PDB-4mi1: Crystal structure of the double mutant (S112A, H303A) of B.anthra...

ID or keywords:

Entry

Database: PDB / ID: 4mi1

Title

Crystal structure of the double mutant (S112A, H303A) of B.anthracis mycrocine immunity protein (MccF) with aspartyl sulfamoyl adenylates

Components

Microcin immunity protein MccF

Keywords

IMMUNE SYSTEM / CSGID / MCCF / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / microcine immunity protein / serine peptidase S66

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: 1.4 Å

Authors

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

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of the double mutant (S112A, H303A) of B.anthracis mycrocine immunity protein (MccF) with aspartyl sulfamoyl adenylates
Authors: Nocek, B. / Severinov, K. / Anderson, W.F. / Joachimiak, A.

History

Deposition	Aug 30, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 23, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jul 17, 2019	Group: Data collection / Derived calculations / Refinement description Category: software / struct_conn Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2	Sep 20, 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
Revision 1.3	Dec 6, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4mi1.cif.gz	304.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4mi1.ent.gz	248.4 KB	Display	PDB format
PDBx/mmJSON format	4mi1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4mi1_validation.pdf.gz	1004 KB	Display	wwPDB validaton report
Full document	4mi1_full_validation.pdf.gz	1007.4 KB	Display
Data in XML	4mi1_validation.xml.gz	30 KB	Display
Data in CIF	4mi1_validation.cif.gz	44.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mi/4mi1 ftp://data.pdbj.org/pub/pdb/validation_reports/mi/4mi1	HTTPS FTP

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Related structure data

Related structure data	3gjzS 4jvo 4mjx S: Starting model for refinement
Similar structure data	3u1b-d 3tyx-d 5k99-d 3tlc-d 3tle-d 3tla-d 4iiy-d 3t5m-d 3tlg-d 3tlz-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	TargetTrack: CSGID-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

hetero molecules

77.8 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)	117.894, 117.894, 55.984
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: 38315.387 Da / Num. of mol.: 2 / Mutation: S112A, H303A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BA_1949, BAS1809, GBAA_1949 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q81RT8, UniProt: A0A6L8PEJ7*PLUS
#2: Chemical	ChemComp-DSZ / 5'-O-(L-alpha-aspartylsulfamoyl)adenosine Mass: 461.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₁₉N₇O₉S
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 482 / 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: 2.54 Å³/Da / Density % sol: 51.55 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20 % Peg 3350, Ammonium Citrate tribasic, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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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: Aug 12, 2013 / 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: 1.4→117 Å / Num. obs: 188639 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / R_merge(I) obs: 0.048 / Net I/σ(I): 30
Reflection shell	Resolution: 1.4→1.42 Å / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	dev_1639	refinement
MOLREP		phasing
CCP4		model building
REFMAC	5.7.0029	refinement
HKL-3000		data reduction
HKL-3000		data scaling
CCP4		phasing
SBC-Collect		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GJZ

3gjz

Resolution: 1.4→26.08 Å / Cor.coef. F_o:F_c: 0.98 / Cor.coef. F_o:F_c free: 0.971 / SU ML: 0.1 / σ(F): 1.35 / Phase error: 18.8 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection
R_free	0.1582	9437	5 %
R_work	0.1278	-	-
obs	0.1293	188639	90.02 %
all	-	136187	-

Solvent computation

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

Displacement parameters

B_iso mean: 20.591 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.26 Å²	0 Å²	0 Å²
2-	-	-0.26 Å²	0 Å²
3-	-	-	0.51 Å²

Refinement step

Cycle: LAST / Resolution: 1.4→26.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5313	0	77	482	5872

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	5652
X-RAY DIFFRACTION	f_angle_d	1.377	7705
X-RAY DIFFRACTION	f_dihedral_angle_d	13.261	2104
X-RAY DIFFRACTION	f_chiral_restr	0.081	834
X-RAY DIFFRACTION	f_plane_restr	0.007	989

