PDB-5usd: Crystal structure of MccF-like protein (BA_5613) in the complex w...

ID or keywords:

Entry

Database: PDB / ID: 5usd

Title

Crystal structure of MccF-like protein (BA_5613) in the complex with aspartyl sulfamoyl adenylate

Components

Peptidase S66

Keywords

HYDROLASE / S66 / MccF-like protein / Microcin C / aspartyl sulfamoyl adenylate /

Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

hydrolase activity
Similarity search - Function

Biological species

Bacillus anthracis (anthrax bacterium)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.095 Å

Authors

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

Citation

Journal: To Be Published
Title: Crystal structure of MccF-like protein (BA_5613) in the complex with aspartyl sulfamoyl adenylate
Authors: Nocek, B. / Anderson, W.F. / Joachimiak, A.

History

Deposition	Feb 13, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 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
Revision 1.2	Nov 15, 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	5usd.cif.gz	747.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5usd.ent.gz	633.7 KB	Display	PDB format
PDBx/mmJSON format	5usd.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/us/5usd ftp://data.pdbj.org/pub/pdb/validation_reports/us/5usd	HTTPS FTP

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Related structure data

Related structure data	5fd8S 4e5s S: Starting model for refinement
Similar structure data	4e5s-2 4img-d 4lal-1 4hk6-2 4lal-2 5fd8-d 4imf-d 4hnn-1 4hnn-3 3nvd-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-idp91764

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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: Peptidase S66

B: Peptidase S66

C: Peptidase S66

D: Peptidase S66

hetero molecules

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

1

A: Peptidase S66

D: Peptidase S66

hetero molecules

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

2

B: Peptidase S66

C: Peptidase S66

hetero molecules

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

Unit cell

Length a, b, c (Å)	74.456, 85.808, 124.804
Angle α, β, γ (deg.)	90.00, 92.32, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Peptidase S66 / Putative carboxypeptidase yocD Mass: 37245.090 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: yocD, GBAA_5613, A8C77_27310, BASH2_00378 / Production host: Bacillus anthracis str. Ames (bacteria) / References: UniProt: Q81JT5, UniProt: A0A6L8PVW7*PLUS
#2: Chemical	ChemComp-DSZ / 5'-O-(L-alpha-aspartylsulfamoyl)adenosine Mass: 461.407 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₄H₁₉N₇O₉S
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 566 / 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: 2.68 Å³/Da / Density % sol: 54.02 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS, 25% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2016 / Details: double mirror
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97945 Å / Relative weight: 1
Reflection	Resolution: 2.095→32.611 Å / Num. obs: 84529 / % possible obs: 92.7 % / Redundancy: 2.6 % / R_merge(I) obs: 0.093 / Net I/σ(I): 10.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5FD8

5fd8

Resolution: 2.095→32.611 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.56

	R_factor	Num. reflection	% reflection
R_free	0.2096	3795	5.06 %
R_work	0.1815	-	-
obs	0.183	74962	91.14 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.095→32.611 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10332	0	68	566	10966

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	10633
X-RAY DIFFRACTION	f_angle_d	0.619	14431
X-RAY DIFFRACTION	f_dihedral_angle_d	14.142	6331
X-RAY DIFFRACTION	f_chiral_restr	0.043	1660
X-RAY DIFFRACTION	f_plane_restr	0.003	1832

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 (%)
2.0948-2.1214	0.2956	84	0.218	1393	X-RAY DIFFRACTION	43
2.1214-2.1493	0.2129	98	0.2112	1927	X-RAY DIFFRACTION	60
2.1493-2.1787	0.2675	100	0.213	1964	X-RAY DIFFRACTION	60
2.1787-2.2098	0.2527	106	0.2146	2027	X-RAY DIFFRACTION	63
2.2098-2.2428	0.261	95	0.2178	2141	X-RAY DIFFRACTION	66
2.2428-2.2778	0.2758	127	0.2134	2245	X-RAY DIFFRACTION	69
2.2778-2.3152	0.2907	110	0.2136	2332	X-RAY DIFFRACTION	72
2.3152-2.3551	0.2704	117	0.2055	2360	X-RAY DIFFRACTION	74
2.3551-2.3979	0.2332	124	0.1997	2445	X-RAY DIFFRACTION	75
2.3979-2.444	0.2106	126	0.2012	2550	X-RAY DIFFRACTION	78
2.444-2.4939	0.2312	141	0.2088	2557	X-RAY DIFFRACTION	79
2.4939-2.5481	0.2513	127	0.2215	2685	X-RAY DIFFRACTION	82
2.5481-2.6073	0.2158	143	0.2048	2761	X-RAY DIFFRACTION	85
2.6073-2.6725	0.2601	165	0.2058	2776	X-RAY DIFFRACTION	87
2.6725-2.7447	0.2415	166	0.2043	2816	X-RAY DIFFRACTION	87
2.7447-2.8254	0.2466	160	0.2078	2885	X-RAY DIFFRACTION	89
2.8254-2.9166	0.2476	159	0.2121	2934	X-RAY DIFFRACTION	90
2.9166-3.0208	0.2392	149	0.2123	2943	X-RAY DIFFRACTION	92
3.0208-3.1416	0.2609	181	0.2052	3004	X-RAY DIFFRACTION	93
3.1416-3.2845	0.2079	175	0.1918	3044	X-RAY DIFFRACTION	93
3.2845-3.4574	0.202	166	0.182	3042	X-RAY DIFFRACTION	94
3.4574-3.6738	0.2015	162	0.1592	3091	X-RAY DIFFRACTION	94
3.6738-3.957	0.1829	174	0.1611	3044	X-RAY DIFFRACTION	94
3.957-4.3544	0.1584	184	0.1473	3059	X-RAY DIFFRACTION	94
4.3544-4.9825	0.163	149	0.1372	3054	X-RAY DIFFRACTION	93
4.9825-6.2702	0.1809	146	0.163	3055	X-RAY DIFFRACTION	92
6.2702-32.615	0.1818	161	0.1635	3033	X-RAY DIFFRACTION	90

