PDB-3u1b: Crystal structure of the S238R mutant of mycrocine immunity prote...

ID or keywords:

Entry

Database: PDB / ID: 3u1b

Title

Crystal structure of the S238R mutant of mycrocine immunity protein (MccF) with AMP

Components

Microcin immunity protein MccF

Keywords

IMMUNE SYSTEM / CSGID /

Structural Genomics / Center for Structural Genomics of Infectious Diseases / microcine immunity protein / MccF-like / AMP

Function / homology

Function and homology information

hydrolase activity /

nucleotide binding
Similarity search - Function

Biological species

Bacillus anthracis (anthrax bacterium)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.604 Å

Authors

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

Citation

Journal: J.Mol.Biol. / Year: 2012
Title: Structural and Functional Characterization of Microcin C Resistance Peptidase MccF from Bacillus anthracis.
Authors: Nocek, B. / Tikhonov, A. / Babnigg, G. / Gu, M. / Zhou, M. / Makarova, K.S. / Vondenhoff, G. / Aerschot, A.V. / Kwon, K. / Anderson, W.F. / Severinov, K. / Joachimiak, A.

History

Deposition	Sep 29, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 30, 2011	Provider: repository / Type: Initial release
Revision 1.1	May 2, 2012	Group: Database references
Revision 1.2	Jul 25, 2012	Group: Database references
Revision 1.3	Sep 13, 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_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	3u1b.cif.gz	288.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3u1b.ent.gz	233.9 KB	Display	PDB format
PDBx/mmJSON format	3u1b.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/u1/3u1b ftp://data.pdbj.org/pub/pdb/validation_reports/u1/3u1b	HTTPS FTP

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Related structure data

Related structure data	3gjzSC 3sr3C 3t5mC 3tyxC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3t5m-d 4mi1-d 3tyx-d 5k99-d 3tla-d 3tlc-d 3tle-d 4gyk-2 3tlg-d 4iiy-d 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	TargetDB: IDP00038

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #57 - Sep 2004 Catalase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: Microcin immunity protein MccF

B: Microcin immunity protein MccF

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	118.550, 118.550, 56.619
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	78
Space group name H-M	P4₃

#1: Protein	Microcin immunity protein MccF Mass: 38093.410 Da / Num. of mol.: 2 / Mutation: S238R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BAS1809, BA_1949, GBAA_1949 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21DE3 / References: UniProt: Q81RT8, UniProt: A0A6L8PEJ7*PLUS
#2: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Comment: AMP*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.61 Å³/Da / Density % sol: 52.89 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 30% Peg 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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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: Apr 20, 2011 / Details: mirrors
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: 1.604→34 Å / Num. all: 102999 / Num. obs: 101972 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / R_merge(I) obs: 0.075 / Net I/σ(I): 21
Reflection shell	Resolution: 1.604→1.63 Å / % possible all: 100

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
MOLREP		phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3GJZ

3gjz

Resolution: 1.604→33.688 Å / SU ML: 0.44 / σ(F): 1.35 / σ(I): 2 / Phase error: 19.17 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1898	5099	5 %	RANDOM
R_work	0.1638	-	-	-
all	0.17	106912	-	-
obs	0.1651	101893	98.75 %	-

Solvent computation

Shrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 51.732 Å² / k_sol: 0.43 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.7321 Å²	-0 Å²	0 Å²
2-	-	-3.7321 Å²	-0 Å²
3-	-	-	7.4643 Å²

Refinement step

Cycle: LAST / Resolution: 1.604→33.688 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5319	0	46	509	5874

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	5529
X-RAY DIFFRACTION	f_angle_d	1.607	7523
X-RAY DIFFRACTION	f_dihedral_angle_d	13.419	2053
X-RAY DIFFRACTION	f_chiral_restr	0.123	818
X-RAY DIFFRACTION	f_plane_restr	0.012	963