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 (%)
1.3998-1.4157	0.2116	92	0.1606	1506	X-RAY DIFFRACTION	16
1.4157-1.4323	0.1807	125	0.1671	2050	X-RAY DIFFRACTION	22
1.4323-1.4498	0.1623	111	0.1716	2503	X-RAY DIFFRACTION	26
1.4498-1.4681	0.2167	148	0.171	2898	X-RAY DIFFRACTION	31
1.4681-1.4875	0.2015	166	0.167	3293	X-RAY DIFFRACTION	35
1.4875-1.5078	0.2019	194	0.1653	3680	X-RAY DIFFRACTION	39
1.5078-1.5294	0.1779	215	0.1679	3967	X-RAY DIFFRACTION	42
1.5294-1.5522	0.1918	250	0.1686	4425	X-RAY DIFFRACTION	47
1.5522-1.5764	0.2	239	0.1712	4708	X-RAY DIFFRACTION	50
1.5764-1.6023	0.2038	247	0.1627	4772	X-RAY DIFFRACTION	51
1.6023-1.6299	0.1848	257	0.1578	4774	X-RAY DIFFRACTION	51
1.6299-1.6595	0.1793	270	0.1594	4752	X-RAY DIFFRACTION	51
1.6595-1.6915	0.2043	259	0.1534	4811	X-RAY DIFFRACTION	51
1.6915-1.726	0.1785	220	0.1509	4931	X-RAY DIFFRACTION	52
1.726-1.7635	0.1636	251	0.1506	5107	X-RAY DIFFRACTION	54
1.7635-1.8045	0.1572	298	0.1367	5336	X-RAY DIFFRACTION	57
1.8045-1.8496	0.1554	292	0.1317	5835	X-RAY DIFFRACTION	62
1.8496-1.8996	0.1599	310	0.13	6352	X-RAY DIFFRACTION	68
1.8996-1.9555	0.145	378	0.1196	7185	X-RAY DIFFRACTION	76
1.9555-2.0186	0.1576	440	0.1162	7491	X-RAY DIFFRACTION	81
2.0186-2.0907	0.1316	413	0.1144	8305	X-RAY DIFFRACTION	87
2.0907-2.1744	0.1478	472	0.1126	8549	X-RAY DIFFRACTION	91
2.1744-2.2733	0.1454	468	0.1168	8680	X-RAY DIFFRACTION	93
2.2733-2.3931	0.1339	463	0.1187	9005	X-RAY DIFFRACTION	95
2.3931-2.5429	0.1555	463	0.1223	9258	X-RAY DIFFRACTION	97
2.5429-2.739	0.1727	506	0.1183	9148	X-RAY DIFFRACTION	98
2.739-3.0143	0.1562	498	0.1352	9259	X-RAY DIFFRACTION	98
3.0143-3.4496	0.1626	463	0.1323	9281	X-RAY DIFFRACTION	98
3.4496-4.3429	0.1568	498	0.1144	8926	X-RAY DIFFRACTION	95
4.3429-26.0846	0.159	431	0.1356	8415	X-RAY DIFFRACTION	89

