PDB-5f1y: Crystal structure of Ba3275, the member of S66 family of serine p...

ID or keywords:

Entry

Database: PDB / ID: 5f1y

Title

Crystal structure of Ba3275, the member of S66 family of serine peptidases

Components

MccC family protein

Keywords

HYDROLASE / MccC family protein / Serine peptidase / Center for Structural Genomics of Infectious Diseases / CSGID /

Structural Genomics

Function / homology

Function and homology information

hydrolase activity /

nucleotide binding
Similarity search - Function

Biological species

Bacillus cereus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.04 Å

Authors

Nocek, B. / Jedrzejczak, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: Crystal structure of S116A mutant of Ba3275, the member of S66 family of serine peptidases
Authors: Nocek, B. / Jedrzejczak, R. / Joachimiak, A.

History

Deposition	Nov 30, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 30, 2015	Provider: repository / Type: Initial release
Revision 1.1	Aug 17, 2016	Group: Structure summary

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5f1y.cif.gz	291 KB	Display	PDBx/mmCIF format
PDB format	pdb5f1y.ent.gz	248 KB	Display	PDB format
PDBx/mmJSON format	5f1y.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f1/5f1y ftp://data.pdbj.org/pub/pdb/validation_reports/f1/5f1y	HTTPS FTP

-
Related structure data

Similar structure data	5f5x-d 5f9m-2 3b8u-2 3b8v-1 2rjg-1 3b8t-1 6p2m-d 4hdr-1 4us5-2 5f9m-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

-
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

hetero molecules

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

1

Idetical with deposited unit
defined by author

2

A: MccC family protein

defined by software
39.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

B: MccC family protein

hetero molecules

defined by software
39.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	71.324, 54.721, 86.260
Angle α, β, γ (deg.)	90.00, 91.94, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	MccC family protein Mass: 39785.242 Da / Num. of mol.: 2 / Mutation: P10A, 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 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q734X3
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.12 Å³/Da / Density % sol: 41.85 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 10% Peg 8000, 100 mM Tris HCL 7.0, 200mM MgCl2

-
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: Mar 3, 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: 2.04→36.3 Å / Num. obs: 42220 / % possible obs: 99.3 % / Redundancy: 3.6 % / R_merge(I) obs: 0.064 / Net I/σ(I): 16.5
Reflection shell	Resolution: 2.04→2.09 Å

-
Processing

Software

Name	Version	Classification
PHENIX	dev_1834	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.04→36.346 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.85 / Phase error: 21.56 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1972	3057	5.01 %
R_work	0.1492	-	-
obs	0.1516	60984	93.56 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.04→36.346 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5516	0	6	332	5854

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5697
X-RAY DIFFRACTION	f_angle_d	0.934	7721
X-RAY DIFFRACTION	f_dihedral_angle_d	14.254	2128
X-RAY DIFFRACTION	f_chiral_restr	0.037	816
X-RAY DIFFRACTION	f_plane_restr	0.004	1007

