PDB-3gjz: Crystal structure of microcin immunity protein MccF from Bacillus...

ID or keywords:

Entry

Database: PDB / ID: 3gjz

Title

Crystal structure of microcin immunity protein MccF from Bacillus anthracis str. Ames

Components

Microcin immunity protein MccF

Keywords

IMMUNE SYSTEM / NIAID Structural Genomic Centers for Infectious Diseases / microcin immunity protein MccF / MccF / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases

Function / homology

Function and homology information

hydrolase activity / nucleotide binding
Similarity search - Function

Biological species

Bacillus anthracis str. Ames (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.1 Å

Authors

Nocek, B. / Zhou, M. / Kwon, K. / Anderson, W. / 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	Mar 9, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 14, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	May 2, 2012	Group: Database references
Revision 1.3	Jul 25, 2012	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

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Data in CIF	3gjz_validation.cif.gz	39.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gj/3gjz ftp://data.pdbj.org/pub/pdb/validation_reports/gj/3gjz	HTTPS FTP

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Related structure data

Related structure data	3sr3C 3t5mC 3tyxC 3u1bC C: citing same article (ref.)
Similar structure data	4jvo-d 4mjx-d 5k99-d 1ofr-2 3tlc-d 1oab-d 3t5m-d 4hk5-2 3aga-d 1ofa-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) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: Microcin immunity protein MccF

B: Microcin immunity protein MccF

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	118.962, 118.962, 55.542
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: 38398.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis str. Ames (bacteria) Strain: Ames / isolate Porton / Gene: BAS1809, BA_1949, GBAA1949 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81RT8, UniProt: A0A6L8PEJ7*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Microcin immunity protein MccF

Mass: 38398.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus anthracis str. Ames (bacteria)
Strain: Ames / isolate Porton / Gene: BAS1809, BA_1949, GBAA1949 / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81RT8, UniProt: A0A6L8PEJ7*PLUS

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.56 Å³/Da / Density % sol: 51.93 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 0.056M Sodium dihydrogen phosphate, 1.344M di-Potassium hydrogen phosphate, pH 8.2, 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 Q315r / Detector: CCD / Date: Dec 10, 2008 / 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: 2.1→40 Å / Num. obs: 45439 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Redundancy: 3.9 % / R_merge(I) obs: 0.093 / Net I/σ(I): 15.2
Reflection shell	Resolution: 2.1→2.14 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.561 / Mean I/σ(I) obs: 2.13 / Num. unique all: 2222 / % possible all: 97.8

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		phasing
SHELX		model building
MLPHARE		phasing
DM		model building
CCP4		model building
ARP/wARP		model building
Coot		model building
REFMAC	5.5.0054	refinement
HKL-3000		data reduction
HKL-3000		data scaling
SHELX		phasing
DM		phasing
CCP4		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.1→40 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.947 / SU B: 12.098 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.21 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23176	2271	5.1 %	RANDOM
R_work	0.18659	-	-	-
all	0.189	44930	-	-
obs	0.18893	42659	98.89 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 21.257 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.23 Å²	0 Å²	0 Å²
2-	-	-0.23 Å²	0 Å²
3-	-	-	0.46 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5330	0	0	230	5560

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	5481
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3759
X-RAY DIFFRACTION	r_angle_refined_deg	1.689	1.966	7436
X-RAY DIFFRACTION	r_angle_other_deg	0.94	3	9198
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.432	5	668
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.903	24.637	248
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.134	15	944
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.687	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.101	0.2	803
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	6047
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1085
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	0.786	1.5	3334
X-RAY DIFFRACTION	r_mcbond_other	0.228	1.5	1343
X-RAY DIFFRACTION	r_mcangle_it	1.374	2	5417
X-RAY DIFFRACTION	r_scbond_it	2.613	3	2147
X-RAY DIFFRACTION	r_scangle_it	3.744	4.5	2018
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.1→2.16 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.322	161	-
R_work	0.265	3111	-
obs	-	-	97.82 %