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	1.6719	-0.407	0.6251	1.2285	-0.5474	2.2131	0.0117	0.0184	-0.0551	0.084	0.1609	-0.1678	0.0312	0.2148	-0.1604	0.1111	-0.0073	-0.0445	0.1813	-0.0162	0.2266	15.9797	3.8407	33.2472
2	0.9652	-0.0857	-0.3368	1.2969	0.2331	0.9509	-0.0408	-0.0052	0.0533	0.1467	0.1693	-0.2183	-0.0698	0.2161	-0.1181	0.1325	-0.0124	-0.022	0.1918	-0.0274	0.1919	16.2411	5.4347	38.6547
3	1.7746	0.0551	-0.1535	2.9308	-0.9876	2.2064	-0.0788	0.22	-0.1017	0.0441	0.0526	0.0749	0.295	-0.0967	-0.0072	0.203	-0.0094	0.0148	0.1978	-0.024	0.1613	4.9473	-9.1811	30.6716
4	3.7211	-0.3516	-0.2683	2.1039	0.5008	1.3819	-0.0765	0.0418	-0.5798	0.0817	-0.0046	0.1107	0.4587	-0.0465	0.0718	0.3369	-0.0175	0.08	0.1647	0.0588	0.2582	3.5126	-17.0962	39.3795
5	0.5068	0.0921	-0.2094	1.3505	0.3574	0.9189	-0.053	-0.04	-0.0224	0.5312	0.042	0.3533	0.113	-0.1444	0.0031	0.2973	0.0128	0.0889	0.1941	0.0252	0.2248	-4.3095	-2.4613	48.4153
6	2.2159	0.6996	-0.6876	2.7679	-1.1066	2.595	-0.0857	0.3269	0.088	-0.1146	0.2035	0.5663	0.1348	-0.3442	-0.1033	0.1425	-0.0074	0.0023	0.2757	0.0142	0.2928	-8.2294	-1.1377	33.5938
7	0.556	0.8986	0.4922	3.3913	0.1335	1.4277	-0.0461	-0.0152	-0.1437	-0.0017	-0.033	-0.1381	0.0091	-0.0989	0.0706	0.1236	-0.0188	0.0387	0.2424	0.0057	0.276	35.3104	-3.1574	17.5405
8	0.6237	0.1774	-0.2512	1.0037	-0.079	0.7566	0.044	-0.119	-0.0166	0.1245	-0.102	0.008	-0.0041	0.0462	0.0506	0.1261	-0.0277	-0.0207	0.2503	0.0099	0.2367	39.9386	-0.1646	17.7662
9	1.4304	0.3826	-0.3295	1.1672	-0.1891	1.2451	-0.0925	0.3471	0.0337	-0.2125	0.1887	0.3113	-0.0232	-0.3874	-0.0758	0.1864	-0.0435	-0.0366	0.4062	0.0408	0.3131	29.6061	1.2286	-0.5888
10	1.9958	-0.3259	0.0808	1.5568	0.175	1.7672	-0.0757	0.1385	-0.2999	-0.0684	-0.0956	0.0488	0.2239	0.0256	0.1601	0.1427	-0.0109	0.0106	0.2237	0.0038	0.3157	52.3848	-4.3699	3.184
11	1.0414	0.4283	-0.0991	0.7897	-0.1261	0.965	-0.0898	0.1911	-0.1154	-0.1123	0.0177	-0.0018	0.0875	-0.1337	0.0634	0.2292	-0.0611	0.0119	0.2809	-0.0048	0.2839	47.4914	2.3378	-5.8985
12	0.9468	0.1291	-0.6159	1.2937	-0.3639	1.2542	-0.215	0.415	-0.0952	-0.3567	0.1638	0.1089	0.1462	-0.3137	0.041	0.2218	-0.1045	-0.0405	0.4121	-0.0341	0.2736	39.4717	-4.1796	-8.3055
13	2.397	-0.1602	0.4622	1.2357	-0.161	1.3913	-0.1101	-0.1183	-0.202	-0.001	-0.0042	-0.1744	-0.0098	0.2282	0.0978	0.1733	-0.0143	0.0096	0.2948	0.064	0.2965	73.3374	17.0387	-14.9682
14	2.5658	-0.8564	0.1979	2.5216	0.0184	1.4365	-0.0761	0.0829	0.0876	-0.0487	-0.0412	-0.2975	-0.182	0.0438	0.1084	0.1881	-0.0466	-0.0076	0.2506	0.062	0.2052	71.3676	27.9317	-18.6608
15	2.2114	-0.1234	0.61	1.9674	-0.409	1.9648	-0.0588	0.4042	-0.1683	-0.3055	-0.0095	-0.0938	0.0745	-0.0064	0.0589	0.2406	-0.0308	0.0266	0.2321	-0.0069	0.1818	63.192	10.1456	-20.927
16	0.7852	0.2494	0.027	1.2606	-0.3633	0.7503	-0.0491	0.0273	-0.1995	-0.1283	-0.1146	-0.3666	0.1443	0.1768	0.1646	0.1921	0.0138	0.0522	0.2353	0.0326	0.3019	70.8865	10.2128	-10.7113
17	0.9576	-0.6181	-0.0221	0.8186	0.1187	1.1048	-0.0446	-0.1828	0.0226	0.0671	-0.0742	-0.2709	-0.238	0.187	0.1158	0.1708	-0.0639	-0.0678	0.2565	0.0645	0.3248	71.9219	28.1596	-2.3452
18	0.5621	0.1932	-0.1792	1.3343	-0.3753	1.872	-0.0354	-0.0705	0.1103	0.2148	-0.1179	-0.2326	-0.2953	0.1801	0.1635	0.1939	-0.0433	-0.0777	0.246	0.0177	0.2944	67.7863	25.1816	7.3013
