PDB-5f9m: Crystal structure of native B3275, member of MccF family of enzymes

ID or keywords:

Entry

Database: PDB / ID: 5f9m

Title

Crystal structure of native B3275, member of MccF family of enzymes

Components

MccC family protein

Keywords

HYDROLASE / serine peptidase / MccF related protein / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

hydrolase activity / nucleotide binding
Similarity search - Function

Biological species

Bacillus cereus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.402 Å

Authors

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

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	HHSN272200700058C	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	HHSN272201200026C	United States

Citation

Journal: To Be Published
Title: Crystal structure of native B3275, member of MccF family of enzymes.
Authors: Nocek, B. / Severinov, K. / Anderson, W.F. / Joachimiak, A.

History

Deposition	Dec 9, 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	Sep 27, 2017	Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5f9m.cif.gz	551.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5f9m.ent.gz	457.6 KB	Display	PDB format
PDBx/mmJSON format	5f9m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5f9m_validation.pdf.gz	442.3 KB	Display	wwPDB validaton report
Full document	5f9m_full_validation.pdf.gz	452.5 KB	Display
Data in XML	5f9m_validation.xml.gz	47.7 KB	Display
Data in CIF	5f9m_validation.cif.gz	64.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f9/5f9m ftp://data.pdbj.org/pub/pdb/validation_reports/f9/5f9m	HTTPS FTP

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Related structure data

Related structure data	5f1yS S: Starting model for refinement
Similar structure data	5f5x-d 6p2m-d 6qky-2 5f1y-d 5jwz-1 3k3c-d 5jgy-d 6p2l-d 2dtj-2 3b8v-1 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-IDP95363

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: MccC family protein

B: MccC family protein

C: MccC family protein

D: MccC family protein

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

1

A: MccC family protein

C: MccC family protein

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

2

B: MccC family protein

D: MccC family protein

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

Unit cell

Length a, b, c (Å)	54.779, 70.858, 85.490
Angle α, β, γ (deg.)	92.12, 90.24, 89.87
Int Tables number	1
Space group name H-M	P1

#1: Protein	MccC family protein Mass: 39366.516 Da / Num. of mol.: 4 / Mutation: S116A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (strain ATCC 10987 / NRS 248) (bacteria) Strain: ATCC 10987 / NRS 248 / Gene: BCE_3281 / Production host: Escherichia coli (E. coli) / References: UniProt: Q734X3
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.11 Å³/Da / Density % sol: 41.57 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M sodium Chloride, 0.1 M BIS-TRIS, 25% Peg 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2015
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.4→37.19 Å / Num. obs: 48084 / % possible obs: 96.5 % / Redundancy: 2.1 % / R_merge(I) obs: 0.1 / Net I/σ(I): 8

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5F1Y

5f1y

Resolution: 2.402→37.19 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.67 / Phase error: 25.83 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2274	3138	4.98 %
R_work	0.1868	-	-
obs	0.1889	62982	92.85 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.402→37.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11041	0	0	160	11201

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	11324
X-RAY DIFFRACTION	f_angle_d	0.598	15344
X-RAY DIFFRACTION	f_dihedral_angle_d	14.416	4217
X-RAY DIFFRACTION	f_chiral_restr	0.024	1624
X-RAY DIFFRACTION	f_plane_restr	0.003	2001

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 (%)
2.4023-2.4399	0.3418	45	0.2663	926	X-RAY DIFFRACTION	21
2.4399-2.4799	0.2742	61	0.2742	1111	X-RAY DIFFRACTION	26
2.4799-2.5226	0.3598	63	0.2641	1304	X-RAY DIFFRACTION	30
2.5226-2.5685	0.2752	73	0.2569	1429	X-RAY DIFFRACTION	33
2.5685-2.6179	0.3237	76	0.27	1602	X-RAY DIFFRACTION	36
2.6179-2.6713	0.2857	85	0.2664	1698	X-RAY DIFFRACTION	40
2.6713-2.7294	0.3563	122	0.267	2041	X-RAY DIFFRACTION	47
2.7294-2.7928	0.3185	107	0.253	2162	X-RAY DIFFRACTION	51
2.7928-2.8626	0.2411	139	0.2411	2383	X-RAY DIFFRACTION	55
2.8626-2.94	0.321	125	0.2476	2486	X-RAY DIFFRACTION	58
2.94-3.0265	0.2352	126	0.2352	2652	X-RAY DIFFRACTION	61
3.0265-3.1241	0.2602	149	0.2294	2791	X-RAY DIFFRACTION	65
3.1241-3.2357	0.2466	153	0.2103	3114	X-RAY DIFFRACTION	71
3.2357-3.3652	0.2467	180	0.1935	3265	X-RAY DIFFRACTION	76
3.3652-3.5182	0.2191	199	0.1822	3510	X-RAY DIFFRACTION	82
3.5182-3.7036	0.2206	222	0.1669	3761	X-RAY DIFFRACTION	87
3.7036-3.9354	0.1815	220	0.1573	3993	X-RAY DIFFRACTION	91
3.9354-4.2388	0.2527	171	0.1494	4025	X-RAY DIFFRACTION	93
4.2388-4.6647	0.1793	216	0.1464	3912	X-RAY DIFFRACTION	91
4.6647-5.338	0.1885	192	0.1523	3900	X-RAY DIFFRACTION	90
5.338-6.7188	0.2072	225	0.1873	3938	X-RAY DIFFRACTION	92
6.7188-37.1943	0.2204	189	0.1851	3841	X-RAY DIFFRACTION	88

