PDB-5z8o: Structural of START superfamily protein MSMEG_0129 from Mycobacte...

ID or keywords:

Entry

Database: PDB / ID: 5z8o

Title

Structural of START superfamily protein MSMEG_0129 from Mycobacterium smegmatis

Components

Cyclase/dehydrase

Keywords

UNKNOWN FUNCTION / MSMEG_0129 / START domain / Mycobacterium smegmatis

Function / homology

Coenzyme Q-binding protein COQ10, START domain / Polyketide cyclase / dehydrase and lipid transport / START-like domain superfamily / Cyclase/dehydrase

Function and homology information

Biological species

Mycobacterium smegmatis str. MC2 155 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Zheng, S. / Liu, W. / Bi, L.

Citation

Journal: FEBS Lett. / Year: 2018
Title: Structural and genetic analysis of START superfamily protein MSMEG_0129 from Mycobacterium smegmatis.
Authors: Zheng, S. / Zhou, Y. / Fleming, J. / Zhou, Y. / Zhang, M. / Li, S. / Li, H. / Sun, B. / Liu, W. / Bi, L.

History

Deposition	Jan 31, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 21, 2018	Provider: repository / Type: Initial release
Revision 1.1	May 9, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Nov 22, 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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5z8o.cif.gz	140 KB	Display	PDBx/mmCIF format
PDB format	pdb5z8o.ent.gz	109.1 KB	Display	PDB format
PDBx/mmJSON format	5z8o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5z8o_validation.pdf.gz	438.9 KB	Display	wwPDB validaton report
Full document	5z8o_full_validation.pdf.gz	442.4 KB	Display
Data in XML	5z8o_validation.xml.gz	18.6 KB	Display
Data in CIF	5z8o_validation.cif.gz	28.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z8/5z8o ftp://data.pdbj.org/pub/pdb/validation_reports/z8/5z8o	HTTPS FTP

-
Related structure data

Related structure data	3tfzS S: Starting model for refinement
Similar structure data	2z62-d 4etx-d 4cnm-d 3qr5-d 2bjc-d 2hd0-4 5e3p-d 1dde-d 2yyn-2 2hd0-3 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Cyclase/dehydrase

B: Cyclase/dehydrase

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	109.760, 109.760, 56.500
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	171
Space group name H-M	P6₂

#1: Protein	Cyclase/dehydrase / MSMEG_0129 Mass: 16341.506 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria) Strain: mc(2)155 / Gene: MSMEI_0126 / Production host: Escherichia coli (E. coli) / References: UniProt: I7FVL6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 486 / 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: 3.01 Å³/Da / Density % sol: 59.08 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 2.0 M sodium formate, 0.1 M MES, pH 6.5

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 10, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 1.95→50 Å / Num. obs: 55131 / % possible obs: 99.3 % / Redundancy: 7.6 % / R_rim(I) all: 0.077 / Net I/σ(I): 19.12
Reflection shell	Resolution: 1.95→2 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 3.6 / R_rim(I) all: 0.622 / % possible all: 97.5

-
Processing

Software

Name	Version	Classification
PHENIX	1.10.1_2155	refinement
XDS		data reduction
XDS		data scaling
Rosetta		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3TFZ

3tfz

Resolution: 1.95→50 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / Phase error: 24.67

	R_factor	Num. reflection	% reflection
R_free	0.2359	2781	-
R_work	0.2102	-	-
obs	-	55053	99.27 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.95→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2277	0	0	486	2763

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	2328
X-RAY DIFFRACTION	f_angle_d	0.785	3166
X-RAY DIFFRACTION	f_dihedral_angle_d	15.137	1412
X-RAY DIFFRACTION	f_chiral_restr	0.053	362
X-RAY DIFFRACTION	f_plane_restr	0.005	412

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 (%)
1.9501-1.9836	0.5565	138	0.5003	2488	X-RAY DIFFRACTION	96
1.9836-2.0197	0.2746	153	0.2713	2669	X-RAY DIFFRACTION	100
2.0197-2.0585	0.3054	148	0.2789	2603	X-RAY DIFFRACTION	100
2.0585-2.1005	0.3474	146	0.2966	2620	X-RAY DIFFRACTION	99
2.1005-2.1461	0.1979	114	0.2267	2596	X-RAY DIFFRACTION	100
2.1461-2.1959	0.2651	149	0.2535	2677	X-RAY DIFFRACTION	100
2.1959-2.2508	0.5245	132	0.4408	2511	X-RAY DIFFRACTION	95
2.2508-2.3115	0.3591	113	0.3019	2519	X-RAY DIFFRACTION	96
2.3115-2.3794	0.236	158	0.2284	2636	X-RAY DIFFRACTION	100
2.3794-2.4561	0.223	178	0.1945	2598	X-RAY DIFFRACTION	100
2.4561-2.5437	0.2799	117	0.2116	2659	X-RAY DIFFRACTION	100
2.5437-2.6453	0.2924	136	0.2227	2621	X-RAY DIFFRACTION	100
2.6453-2.7654	0.2549	139	0.2089	2641	X-RAY DIFFRACTION	100
2.7654-2.9108	0.2072	139	0.2033	2612	X-RAY DIFFRACTION	100
2.9108-3.0925	0.2474	122	0.1998	2669	X-RAY DIFFRACTION	100
3.0925-3.3302	0.241	125	0.1875	2660	X-RAY DIFFRACTION	100
3.3302-3.6634	0.1767	136	0.1637	2629	X-RAY DIFFRACTION	100
3.6634-4.1891	0.1896	145	0.1597	2588	X-RAY DIFFRACTION	100
4.1891-5.2611	0.1495	143	0.1423	2662	X-RAY DIFFRACTION	100
5.2611-19.6841	0.1726	150	0.1814	2614	X-RAY DIFFRACTION	100

