PDB-5fcd: Crystal structure of MccD protein

ID or keywords:

Entry

Database: PDB / ID: 5fcd

Title

Crystal structure of MccD protein

Components

MccD
UNK-UNK-UNK-MSE-UNK
UNK-UNK-UNK-UNK-MSE-UNK

Keywords

TRANSFERASE / MccD protein / methyltransferase fold / SAM binding / McC binding / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

S-adenosylmethionine-dependent methyltransferase activity
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.1 Å

Authors

Nocek, B. / Jedrzejczak, R. / Anderson, W.F. / Severinov, K. / Dubiley, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: Crystal structure of MccD protein.
Authors: Nocek, B. / Jedrzejczak, R. / Anderson, W.F. / Severinov, K. / Dubiley, S. / Joachimiak, A.

History

Deposition	Dec 15, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 30, 2015	Provider: repository / Type: Initial release
Revision 1.1	Feb 8, 2017	Group: Structure summary
Revision 1.2	Nov 13, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5fcd.cif.gz	281.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5fcd.ent.gz	233.8 KB	Display	PDB format
PDBx/mmJSON format	5fcd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5fcd_validation.pdf.gz	441 KB	Display	wwPDB validaton report
Full document	5fcd_full_validation.pdf.gz	443.7 KB	Display
Data in XML	5fcd_validation.xml.gz	20.7 KB	Display
Data in CIF	5fcd_validation.cif.gz	29.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fc/5fcd ftp://data.pdbj.org/pub/pdb/validation_reports/fc/5fcd	HTTPS FTP

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Related structure data

Similar structure data	5u44-2 5p0d-d 4kb8-1 5ozn-d 5p3f-d 6n0p-1 2v7a-1 6kzi-d 5u46-2 2zns-d Search similar-shape structures by Omokage search (details) 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
Other databases	TargetTrack: CSGID-IDP95362

Similar structure data

Other databases

TargetTrack: CSGID-IDP95362

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

D: UNK-UNK-UNK-MSE-UNK

E: UNK-UNK-UNK-UNK-MSE-UNK

A: MccD

B: MccD

hetero molecules

64.4 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

D: UNK-UNK-UNK-MSE-UNK

A: MccD

hetero molecules

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

2

E: UNK-UNK-UNK-UNK-MSE-UNK

B: MccD

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

3

D: UNK-UNK-UNK-MSE-UNK

E: UNK-UNK-UNK-UNK-MSE-UNK

A: MccD

B: MccD

hetero molecules

D: UNK-UNK-UNK-MSE-UNK

E: UNK-UNK-UNK-UNK-MSE-UNK

A: MccD

B: MccD

hetero molecules

D: UNK-UNK-UNK-MSE-UNK

E: UNK-UNK-UNK-UNK-MSE-UNK

A: MccD

B: MccD

hetero molecules

defined by software
193 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	95.100, 95.100, 128.685
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	173
Space group name H-M	P6₃

#1: Protein/peptide	UNK-UNK-UNK-MSE-UNK Mass: 536.525 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The N-terminal part of MccD protein / Source: (gene. exp.) Escherichia coli (E. coli) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Protein/peptide	UNK-UNK-UNK-UNK-MSE-UNK Mass: 621.630 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The N-terminal part of MccD protein / Source: (gene. exp.) Escherichia coli (E. coli) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Protein	MccD / MccD protein Mass: 31602.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mccD Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q83Y56
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.65 Å³/Da / Density % sol: 53.51 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.6 M Na Citrate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.1→39.22 Å / Num. obs: 38222 / % possible obs: 99.3 % / Redundancy: 4.6 % / R_merge(I) obs: 0.049 / Net I/σ(I): 19
Reflection shell	Resolution: 2.1→2.14 Å / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	dev_1888	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.1→39.22 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.86 / Phase error: 23.56 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2228	3270	4.98 %
R_work	0.1993	-	-
obs	0.2004	65623	94.35 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1→39.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3690	0	1	265	3956

