PDB-5c0t: Crystal structure of the mercury-bound form of MerB mutant D99S

ID or keywords:

Entry

Database: PDB / ID: 5c0t

Title

Crystal structure of the mercury-bound form of MerB mutant D99S

Components

Alkylmercury lyase

Keywords

LYASE / METAL BINDING PROTEIN / Bacterial Proteins / Cysteine / Escherichia coli / Lyases / Mercury / Mutation

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 /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.96 Å

Authors

Wahba, H.M. / Lecoq, L. / Stevenson, M. / Mansour, A. / Cappadocia, L. / Lafrance-Vanasse, J. / Wilkinson, K.J. / Sygusch, J. / Wilcox, D.E. / Omichinski, J.G.

Funding support

Canada,

United States, 2items

Citation

Journal: Biochemistry / Year: 2016
Title: Structural and Biochemical Characterization of a Copper-Binding Mutant of the Organomercurial Lyase MerB: Insight into the Key Role of the Active Site Aspartic Acid in Hg-Carbon Bond Cleavage ...
Authors: Wahba, H.M. / Lecoq, L. / Stevenson, M. / Mansour, A. / Cappadocia, L. / Lafrance-Vanasse, J. / Wilkinson, K.J. / Sygusch, J. / Wilcox, D.E. / Omichinski, J.G.

History

Deposition	Jun 12, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 3, 2016	Provider: repository / Type: Initial release
Revision 1.1	Feb 10, 2016	Group: Database references
Revision 1.2	Feb 24, 2016	Group: Database references
Revision 1.3	Mar 2, 2016	Group: Database references
Revision 1.4	Sep 27, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6	Sep 27, 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 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5c0t.cif.gz	180.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5c0t.ent.gz	141.2 KB	Display	PDB format
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Validation report

Summary document	5c0t_validation.pdf.gz	420.9 KB	Display	wwPDB validaton report
Full document	5c0t_full_validation.pdf.gz	421.7 KB	Display
Data in XML	5c0t_validation.xml.gz	19 KB	Display
Data in CIF	5c0t_validation.cif.gz	27.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c0/5c0t ftp://data.pdbj.org/pub/pdb/validation_reports/c0/5c0t	HTTPS FTP

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Related structure data

Related structure data	5c0uC 5c17C 5dsfC 3f0oS 3f0p C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5dsf-1 5u79-1 3fn8-1 5u7c-1 5c0u-2 5u83-2 5u7b-2 5u7a-2 3f2h-2 5u82-2 5dsf-2 5u88-2 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#147 - Mar 2012 Rhodopsin similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #220 - Apr 2018 Dehalogenases 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)
#122 - Feb 2010
Enhanceosome
similarity (1)
#220 - Apr 2018
Dehalogenases
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

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

1

A: Alkylmercury lyase

hetero molecules

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

2

B: Alkylmercury lyase

hetero molecules

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

Unit cell

Length a, b, c (Å)	38.061, 89.113, 51.824
Angle α, β, γ (deg.)	90.000, 100.790, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Alkylmercury lyase / Organomercurial lyase Mass: 23030.258 Da / Num. of mol.: 2 / Mutation: D99S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: merB / 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-BR / BROMIDE ION Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 252 / 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: 1.87 Å³/Da / Density % sol: 34.38 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 23 % polyethylene glycol 2000 MME, 0.2 M sodium acetate pH 5.5, 0.2 M potassium bromide. Before flash freezing, the same precipitant was used except 25 % polyethylene glycol 2000 MME was ...Details: 23 % polyethylene glycol 2000 MME, 0.2 M sodium acetate pH 5.5, 0.2 M potassium bromide. Before flash freezing, the same precipitant was used except 25 % polyethylene glycol 2000 MME was used as a cryo-protectant.