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	1.5803	0.679	0.2048	1.7779	0.3261	0.5291	-0.0711	0.1114	-0.0952	-0.1507	0.0892	-0.0603	-0.0101	0.0311	0.0103	0.1143	-0.0049	0.0022	0.0865	-0.0104	0.0862	-19.6532	11.6762	-6.0687
2	1.2748	0.9167	0.0115	1.5758	0.152	0.5393	-0.0317	-0.0219	-0.1228	0.038	-0.0091	-0.1193	0.038	-0.0065	0.0345	0.1193	0.0117	-0.0133	0.1032	-0.0101	0.1059	-15.5211	12.0095	-1.741
3	1.5609	1.0784	-0.0054	1.629	-0.0289	0.5325	-0.1168	0.0572	0.0011	-0.1524	0.0357	0.0989	-0.0027	-0.0648	0.088	0.1252	0.001	-0.0226	0.1024	-0.0206	0.0992	-22.9105	18.4781	-7.9637
4	2.2449	-0.4255	-0.7922	2.2211	0.3536	0.6629	-0.1501	0.2838	-0.0064	-0.3628	-0.088	0.5252	-0.1137	-0.2713	0.1913	0.174	-0.0409	-0.0825	0.196	-0.0302	0.2647	-39.1062	15.7077	-8.4498
5	2.5945	-1.6299	1.0689	2.4219	-0.8756	1.4979	-0.2219	-0.3757	-0.0561	0.2846	0.1498	0.5298	-0.0618	-0.4373	-0.0654	0.1645	-0.0299	0.0263	0.2666	-0.0552	0.2899	-39.7872	18.3404	4.9349
6	1.4569	0.3027	-0.1004	0.7559	0.2101	0.3085	-0.0553	0.126	0.2461	-0.2145	0.0124	0.2839	-0.0904	-0.1417	0.0446	0.1638	0.0204	-0.0896	0.1424	-0.011	0.1868	-28.558	34.8756	-8.7281
7	0.8083	0.3409	0.5566	1.6047	-0.043	1.139	-0.0055	0.0024	0.2481	-0.0787	-0.0567	0.4638	-0.0825	-0.1552	0.044	0.1221	0.036	-0.0639	0.1672	-0.0399	0.2658	-36.3607	35.2106	-2.5941
8	0.8469	-0.3393	-0.1401	1.8764	0.1267	0.5074	-0.0767	0.0195	0.2398	-0.2285	-0.0706	0.5813	-0.1177	-0.3032	-0.0263	0.1664	0.0546	-0.1406	0.2311	-0.0451	0.3928	-40.3697	36.1243	-6.5494
9	1.8399	-0.2582	-1.1235	0.6289	0.0974	0.6878	-0.1237	0.1916	0.1162	-0.3343	-0.0664	0.3104	-0.0847	-0.1206	0.1438	0.2155	-0.0385	-0.1068	0.204	-0.0388	0.2273	-34.8484	22.3109	-11.7811
10	1.9776	-0.941	0.8918	1.1493	-0.9709	0.8367	0.0524	0.2889	-0.0023	-0.7136	-0.1654	0.4252	0.0342	-0.3419	-0.154	0.3048	-0.0747	-0.2255	0.2568	-0.0487	0.2972	-37.4665	20.8895	-19.12
11	1.8604	0.4108	-0.34	1.8844	-0.4433	1.6993	0.07	0.0319	0.3427	0.0133	0.0034	0.1823	-0.3246	-0.0498	-0.0287	0.2586	0.076	-0.011	0.1579	-0.1146	0.2949	-22.4507	62.3007	7.0076
12	0.6335	-0.1955	0.0168	1.4902	0.1093	0.5005	-0.0356	-0.3763	0.5111	0.0714	-0.0248	0.645	-0.2799	-0.4442	0.0609	0.2448	0.1297	0.0092	0.1764	-0.1894	0.3897	-30.513	59.2557	11.0953
13	1.7021	-0.1532	-0.1476	0.9465	0.3513	0.853	-0.0095	0.0138	0.2393	-0.1411	-0.0481	0.3548	-0.2704	-0.1264	0.0122	0.2315	0.0511	-0.0643	0.1198	-0.0429	0.239	-24.4416	55.4919	-0.446
14	0.8528	0.0625	0.295	0.7467	-0.1057	0.9041	0.0107	-0.1586	0.2252	0.1316	-0.1007	0.0912	-0.2742	-0.033	0.085	0.2517	-0.0006	-0.0064	0.1476	-0.0766	0.1843	-11.0226	58.1827	14.2847
15	2.7654	-0.4465	-0.7501	0.9927	0.608	2.6144	-0.0571	-0.679	-0.0383	0.3041	-0.0253	0.1473	0.0077	0.0824	0.0953	0.2506	-0.0281	0.0125	0.1902	-0.0263	0.1347	-10.3882	47.0739	22.5008
16	1.157	0.3864	0.4236	1.2927	0.2784	0.3483	-0.0195	0.0409	0.0832	-0.1157	-0.0199	0.1457	-0.1199	-0.0018	0.039	0.151	0.0166	-0.0227	0.1069	-0.0166	0.0977	-12.3847	43.477	-1.5392
17	0.7414	0.2718	0.1348	1.6269	0.2254	0.7602	0.0176	-0.0099	0.0532	-0.0016	-0.034	-0.0177	-0.1016	0.0216	0.0167	0.1173	0.0022	-0.0248	0.1041	-0.015	0.0852	-5.9182	43.0194	5.2835
18	3.6466	-4.5541	0.9134	5.8255	-1.0697	2.1262	0.0756	0.0462	0.2106	-0.1551	-0.0654	0.0089	-0.3111	0.0315	-0.0407	0.2037	-0.0271	-0.028	0.1068	0.0089	0.1661	-1.9102	59.3631	3.3734

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 26 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 27 through 82 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 83 through 157 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 158 through 177 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 178 through 198 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 199 through 253 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 254 through 279 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 280 through 302 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 303 through 319 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 320 through 333 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid -2 through 26 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 27 through 82 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 83 through 125 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 126 through 177 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 178 through 198 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 199 through 253 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 254 through 319 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 320 through 333 )

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