PDB-4jme: Enduracididine biosynthesis enzyme MppR complexed with 2-keto-end...

ID or keywords:

Entry

Database: PDB / ID: 4jme

Title

Enduracididine biosynthesis enzyme MppR complexed with 2-keto-enduracididine

Components

Putative uncharacterized protein mppR

Keywords

UNKNOWN FUNCTION / Acetoacetate decarboxylase-like

Function / homology

Function and homology information

lyase activity
Similarity search - Function

Biological species

Streptomyces hygroscopicus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.7 Å

Authors

Silvaggi, N.R.

Citation

Journal: Biochemistry / Year: 2013
Title: Structural and Functional Characterization of MppR, an Enduracididine Biosynthetic Enzyme from Streptomyces hygroscopicus: Functional Diversity in the Acetoacetate Decarboxylase-like Superfamily.
Authors: Burroughs, A.M. / Hoppe, R.W. / Goebel, N.C. / Sayyed, B.H. / Voegtline, T.J. / Schwabacher, A.W. / Zabriskie, T.M. / Silvaggi, N.R.

History

Deposition	Mar 13, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 3, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jul 17, 2013	Group: Database references
Revision 1.2	Nov 13, 2013	Group: Refinement description
Revision 1.3	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.4	Apr 3, 2024	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_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4jme.cif.gz	296.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4jme.ent.gz	247.7 KB	Display	PDB format
PDBx/mmJSON format	4jme.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jm/4jme ftp://data.pdbj.org/pub/pdb/validation_reports/jm/4jme	HTTPS FTP

-
Related structure data

Related structure data	4jm3C 4jmcC 4jmdC C: citing same article (ref.)
Similar structure data	4jmc-1 4jmd-1 4jm3-1 6eej-d 1hr8-1 5j5p-d 5e5u-d 4nd5-1 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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative uncharacterized protein mppR

B: Putative uncharacterized protein mppR

hetero molecules

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

1

A: Putative uncharacterized protein mppR

B: Putative uncharacterized protein mppR

hetero molecules

A: Putative uncharacterized protein mppR

B: Putative uncharacterized protein mppR

hetero molecules

defined by author&software
130 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	109.900, 109.900, 87.600
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Putative uncharacterized protein mppR Mass: 32256.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces hygroscopicus (bacteria) / Gene: mppR / Plasmid: pE-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q643B8
#2: Chemical	ChemComp-ECD / (4R)-4-(2-carboxyethyl)imidazolidin-2-iminium Mass: 158.178 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₂N₃O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 582 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.04 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25-30% PEG 3350, 0.2M (NH4)2SO4, 1-10mM HEPES. Drops contained 2 ul of protein solution at 12-18 mg/mL (~380-750 uM) and 1 ul of crystallization solution, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 12, 2012
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 1.7→33.28 Å / Num. all: 67295 / Num. obs: 67228 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.6 % / R_merge(I) obs: 0.048 / Net I/σ(I): 39.2
Reflection shell	Resolution: 1.7→1.73 Å / Redundancy: 5.2 % / R_merge(I) obs: 0.42 / Mean I/σ(I) obs: 3.8 / % possible all: 100

-
Processing

Software

Name	Version	Classification
MAR345		data collection
PHENIX	(phenix.refine: 1.8_1069)	model building
PHENIX	(phenix.refine: 1.8_1069)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX	1.8_1069	phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: SeMet-SAD model refined to 2.2 Angstrom-resolution

Resolution: 1.7→33.277 Å / SU ML: 0.14 / σ(F): 1.43 / Phase error: 16.66 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1731	3318	4.98 %
R_work	0.15	-	-
obs	0.1511	66622	98.77 %
all	-	67452	-

Solvent computation

Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 24.4 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→33.277 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3925	0	22	582	4529

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	4079
X-RAY DIFFRACTION	f_angle_d	1.297	5574
X-RAY DIFFRACTION	f_dihedral_angle_d	12.882	1456
X-RAY DIFFRACTION	f_chiral_restr	0.08	581
X-RAY DIFFRACTION	f_plane_restr	0.008	744