Crystal

Density Matthews: 1.87 Å³/Da / Density % sol: 34.38 %

Crystal grow

Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 23 % polyethylene glycol 2000 MME, 0.2 M sodium acetate pH 5.5, 0.2 M potassium bromide. Before flash freezing, the same precipitant was used except 25 % polyethylene glycol 2000 MME was ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 1.075 Å

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 21, 2011

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.075 Å / Relative weight: 1

Reflection

Redundancy: 3.7 % / Number: 89865 / R_merge(I) obs: 0.089 / Χ²: 1.11 / D res high: 1.96 Å / D res low: 50 Å / Num. obs: 24414 / % possible obs: 99.6

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	ID	R_merge(I) obs	Chi squared	Redundancy
5.32	50	1	0.048	2.601	3.7
4.22	5.32	1	0.042	1.905	3.5
3.69	4.22	1	0.047	1.722	3.6
3.35	3.69	1	0.056	1.626	3.7
3.11	3.35	1	0.066	1.426	3.7
2.93	3.11	1	0.081	1.17	3.7
2.78	2.93	1	0.098	1.074	3.7
2.66	2.78	1	0.119	1.011	3.7
2.56	2.66	1	0.143	0.961	3.7
2.47	2.56	1	0.166	0.857	3.7
2.39	2.47	1	0.203	0.855	3.7
2.32	2.39	1	0.241	0.851	3.7
2.26	2.32	1	0.259	0.814	3.7
2.21	2.26	1	0.309	0.881	3.7
2.16	2.21	1	0.359	0.827	3.7
2.11	2.16	1	0.408	0.771	3.7
2.07	2.11	1	0.459	0.783	3.7
2.03	2.07	1	0.573	0.773	3.7
1.99	2.03	1	0.637	0.69	3.6
1.96	1.99	1	0.779	0.661	3.6

Reflection

Resolution: 1.96→50 Å / Num. obs: 24414 / % possible obs: 99.6 % / Redundancy: 3.7 % / B_iso Wilson estimate: 27.7 Å² / R_merge(I) obs: 0.089 / R_pim(I) all: 0.054 / R_rim(I) all: 0.104 / Χ²: 1.113 / Net I/av σ(I): 18 / Net I/σ(I): 8 / Num. measured all: 89865

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.96-1.99	3.6	0.779	1245	0.677	0.475	0.914	0.661	98.9
1.99-2.03	3.6	0.637	1181	0.7	0.385	0.746	0.69	99.2
2.03-2.07	3.7	0.573	1224	0.743	0.347	0.671	0.773	99.1
2.07-2.11	3.7	0.459	1205	0.833	0.277	0.537	0.783	99.1
2.11-2.16	3.7	0.408	1226	0.873	0.247	0.478	0.771	99.2
2.16-2.21	3.7	0.359	1181	0.876	0.217	0.42	0.827	99.4
2.21-2.26	3.7	0.309	1245	0.916	0.186	0.361	0.881	99.4
2.26-2.32	3.7	0.259	1180	0.939	0.156	0.303	0.814	99.5
2.32-2.39	3.7	0.241	1237	0.942	0.145	0.282	0.851	99.8
2.39-2.47	3.7	0.203	1205	0.958	0.123	0.238	0.855	99.8
2.47-2.56	3.7	0.166	1220	0.971	0.1	0.194	0.857	99.7
2.56-2.66	3.7	0.143	1212	0.982	0.086	0.167	0.961	99.8
2.66-2.78	3.7	0.119	1239	0.986	0.072	0.139	1.011	99.9
2.78-2.93	3.7	0.098	1226	0.99	0.059	0.115	1.074	100
2.93-3.11	3.7	0.081	1204	0.991	0.049	0.095	1.17	100
3.11-3.35	3.7	0.066	1231	0.994	0.04	0.077	1.426	100
3.35-3.69	3.7	0.056	1238	0.994	0.034	0.066	1.626	100
3.69-4.22	3.6	0.047	1227	0.995	0.029	0.055	1.722	99.8
4.22-5.32	3.5	0.042	1234	0.996	0.026	0.049	1.905	99.6
5.32-50	3.7	0.048	1254	0.996	0.03	0.057	2.601	99.5