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 (%)
1.6036-1.6218	0.3257	172	0.3132	3200	X-RAY DIFFRACTION	98
1.6218-1.6409	0.3187	177	0.2932	3184	X-RAY DIFFRACTION	100
1.6409-1.6609	0.2955	188	0.2759	3246	X-RAY DIFFRACTION	100
1.6609-1.6819	0.293	176	0.2455	3210	X-RAY DIFFRACTION	100
1.6819-1.704	0.2791	158	0.2409	3286	X-RAY DIFFRACTION	100
1.704-1.7274	0.2581	173	0.2297	3266	X-RAY DIFFRACTION	100
1.7274-1.7521	0.2505	175	0.2134	3210	X-RAY DIFFRACTION	100
1.7521-1.7782	0.2863	160	0.2204	3260	X-RAY DIFFRACTION	100
1.7782-1.806	0.2263	185	0.2013	3229	X-RAY DIFFRACTION	100
1.806-1.8356	0.243	179	0.1966	3222	X-RAY DIFFRACTION	100
1.8356-1.8672	0.2256	163	0.1904	3264	X-RAY DIFFRACTION	100
1.8672-1.9012	0.2229	159	0.1788	3253	X-RAY DIFFRACTION	100
1.9012-1.9378	0.2108	161	0.1652	3268	X-RAY DIFFRACTION	100
1.9378-1.9773	0.1866	162	0.1662	3272	X-RAY DIFFRACTION	100
1.9773-2.0203	0.182	188	0.1699	3254	X-RAY DIFFRACTION	100
2.0203-2.0673	0.184	158	0.1641	3225	X-RAY DIFFRACTION	100
2.0673-2.119	0.1933	163	0.1642	3307	X-RAY DIFFRACTION	100
2.119-2.1763	0.1985	170	0.1524	3242	X-RAY DIFFRACTION	100
2.1763-2.2403	0.1794	175	0.149	3255	X-RAY DIFFRACTION	100
2.2403-2.3126	0.1781	184	0.1418	3226	X-RAY DIFFRACTION	100
2.3126-2.3952	0.1733	172	0.1484	3265	X-RAY DIFFRACTION	100
2.3952-2.4911	0.1977	164	0.1466	3291	X-RAY DIFFRACTION	100
2.4911-2.6044	0.1763	178	0.1451	3254	X-RAY DIFFRACTION	100
2.6044-2.7417	0.1822	171	0.1442	3286	X-RAY DIFFRACTION	100
2.7417-2.9134	0.187	156	0.1555	3286	X-RAY DIFFRACTION	100
2.9134-3.1382	0.1833	166	0.1625	3286	X-RAY DIFFRACTION	100
3.1382-3.4537	0.195	164	0.1615	3226	X-RAY DIFFRACTION	98
3.4537-3.9528	0.1827	181	0.1562	3109	X-RAY DIFFRACTION	94
3.9528-4.9775	0.1383	163	0.1349	3041	X-RAY DIFFRACTION	92
4.9775-33.695	0.2034	158	0.192	2871	X-RAY DIFFRACTION	84