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 (%)
1.7-1.76	0.2366	308	0.1908	5960	X-RAY DIFFRACTION	94
1.76-1.8304	0.2051	323	0.1701	6223	X-RAY DIFFRACTION	98
1.8304-1.9137	0.201	327	0.1541	6229	X-RAY DIFFRACTION	98
1.9137-2.0146	0.1807	329	0.1542	6296	X-RAY DIFFRACTION	99
2.0146-2.1408	0.1821	333	0.1471	6362	X-RAY DIFFRACTION	100
2.1408-2.3061	0.1826	335	0.1512	6380	X-RAY DIFFRACTION	100
2.3061-2.5381	0.1952	335	0.1543	6357	X-RAY DIFFRACTION	100
2.5381-2.9052	0.1864	337	0.1602	6413	X-RAY DIFFRACTION	100
2.9052-3.6595	0.1677	339	0.154	6470	X-RAY DIFFRACTION	100
3.6595-33.283	0.1461	352	0.1341	6614	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	1.1342	-0.0529	0.0785	0.412	0.0485	0.5303	0.0708	-0.0392	-0.0777	0.0664	-0.0431	-0.0593	0.0643	0.1372	-0.045	0.1436	0.0291	0.0144	0.1181	0.0127	0.138	45.7092	-68.0819	24.2251
2	2.8298	-1.4009	-0.719	1.4477	-0.6731	1.6145	0.0236	0.1485	-0.5928	-0.002	-0.0369	0.52	0.4838	-0.1147	-0.0419	0.2788	-0.0486	0.0351	0.1024	0.0719	0.2567	25.2054	-88.3875	27.7194
3	1.1697	-0.0491	0.2336	1.6202	0.3258	0.6651	-0.0742	-0.0731	-0.0244	0.065	0.0942	-0.0008	0.092	0.0416	0.0074	0.1398	0.0103	0.0239	0.0959	0.0115	0.0751	37.4405	-66.447	29.2119
4	0.8288	0.3974	-0.1589	1.0617	0.2899	0.4087	-0.0357	-0.042	-0.095	0.0959	0.0928	-0.0289	0.1463	0.054	-0.0544	0.1721	0.0124	0.0179	0.0964	0.0214	0.1227	35.9693	-75.2606	24.5026
5	0.8703	-0.4319	-1.0722	0.2098	0.4478	1.2391	0.0981	-0.1887	0.057	-0.0785	0.0176	-0.1897	-0.1213	0.0204	-0.1136	0.1819	0.0011	0.0093	0.1379	0.0039	0.1542	30.7603	-64.3929	25.8019
6	0.3962	0.4079	0.2022	0.8585	-0.3788	0.7492	-0.0505	-0.0716	0.0487	0.3074	-0.0422	0.282	0.1098	-0.0614	0.0208	0.1756	0.0128	0.06	0.1595	0.0111	0.1396	21.7984	-57.7131	33.8935
7	1.1606	-0.1887	0.0301	1.3767	0.4033	3.5154	-0.1407	0.005	-0.1838	0.1154	-0.1324	0.7155	-0.0448	-0.6168	-0.3395	0.2576	-0.0082	0.1042	0.1402	0.0417	0.1759	19.4715	-65.4073	32.6337
8	0.8826	0.1571	-0.3664	1.0707	-0.2759	2.1857	0.0187	-0.0882	-0.0973	0.0415	0.0507	-0.1419	0.3043	0.1575	-0.0597	0.1911	0.0314	0.0284	0.1008	0.0437	0.2078	37.5495	-79.9509	25.5903
9	0.768	-0.072	-0.1201	1.3631	0.2555	0.7552	0.0203	-0.0955	-0.0646	0.1906	-0.0101	0.0651	0.1705	-0.0313	-0.0006	0.1934	-0.0106	0.0359	0.123	0.0552	0.1229	30.4697	-75.0268	31.7011
10	0.7617	0.3126	0.168	0.7368	0.0095	1.1782	0.0228	0.1289	0.1454	0.1207	-0.2447	0.2861	-0.0928	-0.6935	0.0974	0.1337	0.0639	0.0043	0.3101	-0.0576	0.2092	7.3763	-41.3858	17.8474
11	1.3424	0.0774	0.2728	0.7375	0.3312	0.5255	-0.1423	-0.1108	0.2657	-0.0526	0.0502	-0.0966	-0.3281	0.0501	0.0703	0.2787	-0.028	-0.0475	0.1515	-0.0588	0.181	36.5013	-29.3364	29.3897
12	1.3378	0.1662	-0.1964	1.2515	-0.0669	0.9486	-0.0942	-0.1289	0.0725	0.075	0.0698	0.0511	-0.0962	-0.0577	0.0356	0.1395	0.0083	-0.0009	0.1154	-0.0155	0.0897	27.0308	-43.2299	29.258
13	1.3804	0.5668	0.4807	1.0463	-0.3634	0.7584	-0.0663	-0.0508	0.1762	-0.0314	0.0474	0.0904	-0.2254	-0.1097	0.0061	0.1825	0.0088	-0.0062	0.1229	-0.0152	0.1549	28.176	-34.5504	24.1505
14	1.1003	-0.5179	1.0131	0.513	-0.229	1.3672	0.022	-0.1478	0	-0.0001	0.0818	0.1459	0.0957	-0.0615	-0.1398	0.1704	-0.0072	0.0009	0.1248	-0.0078	0.1545	33.5398	-45.3809	25.5012
15	0.803	0.0526	-0.554	1.1134	0.3954	0.7311	-0.0601	-0.1758	0.0609	0.1678	0.054	-0.1783	0.0153	-0.0914	-0.0359	0.1491	0.0029	-0.0211	0.1831	-0.0166	0.1747	42.9456	-51.7228	33.1232
16	1.355	-0.1979	0.0947	0.9565	-0.0448	4.4185	-0.1976	-0.0286	0.2138	0.1559	-0.0237	-0.541	-0.2133	0.6332	-0.2818	0.2141	-0.0221	-0.045	0.128	-0.0785	0.2192	45.3709	-44.0695	31.4447
17	0.866	0.1051	0.6963	0.9071	0.8214	2.6594	-0.1518	-0.0806	0.2725	-0.0227	0.0943	0.1574	-0.6301	-0.2547	-0.0029	0.2659	0.0237	-0.0274	0.1499	-0.0113	0.2598	26.5017	-29.5095	24.6901
18	1.2395	0.1174	0.4738	1.4066	-0.0775	1.4541	-0.0836	-0.0584	0.1232	0.0901	0.0637	-0.0421	-0.2976	0.0153	0.018	0.2262	0.004	-0.0238	0.1403	-0.0612	0.1449	34.4605	-34.9236	31.1898

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 34:68 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 69:89 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 90:127 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 128:152 )
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 153:168 OR RESID 500)
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 169:190 )
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESID 191:204 )
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESID 205:233 )
9	X-RAY DIFFRACTION	9	CHAIN A AND (RESID 234:295 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 30:55 )
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID 56:89 )
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 90:127 )
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESID 128:152 )
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESID 153:168 OR RESID 500)
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESID 169:190 )
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESID 191:204 )
17	X-RAY DIFFRACTION	17	CHAIN B AND (RESID 205:233 )
18	X-RAY DIFFRACTION	18	CHAIN B AND (RESID 234:294 )

-
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