19	1.557	0.749	1.075	0.5991	0.1401	1.8401	-0.1452	-0.0824	-0.1646	0.1215	-0.0626	-0.2572	0.151	0.2238	0.1717	0.1276	0.021	0.0085	0.2263	0.0547	0.2932	65.0875	3.6557	1.8142
20	0.4577	0.0136	-0.0939	0.5758	-0.141	0.3201	-0.1114	0.0724	0.0594	0.0123	-0.018	-0.105	-0.11	-0.0278	0.1255	0.1574	-0.0027	-0.0496	0.2677	0.0456	0.2577	58.0665	13.3373	7.1681
21	0.7512	0.0442	0.1909	1.2386	-0.2849	0.9066	0.0537	-0.1289	-0.1995	0.262	-0.1101	-0.0564	-0.0641	0.1044	0.0275	0.162	0.0024	-0.048	0.229	0.0479	0.2575	63.3173	11.6543	10.6267
22	0.5679	0.2138	-0.1244	0.9602	-1.0754	1.9292	-0.0264	-0.1752	0.0421	0.1209	-0.1067	-0.074	-0.1021	0.0845	0.12	0.1802	-0.01	-0.0656	0.2496	0.0132	0.2529	64.2289	17.6852	12.7374
23	2.3924	-0.1073	-0.6645	0.8811	0.1242	2.49	-0.0798	-0.1539	0.1606	0.0932	-0.1163	-0.278	-0.0935	0.3263	0.1134	0.1646	-0.0785	-0.102	0.3891	0.1036	0.3973	78.1632	17.2731	9.3182
24	0.2389	0.0173	-0.1885	0.5636	0.2885	0.4585	-0.0008	-0.2626	0.0277	0.5489	0.0666	0.0479	0.2276	-0.1167	0.0299	1.4144	-0.0742	0.4862	0.3242	0.1032	0.1618	-8.9221	-7.2517	79.0909
25	0.4036	0.0947	-0.1779	0.9932	0.0883	0.5397	0.0029	-0.2721	0.1102	1.1274	0.0159	0.0153	0.4267	0.134	-0.0344	1.117	0.0897	0.1155	0.3185	-0.0387	0.1559	4.3336	0.6976	74.4315
26	0.2903	-0.2248	-0.0448	0.7298	-0.5293	0.6121	0.0478	-0.1617	0.0288	0.7388	0.107	-0.2013	0.4546	0.313	-0.1639	0.8556	0.1243	-0.0818	0.355	-0.0795	0.2992	15.2524	7.3	70.9466

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 25 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 26 through 137 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 138 through 172 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 173 through 193 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 194 through 305 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 306 through 328 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid -1 through 25 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 26 through 137 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 138 through 203 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 204 through 222 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 223 through 272 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 273 through 328 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 0 through 25 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 26 through 45 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 46 through 72 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 73 through 137 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 138 through 175 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 176 through 203 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 204 through 222 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 223 through 247 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 248 through 272 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 273 through 305 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 306 through 328 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid -1 through 72 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 73 through 247 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 248 through 328 )

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