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	2.6447	-0.264	-0.1721	2.3599	-0.366	1.4155	0.0886	0.2429	0.0368	-0.1008	-0.0846	0.1314	-0.0735	-0.0147	-0.0054	0.183	-0.0038	-0.0238	0.2556	0.011	0.1737	-6.3271	-0.4862	-10.327
2	2.7008	-0.1626	1.342	0.1261	-0.0535	1.3609	-0.0935	-0.4905	0.1304	0.0543	0.1029	0.05	-0.159	-0.2486	-0.0375	0.2685	0.0102	0.0176	0.3035	-0.0701	0.3115	-8.0206	4.5613	8.9065
3	2.2976	-0.6813	0.5084	2.307	-0.2187	2.3048	-0.1014	-0.2121	0.1248	0.1478	0.0122	-0.0802	-0.0908	0.1226	0.091	0.1743	-0.0136	-0.0466	0.2532	0.0046	0.2049	8.849	-2.347	7.2651
4	2.4689	0.2862	-0.3815	1.4936	0.171	1.6826	0.0869	-0.2815	-0.0561	0.0623	-0.0609	0.117	-0.0039	0.0353	-0.0298	0.187	0.0052	0.0158	0.2383	0.023	0.2141	-33.5355	-0.0265	-30.2708
5	3.0185	-0.1269	-0.6263	1.5041	0.2169	2.0248	-0.0179	0.4485	0.018	-0.2132	0.1303	0.0031	0.1943	-0.3443	0.0157	0.2038	-0.0258	0.0057	0.3	-0.0348	0.2795	-37.6406	-5.2026	-48.3354
6	2.8592	0.4219	-0.6108	3.0477	0.1389	2.697	-0.0314	0.2961	-0.0417	-0.1723	-0.0449	-0.0161	0.0853	0.1526	0.075	0.1347	-0.0026	0.028	0.251	0.0186	0.1924	-18.0997	1.5513	-48.4805
7	2.5467	-0.4943	-0.5087	1.477	-0.4067	3.1895	-0.0925	0.0896	-0.3217	-0.282	-0.1899	-0.2561	0.276	-0.1072	0.105	0.3816	-0.0111	-0.0251	0.2015	-0.0123	0.3591	31.2379	-33.1712	8.1945
8	2.719	-0.084	-0.9816	0.7726	-0.1662	2.2986	0.0781	-0.1315	-0.7603	-0.2811	0.1715	-0.2314	0.5814	0.3647	0.1825	0.422	-0.0334	0.0253	0.2255	0.0486	0.4347	30.5538	-40.9424	16.9995
9	0.7175	-1.0061	0.6804	2.0827	-0.2516	1.7343	-0.0239	-0.1108	-0.0588	0.1349	-0.0848	-0.3084	-0.0567	0.1245	0.0599	0.278	0.0082	-0.0354	0.261	0.0416	0.2812	30.9987	-23.0542	12.7245
10	1.3202	0.0809	0.4656	1.7751	0.0204	1.405	0.0638	0.171	-0.2628	-0.2139	-0.0903	-0.1355	0.3369	0.0519	0.0352	0.3615	0.0815	-0.006	0.2805	-0.0876	0.3843	26.7778	-35.152	2.4281
11	1.3553	-0.6873	1.7398	1.7016	-0.4037	4.3441	-0.0052	-0.0646	-0.227	-0.0536	0.1064	0.1261	0.4834	-0.3807	-0.2367	0.384	-0.0677	-0.0339	0.2951	0.0086	0.469	10.6931	-42.5821	9.7835
12	2.3939	0.0074	0.5079	4.1375	1.0059	3.4952	-0.2808	0.2215	0.0298	-0.2057	-0.1116	0.1311	-0.0501	-0.0684	0.2003	0.3399	0.0327	-0.022	0.1845	0.0184	0.2206	18.2724	-23.7646	-4.8209
13	3.4025	-0.1817	0.8373	3.2179	-0.3507	1.4256	0.2234	0.1006	-0.0837	-0.2533	-0.0866	0.1454	0.1316	-0.0762	-0.0411	0.3166	0.0213	-0.0882	0.2204	-0.032	0.279	9.8856	-26.4635	-3.8629
14	3.0609	-0.128	0.8491	3.0646	-0.7524	3.0468	0.2968	0.2655	-0.4281	-0.4854	-0.1645	0.4559	0.2949	-0.4437	-0.2493	0.3976	-0.0106	-0.1336	0.3483	-0.0164	0.4059	3.4987	-31.2345	-7.5426
15	2.8592	0.6562	1.0427	2.337	0.1156	1.8738	0.2508	0.5134	-0.7821	-0.5487	-0.0104	0.261	0.5128	0.1213	-0.257	0.6076	0.0877	-0.0635	0.2687	-0.1209	0.5054	19.2193	-39.4567	-6.7786
16	2.1546	-0.4779	0.5666	1.0281	1.2264	3.6232	0.0872	-0.1171	0.1185	0.0926	-0.1548	-0.2501	-0.367	0.0433	0.0896	0.3509	-0.1008	0.0319	0.2883	0.0908	0.2885	4.2176	32.6592	-48.7479
17	5.3338	-0.1398	2.5851	2.1704	-0.4758	3.6246	0.3612	0.3363	0.6208	-0.0335	-0.1077	-0.112	-0.528	0.4419	-0.2289	0.3299	0.0143	0.04	0.2359	0.0231	0.3656	3.5991	40.4281	-57.52
18	0.0159	0.2129	0.0274	1.4933	0.3276	1.7275	0.0706	0.1149	-0.0068	-0.2564	-0.1513	-0.3417	-0.0625	0.2165	0.0497	0.2768	-0.0067	0.0215	0.2572	0.0637	0.2784	3.9835	22.5365	-53.3207