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
HKL-2000		data reduction
PHASER		phasing
PHENIX	1.9_1692	refinement
PDB_EXTRACT	3.15	data extraction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3F0O

3f0o

Resolution: 1.96→44.203 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.7 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2084	3882	8.21 %	Random selection
R_work	0.1636	43430	-	-
obs	0.1673	47312	97.97 %	-

Solvent computation

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

Displacement parameters

B_iso max: 164.61 Å² / B_iso mean: 36.15 Å² / B_iso min: 15.78 Å²

Refinement step

Cycle: final / Resolution: 1.96→44.203 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3174	0	3	252	3429
B_iso mean	-	-	33.14	39.05	-
Num. residues	-	-	-	-	416

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3271
X-RAY DIFFRACTION	f_angle_d	1.111	4454
X-RAY DIFFRACTION	f_chiral_restr	0.04	527
X-RAY DIFFRACTION	f_plane_restr	0.005	572
X-RAY DIFFRACTION	f_dihedral_angle_d	12.753	1166

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 (%)
1.9567-1.9805	0.3223	134	0.3036	1490	X-RAY DIFFRACTION	91
1.9805-2.0056	0.3039	131	0.2813	1487	X-RAY DIFFRACTION	95
2.0056-2.032	0.3274	135	0.2497	1481	X-RAY DIFFRACTION	97
2.032-2.0598	0.2815	139	0.2366	1584	X-RAY DIFFRACTION	96
2.0598-2.0893	0.286	137	0.2281	1499	X-RAY DIFFRACTION	98
2.0893-2.1204	0.2369	131	0.2303	1554	X-RAY DIFFRACTION	97
2.1204-2.1536	0.2574	141	0.2275	1559	X-RAY DIFFRACTION	98
2.1536-2.1889	0.2911	132	0.2139	1495	X-RAY DIFFRACTION	97
2.1889-2.2266	0.2711	142	0.2034	1592	X-RAY DIFFRACTION	98
2.2266-2.2671	0.2345	139	0.1905	1553	X-RAY DIFFRACTION	97
2.2671-2.3107	0.2345	138	0.1919	1530	X-RAY DIFFRACTION	99
2.3107-2.3579	0.3005	141	0.1957	1586	X-RAY DIFFRACTION	99
2.3579-2.4091	0.2229	139	0.1793	1532	X-RAY DIFFRACTION	98
2.4091-2.4652	0.2622	141	0.1823	1564	X-RAY DIFFRACTION	99
2.4652-2.5268	0.2221	143	0.1773	1599	X-RAY DIFFRACTION	99
2.5268-2.5951	0.2515	136	0.1771	1522	X-RAY DIFFRACTION	99
2.5951-2.6715	0.2356	142	0.1776	1580	X-RAY DIFFRACTION	99
2.6715-2.7577	0.2473	141	0.1786	1560	X-RAY DIFFRACTION	99
2.7577-2.8563	0.2464	144	0.1806	1565	X-RAY DIFFRACTION	99
2.8563-2.9706	0.2314	138	0.1683	1580	X-RAY DIFFRACTION	99
2.9706-3.1058	0.1753	136	0.1605	1559	X-RAY DIFFRACTION	99
3.1058-3.2695	0.2097	140	0.1598	1567	X-RAY DIFFRACTION	99
3.2695-3.4742	0.2071	144	0.1462	1604	X-RAY DIFFRACTION	99
3.4742-3.7423	0.1968	139	0.1476	1531	X-RAY DIFFRACTION	99
3.7423-4.1187	0.1725	138	0.1257	1581	X-RAY DIFFRACTION	99
4.1187-4.7141	0.1719	141	0.1188	1555	X-RAY DIFFRACTION	97
4.7141-5.937	0.1381	140	0.128	1551	X-RAY DIFFRACTION	100