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	2.8591	0.6512	0.1026	2.0078	1.1611	1.3248	0.0643	-0.2127	-0.3752	0.0431	0.0421	-0.0666	0.4435	0.0542	-0.1064	0.3137	-0.0023	-0.0111	0.1289	-0.0096	0.2622	41.108	-8.7721	2.8006
2	1.8089	0.0835	-0.9166	1.1599	-0.7721	1.1819	-0.0124	0.2551	-0.1948	-0.2945	-0.0341	0.2433	0.1469	-0.2324	0.0465	0.2654	-0.0387	-0.0751	0.1799	-0.1155	0.231	31.0627	-0.0218	-10.0655
3	1.4977	-2.3677	0.3393	3.8227	-0.4815	0.1151	0.1478	0.061	-0.223	-0.2142	-0.2212	0.5084	0.0315	-0.073	0.0734	0.1784	-0.0539	-0.0463	0.3579	-0.1498	0.4615	21.3969	10.5391	-0.0091
4	1.3312	-0.6867	-0.5314	2.4117	0.4238	2.2253	-0.069	-0.0369	-0.2004	0.0991	0.0728	0.2851	0.2358	-0.1308	-0.0039	0.2152	-0.0386	0.009	0.1367	-0.0356	0.2526	30.7471	0.3514	6.8458
5	1.2114	0.1515	-0.0323	1.2402	0.3767	1.9434	-0.0458	-0.0186	-0.1879	0.0759	0.0155	0.0675	0.0863	-0.0343	0.0303	0.229	-0.0043	-0.0026	0.1465	-0.0243	0.2424	39.8724	2.2403	3.7456
6	1.4153	-1.1418	2.084	4.662	-5.6006	9.2839	-0.0409	0.1513	-0.2435	-0.4692	-0.1527	-0.3474	0.5704	0.0228	0.1936	0.3084	0.0006	0.0312	0.1054	-0.0948	0.2439	47.4203	-2.0859	-10.3241
7	3.2023	0.4328	0.0317	9.3666	-3.0381	0.998	0.0353	0.0578	-0.1199	-0.5265	0.0956	0.356	0.2015	-0.0164	-0.1309	0.309	0.0243	-0.0167	0.2287	-0.0359	0.2713	58.1627	-3.834	-0.1925
8	0.721	0.5055	-1.4244	1.9802	-1.0243	2.8202	0.1278	0.0138	0.0999	-0.3828	0.0622	-0.1842	-0.1899	-0.016	-0.19	0.3119	0.044	0.0131	0.1912	-0.0532	0.2269	49.3336	11.4994	-14.7171
9	4.6584	2.5172	-0.5241	3.8486	0.4447	1.52	-0.2698	0.4443	0.4413	-0.5302	0.2243	0.3527	-0.1096	-0.1283	0.0456	0.3254	0.0406	-0.0189	0.2386	0.0081	0.1813	45.5529	11.316	-19.2613
10	0.8083	-0.1574	-0.4519	2.5725	-1.2037	1.5717	0.1119	-0.1268	-0.0099	0.0893	0.0767	-0.1522	-0.0206	0.0983	-0.1886	0.1738	0.0108	-0.0034	0.2048	-0.0918	0.2607	60.5292	11.0514	4.5181
11	3.6368	-1.2532	-0.4886	0.5378	0.4963	1.1334	-0.1087	-0.11	-0.1416	0.0406	0.0482	0.0683	-0.0023	0.1798	0.0605	0.2326	-0.0177	0.0184	0.2237	-0.0308	0.2541	41.0946	13.1518	11.6181
12	3.05	-3.5948	4.1462	5.2545	-6.3179	9.0533	0.0959	-0.0526	0.1046	0.0147	-0.008	-0.0329	0.113	-0.0604	-0.0879	0.1897	-0.0184	0.0012	0.1959	-0.0565	0.2301	49.1189	14.1561	6.6213
13	1.0719	-0.0563	0.2032	1.9276	-0.0046	2.2389	-0.0282	-0.0118	0.0589	-0.0547	0.0228	-0.1107	-0.0245	0.0285	0.0054	0.1845	0.0002	0.0404	0.208	-0.021	0.2145	47.7724	23.5171	9.419
14	1.0238	-0.1497	0.6895	2.0251	0.5487	1.0514	0.0932	0.0143	-0.0407	-0.1101	0.0331	-0.1204	-0.023	0.117	-0.1263	0.1762	-0.0222	0.0613	0.2029	-0.0419	0.2161	54.3707	22.259	2.3101
15	1.1017	-0.2127	0.3497	0.9743	-0.7665	1.7424	-0.0182	-0.0379	-0.0607	0.0317	0.0483	-0.0998	0.0234	-0.0098	-0.03	0.22	0.0238	0.0052	0.1521	-0.0552	0.2336	53.3978	7.5193	-0.111
16	4.304	4.6908	-0.4712	9.5805	-2.666	1.2118	0.0167	-0.0878	-0.4275	0.2795	-0.0479	-0.4298	0.0018	0.1642	0.0312	0.304	0.1277	-0.0038	0.2734	-0.0251	0.2556	57.2992	-0.5302	3.8836