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	2.6792	-0.1732	0.5232	0.4728	0.0532	0.4895	-0.2143	-0.3106	-0.0739	0.23	-0.084	0.2503	-0.1543	-0.0723	-0.4142	0.3513	-0.0429	-0.0371	-0.0179	0.0911	0.3014	16.6529	68.9431	-3.278
2	0.1255	0.0195	-0.0928	0.1487	0.0089	0.0723	-0.0066	0.116	0.2167	-0.0412	-0.0512	-0.3281	-0.2514	0.1974	-0.0011	0.3289	-0.0671	0.0537	0.3022	0.0954	0.4113	28.4328	55.9938	-18.0676
3	0.0623	-0.0803	-0.1131	0.1028	0.145	0.207	0.1589	0.0529	0.1655	-0.1646	-0.1187	-0.1324	-0.3054	0.0531	-0.0073	0.4233	-0.0905	0.011	0.2685	0.1258	0.4776	27.8428	65.5871	-15.453
4	0.0433	0.0627	-0.0939	0.1967	-0.3181	0.5142	0.0409	-0.042	0.1702	0.0447	-0.227	-0.9745	-0.2126	0.311	-0.0141	0.318	-0.0958	-0.0427	0.2775	0.0892	0.5389	34.8661	56.5819	-4.9696
5	0.1758	0.091	0.1104	0.058	0.0454	0.1669	-0.0194	0.093	0.137	-0.069	-0.0244	-0.4434	-0.2142	0.108	0.0007	0.2984	-0.0536	-0.0286	0.25	0.0645	0.364	26.7028	53.4545	-4.3529
6	0.0676	0.0044	-0.0131	0.0234	0.0266	0.0866	-0.0516	-0.104	0.349	0.1571	-0.1495	-0.1956	-0.4268	0.0596	-0.0007	0.4913	-0.0743	-0.1275	0.2425	0.0003	0.4356	26.8718	63.2716	5.8246
7	0.2563	-0.1002	-0.0069	0.5011	-0.1956	0.1157	-0.0558	0.0253	0.1441	0.0613	-0.0005	-0.2629	-0.2064	0.0968	-0.0001	0.3315	-0.0316	-0.0273	0.2218	0.0312	0.2821	19.3882	56.4278	-5.5817
8	0.0362	-0.0317	-0.0225	0.0519	0.0475	0.0455	-0.2184	0.0786	0.2178	-0.2477	-0.0354	0.3976	-0.1025	0.0416	0.0005	0.4243	0.0038	-0.0055	0.2231	0.0586	0.3025	11.9353	59.7187	-20.0598
9	0.0423	0.0189	0.0048	0.0257	-0.0185	0.0237	0.1416	0.053	0.309	0.2404	-0.0028	0.1369	-0.4699	-0.196	-0.0002	0.4743	0.0636	-0.0064	0.2516	0.0117	0.3304	5.6158	66.6584	-8.4805
10	0.2861	0.2845	0.1978	0.4383	-0.0597	0.5283	0.0985	0.1564	-0.0454	-0.2939	-0.1041	-0.0224	-0.1527	-0.0664	-0	0.3935	0.0078	0.0305	0.2991	0.0312	0.2049	11.4177	49.0882	-23.7075
11	0.1808	-0.0018	0.0213	0.6182	-0.4806	0.3647	-0.0063	-0.018	0.0562	0.134	-0.0085	-0.091	-0.0683	-0.0567	0	0.2784	-0.0035	-0.0299	0.2227	0.0004	0.2075	10.4014	47.1816	1.0586
12	0.0158	0.0072	-0.0102	0.0057	0.0123	0.1371	-0.1154	-0.1962	0.1495	0.2551	0.0877	0.106	-0.2548	0.1761	0.0015	0.378	0.0222	-0.0265	0.3016	0.0108	0.2467	7.3745	49.736	9.45
13	0.1332	-0.2108	0.167	0.3277	-0.2667	0.2146	-0.0369	0.0077	-0.0325	-0.0451	-0.0126	-0.1755	-0.0132	0.0515	0	0.2365	-0.0044	-0.0131	0.2227	0.0182	0.2025	13.041	38.2969	-2.0694
14	0.1636	-0.329	0.2006	0.6832	-0.3309	0.5536	0.0303	0.0204	-0.04	-0.0589	-0.0321	-0.0183	-0.0479	-0.0958	-0	0.2564	0.0007	-0.0131	0.237	0.0166	0.1879	6.179	40.7109	-6.9982
15	0.2017	-0.2347	0.1922	0.3018	-0.2557	0.2457	-0.0488	-0.1894	0.0942	0.1092	0.0764	0.0386	-0.2306	-0.1329	-0	0.3685	0.0291	-0.0231	0.2374	-0.0178	0.2367	2.6458	58.1349	-2.2518
16	0.1173	-0.0039	0.0146	0.0229	0.0327	0.0469	-0.1683	-0.4882	-0.153	0.2412	-0.198	0.1377	0.0993	-0.2708	0.0009	0.3696	0.0761	0.0378	0.3622	-0.0055	0.3004	23.6678	12.4265	21.001
17	0.1847	-0.0856	0.0779	0.1083	-0.124	0.1351	-0.0098	-0.0063	-0.0918	-0.1721	-0.0208	0.0276	0.1229	0.0245	0.0001	0.3012	0.0136	0.0165	0.2219	0.0254	0.2234	21.3018	8.1666	0.2711
18	0.0043	-0.0134	-0.0154	0.0906	0.0569	0.0508	0.0336	0.0535	-0.3245	-0.2274	0.1186	0.161	0.0403	-0.0361	-0.0002	0.3367	-0.0205	-0.0295	0.2813	0.0071	0.2873	10.5851	13.0575	-3.6749
19	0.112	-0.3157	0.0693	0.8457	-0.2677	0.5119	-0.0897	-0.0532	-0.0785	-0.0102	0.1018	0.0797	0.0096	-0.0326	0.0002	0.2378	0.0071	-0.0075	0.2242	0.0289	0.2015	11.8536	19.7342	6.2213
20	0.2005	-0.3267	0.1299	0.5342	-0.2377	0.3834	-0.1826	-0.0383	0.0246	0.1064	0.0331	-0.152	0.0539	0.0351	-0	0.2716	0.029	-0.0065	0.2494	0.0277	0.2285	22.78	19.1622	9.4735
21	0.0319	-0.0553	0.0306	0.0934	-0.0489	0.0591	0.0015	-0.0271	-0.1841	-0.1352	-0.201	-0.4865	-0.0097	0.0428	-0.0007	0.2808	0.0479	0.0657	0.2659	0.0669	0.3228	35.9641	9.6866	3.3484
22	1.733	0.0002	-1.0386	0.2295	0.5403	1.9006	-0.292	-0.0215	-0.013	0.6214	-0.1298	-0.5157	0.1413	0.2922	-0.3854	0.3918	0.0708	-0.084	0.2966	0.1027	0.3446	34.5933	10.7863	18.1817
23	0.4275	0.3757	0.0505	0.8153	0.3307	0.1785	-0.1258	0.0015	-0.0463	-0.0678	0.1217	-0.5419	-0.1811	0.0264	0.1915	0.2833	0.0831	-0.0048	0.3061	0.1248	0.4429	40.9154	18.2902	2.5804
24	0.0043	0.0153	-0.02	0.0552	-0.0633	0.1672	-0.0275	0.4281	-0.2024	-0.6964	0.1603	-0.4115	-0.007	0.1734	-0.0039	0.5021	0.0632	0.1724	0.367	-0.0322	0.3524	32.7252	11.5595	-12.5431
25	0.1583	-0.0204	-0.0532	0.6997	-0.4876	0.5823	-0.0848	-0.0717	0.0837	0.1245	-0.0375	-0.3662	-0.0153	0.1421	-0.0016	0.2088	0.0077	-0.0701	0.264	0.0264	0.3601	33.0544	29.6637	8.4566
26	0.4772	-0.3334	-0.4121	0.4602	0.1172	0.483	-0.1939	-0.3668	0.3125	0.2883	-0.1895	0.0484	-0.1943	-0.0135	-0.1017	0.4471	0.0447	-0.2081	0.3924	-0.0401	0.4212	28.9564	35.5973	19.8334
27	0.1486	0.0262	-0.0163	0.4427	-0.3424	0.2627	-0.0708	-0.0166	0.0647	-0.0271	-0.1154	-0.302	-0.0379	0.1524	0.0001	0.2302	-0.0172	-0.0665	0.2455	0.0421	0.3403	30.4033	37.1716	2.8281
28	0.0889	-0.0921	0.012	0.6808	-0.3684	0.2276	-0.0771	-0.0192	0.1332	0.0194	-0.153	-0.5535	0.0295	0.2651	-0.0104	0.2296	-0.0166	-0.0574	0.3057	0.0877	0.5023	38.1335	36.2331	1.722
29	0.0963	0.0507	-0.0806	0.0268	-0.0421	0.0675	0.0081	-0.1059	0.039	-0.0786	-0.0047	-0.292	-0.0525	0.6497	-0.0031	0.3798	-0.1266	-0.0718	0.4245	0.0638	0.6831	42.3115	43.9314	11.8133
30	0.2969	0.1061	-0.3641	0.1818	0.059	0.6929	-0.1757	0.0435	0.0355	0.0645	-0.0972	-0.4077	0.1284	0.1983	-0.2347	0.247	0.0499	-0.1076	0.2857	0.0673	0.3781	37.0702	23.1146	13.1939