5.937-44.2144	0.1421	140	0.1281	1570	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	0.0365	0.0064	0.0021	-0.0041	0.0097	0.1262	-0.0778	-0.1049	-0.3246	-0.2538	-0.005	-0.0844	-0.3925	-0.1578	-0.0016	0.2708	0.026	0.068	0.3346	-0.0065	0.3466	-0.8263	2.1069	41.2478
2	0.0829	-0.0312	0.1302	0.1891	0.0107	0.4933	-0.1271	-0.0701	-0.1053	0.5604	0.0752	-0.0281	0.2152	0.1367	-0.0119	0.4542	0.0223	-0.0139	0.1836	-0.0239	0.253	12.9181	-16.5012	37.524
3	1.0505	-0.2928	0.6649	0.2642	-0.4103	0.8293	-0.0994	0.7255	0.7293	0.3182	-0.4737	0.5813	0.6434	-0.1906	-0.3011	0.3268	-0.1006	0.1574	-0.0175	-0.3259	0.4025	6.404	-19.021	30.5894
4	-0.0013	0.0378	-0.0003	0.0532	0.0399	0.0082	0.1301	0.087	-0.148	0.2167	-0.2331	0.397	-0.1312	0.1116	-0	0.2678	0.0274	0.0071	0.2274	-0.0387	0.2716	12.4375	-11.5307	27.4092
5	0.0477	-0.1911	-0.1189	0.6294	0.0698	0.6295	0.0614	0.1258	0.0618	-0.0698	-0.0575	-0.103	0.1326	0.2399	-0.0002	0.2326	0.0255	-0.0156	0.2181	0.0003	0.1855	17.2189	3.1185	30.4742
6	0.9266	-0.3241	-0.0383	0.3687	-0.0993	0.6364	-0.0457	-0.0003	-0.1105	0.0971	0.0153	0.223	-0.0147	-0.1935	0.0001	0.2428	0.0048	0.001	0.212	-0.018	0.2565	3.3228	5.4438	33.9097
7	0.069	0.0663	-0.0412	0.049	0.0358	0.1094	0.0982	-0.6046	-0.1403	-0.0817	0.0388	0.2037	-0.1644	-0.0894	0.0001	0.364	0.057	0.0366	0.4415	0.1597	0.3713	4.9688	1.2905	0.3363
8	0.1731	-0.0899	0.3583	0.2111	-0.0622	0.7627	0.2673	0.1978	0.0251	-0.3816	-0.2121	0.1069	0.2235	-0.0565	0.0003	0.2546	0.076	-0.0145	0.251	0.0386	0.2607	3.922	-21.0024	7.2563
9	0.4434	-0.3264	0.0354	1.7073	-0.4513	0.1771	-0.0033	-0.0023	0.0143	-0.0014	0.0226	-0.0268	0.0404	-0.1003	-0	0.1995	0.035	0.0228	0.2796	0.0237	0.1957	-4.4961	-9.8419	13.3818
10	0.0928	0.1756	0.1494	0.4354	0.3937	0.509	-0.6716	-0.1695	-0.2669	-0.36	-0.3746	-0.6746	-0.0224	0.5959	-0.4352	0.1988	0.0658	0.2342	0.5556	0.373	0.5407	6.7866	2.2551	8.1075
11	0.3564	0.2222	0.1041	0.4999	-0.4938	0.6291	0.0023	0.037	0.2362	-0.1525	-0.0268	-0.0844	-0.1117	0.2213	-0.0046	0.2407	0.0336	-0.0296	0.3626	0.0537	0.2425	-1.2944	2.6914	7.579

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 14 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 15 through 49 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 50 through 69 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 70 through 79 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 80 through 141 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 142 through 208 )	A
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 14 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 15 through 49 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 50 through 141 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 142 through 153 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 154 through 208 )	B

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