17	7.4177	-2.4321	-2.0681	8.162	-6.8258	9.0392	-0.2655	-0.666	-0.1341	0.1202	0.1992	-0.3792	0.1787	0.2042	0.0663	0.2615	0.0503	-0.0698	0.3123	-0.0546	0.2386	36.0754	47.4	28.2004
18	0.6742	-0.5284	-0.1408	1.4021	0.5603	0.659	-0.0301	0.0281	0.1359	-0.3476	0.028	-0.1047	-0.1983	0.0545	0.0021	0.2734	-0.0142	0.0007	0.147	-0.0146	0.2137	42.2159	47.8016	6.2859
19	0.7467	-0.461	0.2105	1.8173	0.6055	1.617	-0.0561	-0.0922	0.0825	0.0064	0.0982	-0.2225	-0.0503	0.0791	-0.0421	0.1889	0.0015	0.0197	0.1841	-0.0486	0.2201	46.8682	40.6045	16.5958
20	0.7814	-0.2018	0.1342	2.4766	0.0275	0.388	-0.1093	-0.0931	0.0763	-0.0311	-0.0138	0.0037	-0.051	-0.0285	0.123	0.1937	0.0224	0.0006	0.2035	-0.0405	0.2018	36.7742	40.3648	16.8479
21	1.6082	-1.6005	1.1691	2.5872	-3.0322	6.1226	0.3583	-0.0071	0.1272	-0.4483	-0.1383	0.3622	0.0824	0.0053	-0.22	0.3096	0.082	-0.1153	0.1639	-0.1321	0.4697	23.7362	49.7468	10.6587
22	7.3118	3.78	-3.8773	8.5551	-4.6479	4.3296	-0.0401	-0.0788	0.2392	0.1522	0.0654	0.7025	-0.2181	-0.4595	-0.0252	0.2087	0.0493	-0.0151	0.2077	-0.0654	0.2545	25.1663	48.7427	25.5298
23	0.7841	-0.7585	-0.0716	1.9291	1.1488	8.2799	-0.0586	-0.0379	0.102	-0.2587	-0.0188	0.3746	-0.2213	0.0089	0.0774	0.2377	0.0168	-0.1032	0.1163	-0.0353	0.3212	19.4623	41.9267	8.5704
24	9.8082	0.405	-0.8243	2.9502	0.0024	1.1107	-0.3151	0.9578	0.228	-0.9227	0.2302	0.2251	-0.1201	-0.4123	0.0849	0.4569	-0.0214	-0.1362	0.3158	-0.0041	0.2167	23.1529	46.1861	-3.5357
25	0.6369	0.7031	0.3353	0.831	0.5507	2.5152	-0.047	-0.0981	0.0378	0.0035	-0.1193	0.161	-0.0077	-0.0956	0.1663	0.1646	0.0278	0.0585	0.1987	-0.034	0.3435	19.8767	30.3967	18.5037
26	1.9875	-0.3098	-0.9181	2.5653	-0.2475	0.4999	-0.0694	-0.1847	-0.2303	0.1108	0.0212	0.158	0.0181	0.0364	0.0482	0.2374	0.0099	0.0289	0.26	0.0076	0.2704	39.046	25.0487	17.9029
27	1.0918	-0.0238	0.1856	1.5348	-0.5814	9.9464	-0.0124	-0.1064	-0.0762	0.0282	-0.0541	0.1207	-0.0305	0.1933	0.0665	0.1741	0.0117	0.0062	0.2051	-0.0162	0.2554	28.1102	27.3081	15.8405
28	1.2819	-0.6294	-0.1703	2.759	0.7408	1.675	-0.0523	-0.045	-0.0872	-0.0174	-0.0442	0.2008	0.1609	-0.0606	0.0965	0.1442	-0.0106	0.0288	0.1939	-0.0251	0.233	27.1538	21.6287	13.7925
29	1.9353	-0.1098	-0.4272	3.0839	2.3955	1.9658	-0.1671	0.3118	-0.0992	-0.2714	-0.1657	0.4517	-0.181	-0.2962	0.3327	0.157	0.0023	-0.0716	0.3612	-0.0331	0.3259	19.6361	22.1742	4.298
30	11.4717	2.3344	-0.8916	11.7084	0.571	14.1165	-0.0007	-0.3307	-0.3071	0.5666	-0.2863	0.4747	0.2765	-0.8318	0.287	0.2527	-0.0229	0.0009	0.2638	-0.0011	0.2881	17.7956	14.8208	18.4637
31	0.3652	-0.3336	0.3871	2.8935	-0.1172	0.4384	-0.0817	-0.0587	0.0818	0.0052	-0.0523	0.2779	-0.0619	-0.0642	0.134	0.1595	0.0325	0.0039	0.2494	-0.0572	0.2586	23.6501	35.3341	17.1005
32	3.2945	2.9452	-0.9044	3.5785	-0.3904	0.75	0.0495	-0.3088	-0.1512	0.1307	-0.2312	0.0043	-0.0801	-0.2227	0.1817	0.2084	0.0838	0.032	0.369	-0.0673	0.2813	21.3183	37.9044	26.3782

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-1 - 16
2	X-RAY DIFFRACTION	2	A	17 - 51
3	X-RAY DIFFRACTION	3	A	52 - 63
4	X-RAY DIFFRACTION	4	A	64 - 103
5	X-RAY DIFFRACTION	5	A	104 - 140
6	X-RAY DIFFRACTION	6	A	141 - 160
7	X-RAY DIFFRACTION	7	A	161 - 168
8	X-RAY DIFFRACTION	8	A	169 - 179
9	X-RAY DIFFRACTION	9	A	180 - 193
10	X-RAY DIFFRACTION	10	A	194 - 206
11	X-RAY DIFFRACTION	11	A	207 - 225
12	X-RAY DIFFRACTION	12	A	226 - 240
13	X-RAY DIFFRACTION	13	A	241 - 257
14	X-RAY DIFFRACTION	14	A	258 - 294
15	X-RAY DIFFRACTION	15	A	295 - 321
16	X-RAY DIFFRACTION	16	A	322 - 332
17	X-RAY DIFFRACTION	17	B	1 - 8
18	X-RAY DIFFRACTION	18	B	9 - 63
19	X-RAY DIFFRACTION	19	B	64 - 102
20	X-RAY DIFFRACTION	20	B	103 - 142
21	X-RAY DIFFRACTION	21	B	143 - 153
22	X-RAY DIFFRACTION	22	B	154 - 164
23	X-RAY DIFFRACTION	23	B	165 - 179
24	X-RAY DIFFRACTION	24	B	180 - 190
25	X-RAY DIFFRACTION	25	B	191 - 211
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