIFFRACTION	9	A	149 - 156
10	X-RAY DIFFRACTION	10	A	157 - 204
11	X-RAY DIFFRACTION	11	A	205 - 209
12	X-RAY DIFFRACTION	12	B	1 - 13
13	X-RAY DIFFRACTION	13	B	14 - 25
14	X-RAY DIFFRACTION	14	B	26 - 40
15	X-RAY DIFFRACTION	15	B	41 - 58
16	X-RAY DIFFRACTION	16	B	59 - 78
17	X-RAY DIFFRACTION	17	B	79 - 91
18	X-RAY DIFFRACTION	18	B	92 - 112
19	X-RAY DIFFRACTION	19	B	113 - 149
20	X-RAY DIFFRACTION	20	B	150 - 169
21	X-RAY DIFFRACTION	21	B	170 - 202
22	X-RAY DIFFRACTION	22	B	203 - 209

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