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	3794
X-RAY DIFFRACTION	f_angle_d	0.702	5138
X-RAY DIFFRACTION	f_dihedral_angle_d	13.283	1347
X-RAY DIFFRACTION	f_chiral_restr	0.027	552
X-RAY DIFFRACTION	f_plane_restr	0.002	668

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 (%)
2.1005-2.1318	0.3004	60	0.2619	1196	X-RAY DIFFRACTION	37
2.1318-2.1651	0.3104	83	0.2532	1620	X-RAY DIFFRACTION	52
2.1651-2.2006	0.2718	101	0.2469	1884	X-RAY DIFFRACTION	61
2.2006-2.2386	0.2727	114	0.2475	2135	X-RAY DIFFRACTION	68
2.2386-2.2793	0.27	120	0.2382	2449	X-RAY DIFFRACTION	77
2.2793-2.3231	0.2964	158	0.2622	2666	X-RAY DIFFRACTION	85
2.3231-2.3705	0.2565	122	0.2551	2913	X-RAY DIFFRACTION	92
2.3705-2.422	0.3011	130	0.2503	2960	X-RAY DIFFRACTION	93
2.422-2.4784	0.2616	132	0.2408	2910	X-RAY DIFFRACTION	94
2.4784-2.5404	0.2744	159	0.2284	2976	X-RAY DIFFRACTION	94
2.5404-2.609	0.2232	171	0.2193	2939	X-RAY DIFFRACTION	94
2.609-2.6858	0.1859	156	0.2156	2942	X-RAY DIFFRACTION	94
2.6858-2.7724	0.259	176	0.2103	2943	X-RAY DIFFRACTION	95
2.7724-2.8715	0.2383	155	0.2029	2978	X-RAY DIFFRACTION	95
2.8715-2.9864	0.212	174	0.2071	2973	X-RAY DIFFRACTION	95
2.9864-3.1223	0.2182	132	0.195	2965	X-RAY DIFFRACTION	95
3.1223-3.2868	0.2423	143	0.188	3027	X-RAY DIFFRACTION	95
3.2868-3.4927	0.1845	143	0.177	2998	X-RAY DIFFRACTION	95
3.4927-3.7621	0.1713	168	0.1537	2949	X-RAY DIFFRACTION	95
3.7621-4.1403	0.1869	175	0.1531	2978	X-RAY DIFFRACTION	95
4.1403-4.7386	0.1719	172	0.1508	2973	X-RAY DIFFRACTION	95
4.7386-5.9667	0.2195	144	0.1966	3011	X-RAY DIFFRACTION	95
5.9667-39.2271	0.2574	182	0.2321	2968	X-RAY DIFFRACTION	95