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 (%)
2.0402-2.0721	0.1893	69	0.1722	918	X-RAY DIFFRACTION	27
2.0721-2.1061	0.2182	57	0.1672	1236	X-RAY DIFFRACTION	34
2.1061-2.1424	0.2092	75	0.1795	1372	X-RAY DIFFRACTION	39
2.1424-2.1813	0.2247	69	0.1749	1490	X-RAY DIFFRACTION	42
2.1813-2.2233	0.1838	89	0.184	1632	X-RAY DIFFRACTION	46
2.2233-2.2687	0.2167	85	0.1913	1846	X-RAY DIFFRACTION	51
2.2687-2.318	0.2226	109	0.1838	2025	X-RAY DIFFRACTION	56
2.318-2.3719	0.2305	122	0.1873	2250	X-RAY DIFFRACTION	62
2.3719-2.4312	0.2338	136	0.186	2460	X-RAY DIFFRACTION	69
2.4312-2.4969	0.3036	144	0.1801	2666	X-RAY DIFFRACTION	74
2.4969-2.5704	0.278	135	0.1777	2879	X-RAY DIFFRACTION	81
2.5704-2.6533	0.265	168	0.1778	3062	X-RAY DIFFRACTION	85
2.6533-2.7481	0.2037	141	0.1844	3231	X-RAY DIFFRACTION	89
2.7481-2.8581	0.2024	202	0.1808	3270	X-RAY DIFFRACTION	93
2.8581-2.9881	0.2677	196	0.1779	3377	X-RAY DIFFRACTION	94
2.9881-3.1456	0.2109	180	0.1741	3405	X-RAY DIFFRACTION	96
3.1456-3.3425	0.2295	154	0.1544	3469	X-RAY DIFFRACTION	96
3.3425-3.6004	0.169	179	0.1347	3458	X-RAY DIFFRACTION	96
3.6004-3.9623	0.1878	199	0.1116	3445	X-RAY DIFFRACTION	96
3.9623-4.5348	0.1342	170	0.106	3506	X-RAY DIFFRACTION	98
4.5348-5.7098	0.1584	188	0.1132	3516	X-RAY DIFFRACTION	98
5.7098-36.3521	0.1733	190	0.1516	3414	X-RAY DIFFRACTION	95