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid -2:15)
2	X-RAY DIFFRACTION	2	(chain A and resid 16:37)
3	X-RAY DIFFRACTION	3	(chain A and resid 38:51)
4	X-RAY DIFFRACTION	4	(chain A and resid 52:77)
5	X-RAY DIFFRACTION	5	(chain A and resid 78:94)
6	X-RAY DIFFRACTION	6	(chain A and resid 95:105)
7	X-RAY DIFFRACTION	7	(chain A and resid 106:142)
8	X-RAY DIFFRACTION	8	(chain A and resid 143:153)
9	X-RAY DIFFRACTION	9	(chain A and resid 154:166)
10	X-RAY DIFFRACTION	10	(chain A and resid 167:193)
11	X-RAY DIFFRACTION	11	(chain A and resid 194:224)
12	X-RAY DIFFRACTION	12	(chain A and resid 225:231)
13	X-RAY DIFFRACTION	13	(chain A and resid 232:256)
14	X-RAY DIFFRACTION	14	(chain A and resid 257:309)
15	X-RAY DIFFRACTION	15	(chain A and resid 310:333)
16	X-RAY DIFFRACTION	16	(chain B and resid 1:8)
17	X-RAY DIFFRACTION	17	(chain B and resid 9:45)
18	X-RAY DIFFRACTION	18	(chain B and resid 46:53)
19	X-RAY DIFFRACTION	19	(chain B and resid 54:102)
20	X-RAY DIFFRACTION	20	(chain B and resid 103:142)
21	X-RAY DIFFRACTION	21	(chain B and resid 143:153)
22	X-RAY DIFFRACTION	22	(chain B and resid 154:164)
23	X-RAY DIFFRACTION	23	(chain B and resid 165:177)
24	X-RAY DIFFRACTION	24	(chain B and resid 178:186)
25	X-RAY DIFFRACTION	25	(chain B and resid 187:224)
26	X-RAY DIFFRACTION	26	(chain B and resid 225:231)
27	X-RAY DIFFRACTION	27	(chain B and resid 232:256)
28	X-RAY DIFFRACTION	28	(chain B and resid 257:288)
29	X-RAY DIFFRACTION	29	(chain B and resid 289:293)
30	X-RAY DIFFRACTION	30	(chain B and resid 294:333)

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