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	0.0468	-0.103	0.0059	0.2321	-0.0138	0.0007	0.0195	0.0463	0.0045	-0.4241	0.408	-1.0236	0.2061	0.9695	-0.448	0.609	-0.0361	0.0403	0.9362	0.0267	1.26	35.807	0.8143	7.3697
2	8.0592	0.0583	1.1261	0.0107	-0.1103	2.7449	0.0966	0.4426	-0.0664	-0.0912	-0.0617	0.2072	0.144	-0.1093	-0.0525	1.2102	-0.0144	0.2319	0.9683	0.2521	0.901	18.8445	-25.0322	-37.0506
3	2.2191	1.8951	0.4587	4.6396	-0.3227	3.9003	-0.0891	-0.0767	-0.1365	0.0805	0.049	-0.4033	-0.0451	0.2584	0.015	0.1585	0.0318	-0.0071	0.2652	-0.0001	0.2062	22.5173	-5.2208	8.1708
4	2.2613	-0.1651	0.0999	2.7304	-0.0603	3.3009	-0.0549	-0.0277	-0.2842	0.0002	0.0313	-0.3038	0.2815	0.1995	-0.006	0.2116	0.0689	0.0141	0.2505	0.0266	0.2313	21.5271	-17.5985	8.8116
5	1.8844	1.1073	0.3813	2.8607	-0.3927	3.9714	-0.0242	0.2669	-0.166	-0.2305	0.1253	-0.1895	0.2944	0.1844	-0.1158	0.1855	0.0749	0.008	0.2716	0.0016	0.1882	16.0979	-9.0845	-5.2386
6	4.3427	0.4318	-0.2466	1.8798	-0.8632	2.7082	0.1568	0.7343	0.2519	-0.3038	-0.125	-0.3565	-0.0224	0.4367	-0.0533	0.2659	0.0621	0.0559	0.3772	0.0642	0.2682	29.1359	1.0637	-8.6645
7	5.8707	-2.1421	0.0088	1.4431	0.2447	0.1788	-0.013	0.1915	0.3618	0.019	0.023	-0.7221	-0.1073	0.2439	-0.0562	0.2884	-0.021	-0.0058	0.3613	0.0353	0.5966	38.2173	-0.5138	1.125
8	3.4857	-3.4938	1.1851	3.8316	-0.6521	1.8353	0.3364	0.9013	-0.3924	-0.0958	0.1152	-0.4854	0.0886	0.1243	-0.4757	0.2919	-0.0083	0.0411	0.6666	-0.0724	0.9651	48.5915	-6.6141	-4.9612
9	5.0908	2.0597	0.8339	2.9094	-0.2929	2.7339	0.0272	0.0301	0.4932	-0.1937	-0.2537	-0.1628	-0.2655	0.1339	0.1963	0.2884	0.0561	0.0344	0.1583	0.0319	0.2536	21.042	3.8018	-0.9011
10	1.8614	0.382	0.0453	2.2647	-0.169	2.3568	-0.0034	-0.1077	-0.0831	0.0029	-0.0088	-0.2203	0.1109	0.3034	0.0311	0.1194	0.0525	0.0003	0.2568	0.0381	0.1621	22.2896	-7.3551	-34.1233
11	5.1651	0.9268	0.6526	1.8569	-0.2938	4.0044	0.2484	0.575	0.2002	-0.1842	-0.3598	-0.4745	-0.2633	1.3238	0.3385	0.6524	0.3543	-0.117	1.547	0.6339	0.5525	23.2141	-29.9316	-15.7829
12	1.3951	2.8007	0.8107	6.687	-1.2075	7.823	-0.1572	-0.3845	-0.3865	0.8208	0.6178	-0.1899	0.7918	-0.0257	-0.3198	0.358	0.0838	0.0004	0.4103	0.0892	0.2981	12.5583	-16.6478	-20.297
13	2.1852	-1.5645	0.6493	1.4456	-0.4915	0.2555	0.1888	-0.2224	-0.5789	0.0751	0.0975	-0.6237	0.4002	-0.0679	-0.272	0.4307	0.0383	-0.0897	0.2463	0.0406	0.8582	20.0393	-26.9046	-33.028
14	1.2066	-0.7051	-0.0024	1.5353	0.476	1.2248	0.229	-0.1365	-0.4238	0.5037	0.302	-1.1403	0.2586	-0.1336	-0.2404	0.7251	0.1518	-0.4705	0.1469	0.2062	1.1629	27.23	-34.3638	-26.3551
15	2.0602	1.5524	-0.5728	7.2223	0.6844	4.1257	0.0246	-0.0545	0.0116	-0.0033	0.001	0.5228	0.2524	-0.3914	-0.0464	0.127	-0.0102	-0.031	0.2698	0.0469	0.1941	9.9799	-11.7114	-30.8924

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'D' and (resid -1 through 3 )
2	X-RAY DIFFRACTION	2	chain 'E' and (resid -3 through 2 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 29 through 62 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 63 through 106 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 107 through 144 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 145 through 191 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 192 through 224 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 236 through 256 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 257 through 267 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 30 through 163 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 164 through 174 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 175 through 192 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 193 through 225 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 236 through 256 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 257 through 267 )

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