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	0.0207	0.0181	0.0299	0.072	-0.0307	0.0534	-0.0475	0.1337	0.1945	0.1409	0.0488	-0.1681	0.1236	-0.089	-0.0104	0.3604	-0.0293	-0.0324	0.2647	0.0353	0.22	11.211	61.0081	29.9068
2	0.0338	0.1625	-0.1479	0.0831	-0.3514	0.1494	-0.1967	0.0854	-0.1527	-0.2337	0.0631	-0.0837	0.1355	-0.0633	-0.0003	0.2175	-0.0358	0.0259	0.1664	0.0088	0.1705	8.0403	44.4539	27.4071
3	1.0264	0.058	-0.1187	0.7829	0.1428	0.4895	0.0404	0.0709	-0.2268	-0.2078	-0.1001	-0.0957	-0.0492	-0.0499	-0.2323	0.1372	-0.0269	0.0345	0.1236	-0.0085	0.1101	2.019	45.9701	35.9651
4	0.2174	0.0366	-0.0475	0.326	0.1646	0.1814	-0.1997	-0.0569	-0.0067	0.3094	-0.2237	0.0799	-0.0786	-0.0715	-0.2007	0.1817	-0.0407	0.0195	0.1353	0.0321	0.1328	3.2177	51.478	40.0831
5	0.2061	0.3927	-0.031	0.4661	-0.1439	0.2572	-0.149	0.0342	0.0841	0.1376	-0.0503	0.0709	-0.5515	0.0379	-0.0198	0.2418	-0.0475	0.011	0.1884	0.012	0.1424	6.3246	57.3641	30.0721
6	0.076	0.0151	0.0456	0.1821	0.2375	0.3267	-0.1398	0.0136	0.1423	0.0333	-0.2639	-0.1119	-0.1272	-0.0025	-0.1016	0.9746	-0.3342	-0.4142	0.4227	-0.0406	0.2058	14.6049	58.2288	51.3327
7	0.3043	0.0571	-0.154	0.3217	-0.0005	0.0947	-0.0049	0.1948	-0.1516	-0.1144	-0.1036	-0.3288	-0.2427	0.3405	-0.2486	0.1878	-0.084	0.0107	0.0976	0.0657	0.199	16.3794	53.4588	29.6547
8	0.4066	-0.126	0.2962	0.0737	-0.1331	0.2599	-0.1991	-0.3507	-0.2478	-0.151	-0.006	-0.2348	0.1181	-0.3215	-0.078	0.2175	-0.0065	0.1035	0.2856	0.1407	0.4676	-4.1801	20.6244	60.909
9	0.0604	-0.0225	0.02	0.2334	0.119	0.1861	-0.0466	-0.1451	-0.0101	0.1273	0.0363	0.0261	0.0129	0.2041	0	0.1696	0.0046	0.0431	0.1999	0.0255	0.132	-1.1651	38.373	62.1753
10	0.1677	-0.1669	-0.0319	0.8018	0.0075	0.4341	-0.0092	-0.1213	0.0136	0.0393	0.0202	0.1761	0.0588	0.0626	-0.0121	0.134	0.0169	0.0449	0.0993	0.0109	0.14	-2.9289	36.4742	50.779
11	0.402	0.249	0.1176	0.1716	-0.1049	0.0681	-0.1169	-0.0854	-0.2198	0.0698	0.0687	0.0073	0.184	-0.1103	-0.0001	0.1851	0.0072	0.0635	0.1585	0.0354	0.2792	-4.1566	25.325	56.4227
12	0.664	0.2253	-0.2035	1.2978	-0.8291	0.6889	-0.0111	-0.7338	-0.6919	0.8935	-0.4357	-0.5474	-0.125	0.7072	-0.7487	-0.0083	0.0951	0.0758	0.2994	0.1226	0.3248	3.0763	27.0629	64.0553

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -3 through 7 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 8 through 36 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 37 through 71 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 72 through 82 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 83 through 110 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 111 through 115 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 116 through 142 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid -3 through 7 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 8 through 36 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 37 through 82 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 83 through 115 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 116 through 143 )

-
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