19	3.0575	0.3428	-0.6945	2.8228	-0.0892	1.9698	0.214	-0.428	-0.2601	0.3456	-0.1935	-0.2492	0.084	0.2507	-0.0628	0.3186	-0.0703	-0.0393	0.3536	-0.0271	0.3283	3.1405	24.3213	-41.8554
20	1.2389	0.0773	-0.2866	1.0739	-0.508	4.5442	0.0301	-0.2094	0.2074	0.1357	-0.2236	0.0313	-0.8422	-0.4087	0.2241	0.3812	-0.0796	0.0515	0.2683	-0.0435	0.5219	-3.5804	38.2545	-49.391
21	1.4869	-0.3454	-0.9607	0.6128	-0.3196	1.3214	0.0794	-0.0899	0.4359	0.3397	0.125	0.0713	-0.2412	0.247	-0.1754	0.4297	-0.0556	0.0801	0.2385	-0.051	0.522	-6.9964	43.457	-45.0743
22	1.4182	0.0075	-1.1819	1.6446	-0.0574	4.8782	-0.0543	-0.0561	0.355	0.3054	0.0365	-0.0843	-0.5045	-0.2829	0.028	0.3789	0.0653	0.1051	0.248	-0.0129	0.4333	-17.0085	42.8603	-47.6831
23	1.7453	0.7857	-0.4025	4.9557	2.1364	4.9383	-0.2841	-0.1986	-0.1213	0.0639	0.0392	0.0295	-0.0381	0.1345	0.2237	0.208	-0.0284	0.0423	0.1895	0.0213	0.3118	-8.7223	23.1087	-35.5826
24	4.167	-0.2255	0.5835	2.8736	0.5191	0.6176	0.2239	-0.1099	0.1834	0.0914	-0.3998	-0.0501	0.2259	0.0661	0.1572	0.4129	-0.0665	0.1659	0.2974	0.0381	0.2962	-12.6448	26.1316	-36.5262
25	2.2776	-0.1115	-0.1644	3.5617	-0.7827	1.5992	0.2566	-0.1653	0.1823	0.2358	-0.1446	0.3291	-0.2826	0.0047	-0.1461	0.3329	-0.0185	0.0937	0.2515	-0.0272	0.3088	-21.9798	27.6241	-34.5834
26	2.8046	-1.0764	-0.1554	2.1384	-0.4202	2.4639	0.2215	-0.2719	0.6601	0.6815	0.0506	0.2647	-0.5576	0.2117	-0.1954	0.5636	-0.1221	0.0588	0.2621	-0.0855	0.5655	-8.3232	38.7837	-34.5549

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 150 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 151 through 207 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 208 through 343 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 150 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 151 through 200 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 201 through 343 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 1 through 30 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 31 through 51 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 52 through 100 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 101 through 171 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 172 through 207 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 208 through 232 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 233 through 284 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 285 through 313 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 314 through 343 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 1 through 30 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 31 through 51 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 52 through 100 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 101 through 129 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 130 through 150 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 151 through 184 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 185 through 207 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 208 through 232 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 233 through 251 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 252 through 310 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 311 through 343 )

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