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	1.3352	0.2252	0.0866	1.0971	0.1432	1.3908	-0.0759	-0.0459	-0.271	0.1935	0.1573	-0.1818	0.0612	0.2308	0.0106	0.2397	0.0887	0.0299	0.2204	-0.0179	0.2598	67.0181	-30.9754	14.1218
2	0.7245	0.2301	0.2143	0.8895	-0.1395	0.9346	-0.1788	0.1013	-0.2837	-0.1404	0.2457	-0.4473	0.1547	0.2571	-0.1231	0.2379	0.0176	0.0788	0.2699	-0.0587	0.3493	71.2733	-30.8714	5.1017
3	1.7509	-0.2632	-0.082	1.0498	0.4401	0.9058	-0.1985	-0.0534	-0.1788	0.1768	0.1315	-0.0174	0.2465	0.0956	0.0349	0.219	0.048	0.0354	0.1719	0.0063	0.2289	57.5181	-30.2171	15.0185
4	0.0238	0.1106	0.1756	0.6209	0.3863	1.5942	-0.1702	-0.2961	0.0617	0.1111	0.2251	-0.3355	-0.0181	0.6066	-0.0774	0.2038	0.1148	-0.0217	0.3255	-0.0468	0.3309	72.2941	-23.4764	14.1005
5	0.7174	0.0409	0.2103	1.0877	0.5266	0.2867	-0.1005	-0.2066	0.116	0.1439	0.2684	-0.6248	0.0051	0.3601	0.2235	0.2078	0.1033	-0.0835	0.4201	-0.1228	0.4565	77.9692	-19.8956	18.4349
6	0.3964	0.1614	0.5361	1.4271	0.7532	0.916	-0.0667	-0.3826	0.2899	0.0097	0.3516	-0.7152	-0.2729	0.6503	0.5932	0.2225	0.0601	-0.1274	0.5116	-0.2152	0.5358	76.6979	-10.7427	18.6822
7	4.2566	-0.5759	1.6537	1.4541	0.1261	2.6983	-0.186	-0.2129	-0.1325	0.3726	0.065	0.0259	0.2811	0.0797	0.0966	0.2352	0.0797	-0.0001	0.1925	-0.0376	0.1559	55.1808	-18.6012	25.454
8	2.0813	0.2926	-0.3633	2.221	-0.5324	2.5282	-0.154	-0.2701	0.2622	0.2888	0.2935	-0.0878	-0.0534	0.0814	-0.1146	0.2014	0.0995	-0.068	0.2969	-0.0911	0.2179	60.6223	-14.3144	26.6016
9	1.735	-0.3472	-0.0851	0.9076	0.18	0.5233	-0.153	-0.3703	0.4325	0.3897	0.3241	-0.4058	-0.0651	0.3415	-0.0312	0.1865	0.0728	-0.1157	0.3212	-0.1558	0.3406	63.8426	-7.9076	27.5782
10	0.76	-0.6308	-0.0752	0.5807	-0.0513	0.2387	-0.0941	-0.3747	0.1729	0.2259	0.2308	-0.2294	0.1065	0.1573	0.5557	0.3629	0.3879	-0.3466	0.6609	-0.2001	0.454	75.5584	-19.0434	34.3153
11	1.3198	-0.4029	0.0801	1.8091	0.1197	1.1708	-0.1278	-0.1176	0.2274	0.2797	0.0845	0.0476	0.0647	-0.0816	-0.0053	0.2085	-0.0035	0.0478	0.1059	-0.0158	0.1514	30.9721	6.9477	32.6364
12	1.6445	0.6676	-0.6155	0.7591	0.1246	1.2516	0.0608	0.0334	0.3225	0.3374	0.0069	-0.0396	-0.2657	-0.0283	-0.0329	0.216	0.0004	0.0129	0.1115	-0.0321	0.1921	32.1335	16.8404	32.1301
13	4.2914	-0.0195	-0.6335	1.1563	0.2752	1.5572	-0.1379	-0.6397	0.2538	0.5425	0.2858	-0.4223	0.2826	0.3202	-0.0938	0.3252	0.085	-0.0657	0.1901	-0.096	0.2201	44.1611	6.0655	39.6486
14	1.9967	-0.101	0.1999	0.9533	-0.5018	1.0693	-0.0239	-0.2611	0.2002	0.4354	0.151	-0.0616	0.2279	0.1014	0.0422	0.2631	0.0163	-0.0169	0.1242	-0.0401	0.0659	37.1368	3.3059	36.2315
15	1.2607	-0.3287	-0.3394	1.1604	0.8592	0.6152	-0.0323	-0.0073	0.0177	0.1513	0.0445	0.1051	0.0905	-0.1284	-0.0181	0.1787	-0.009	0.0408	0.1169	-0.0117	0.103	32.3781	1.9671	29.9152
16	1.1806	-0.468	-0.2122	1.7034	0.4444	1.6671	0.2204	0.1229	-0.0148	-0.2303	-0.2785	0.2093	-0.2029	-0.3269	0.0701	0.1881	0.0547	-0.0189	0.1949	-0.0464	0.1964	26.9849	8.5459	17.4861
17	0.799	0.4679	-0.2367	2.0588	0.6137	0.8983	0.1425	0.4083	0.1694	-0.5349	-0.1606	0.5586	-0.3609	-0.2668	-0.0593	0.2998	0.0501	-0.0604	0.3692	-0.041	0.2076	30.5165	3.1149	8.4526
18	3.8442	0.2326	0.966	1.3076	0.4872	1.4182	-0.0599	-0.1114	-0.0421	0.2553	0.0006	-0.0206	0.3577	0.0255	0.0561	0.229	-0.0029	0.0354	0.1118	-0.0226	0.1377	40.1027	-9.957	25.7817
19	1.9605	-1.1134	0.0184	2.291	0.4746	1.6199	0.0449	0.1091	0.0468	-0.1525	-0.1016	-0.0222	0.1143	0.0074	0.0889	0.1444	0.0076	0.0206	0.1301	-0.0239	0.0958	40.8521	-9.7652	13.1756
20	1.4013	-0.8682	-0.0694	1.7835	0.0828	0.9835	0.1048	0.2944	-0.1465	-0.1597	-0.3223	0.3486	0.0762	-0.3969	0.1236	0.1688	-0.0194	-0.0012	0.2588	-0.0901	0.183	27.7779	-6.5816	14.1462

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 29 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 30 through 57 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 58 through 127 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 128 through 149 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 150 through 183 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 184 through 210 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 211 through 231 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 232 through 250 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 251 through 326 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 327 through 343 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 1 through 29 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 30 through 57 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 58 through 75 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 76 through 99 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 100 through 149 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 150 through 186 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 187 through 210 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 211 through 231 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 232 through 298 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 299 through 343 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi