PDB-4jm3: Enduracididine Biosynthesis Enzyme MppR with HEPES Buffer Bound

ID or keywords:

Entry

Database: PDB / ID: 4jm3

Title

Enduracididine Biosynthesis Enzyme MppR with HEPES Buffer Bound

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 /

MOLECULAR REPLACEMENT / Resolution: 1.85 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 15, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4jm3.cif.gz	302.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4jm3.ent.gz	253.7 KB	Display	PDB format
PDBx/mmJSON format	4jm3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4jm3_validation.pdf.gz	446.6 KB	Display	wwPDB validaton report
Full document	4jm3_full_validation.pdf.gz	449 KB	Display
Data in XML	4jm3_validation.xml.gz	26.5 KB	Display
Data in CIF	4jm3_validation.cif.gz	39.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jm/4jm3 ftp://data.pdbj.org/pub/pdb/validation_reports/jm/4jm3	HTTPS FTP

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Related structure data

Related structure data	4jmcC 4jmdC 4jmeC C: citing same article (ref.)
Similar structure data	4jmd-1 4jmc-1 4jme-1 5e5u-d 5j5q-1 4r1d-d 1guy-1 3ig4-6 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative uncharacterized protein mppR

B: Putative uncharacterized protein mppR

hetero molecules

65 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)	109.790, 109.790, 87.690
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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.36 Å³/Da / Density % sol: 47.99 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25-30% PEG 3350, 0.2M (NH4)2SO4, 1-10mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-D / Wavelength: 0.9795 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 1, 2011

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 1.85→34.26 Å / Num. all: 52362 / Num. obs: 52362 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.2 % / R_merge(I) obs: 0.109 / Net I/σ(I): 9.4

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Diffraction-ID	% possible all
1.85-1.95	6.2	0.32	4.2	7559	1	100
5.85-34.26	5.7	0.086	13.9	1769	1	99.4

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Processing

Software

Name	Version	Classification
MAR345		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8_1069)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: SeMet SAD model refined to 2.2 Angstrom-resolution

Resolution: 1.85→34.259 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 16.53 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.176	1997	3.82 %	RANDOM
R_work	0.1451	-	-	-
obs	0.1463	52325	99.98 %	-
all	-	52362	-	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.85→34.259 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3964	0	30	555	4549

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	4142
X-RAY DIFFRACTION	f_angle_d	1.301	5662
X-RAY DIFFRACTION	f_dihedral_angle_d	14.269	1482
X-RAY DIFFRACTION	f_chiral_restr	0.08	589
X-RAY DIFFRACTION	f_plane_restr	0.007	751

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 (%)
1.85-1.8963	0.2094	139	0.1674	3536	X-RAY DIFFRACTION	100
1.8963-1.9475	0.1826	141	0.156	3543	X-RAY DIFFRACTION	100
1.9475-2.0048	0.2043	143	0.157	3582	X-RAY DIFFRACTION	100
2.0048-2.0695	0.1909	140	0.1451	3558	X-RAY DIFFRACTION	100
2.0695-2.1435	0.1831	138	0.1436	3548	X-RAY DIFFRACTION	100
2.1435-2.2293	0.2078	145	0.1478	3593	X-RAY DIFFRACTION	100
2.2293-2.3307	0.1895	142	0.1438	3552	X-RAY DIFFRACTION	100
2.3307-2.4536	0.1801	139	0.1491	3568	X-RAY DIFFRACTION	100
2.4536-2.6073	0.1966	142	0.1529	3600	X-RAY DIFFRACTION	100
2.6073-2.8085	0.1898	143	0.1562	3612	X-RAY DIFFRACTION	100
2.8085-3.091	0.2108	146	0.1563	3591	X-RAY DIFFRACTION	100
3.091-3.5378	0.1668	143	0.1492	3615	X-RAY DIFFRACTION	100
3.5378-4.4558	0.1326	144	0.1273	3661	X-RAY DIFFRACTION	100
4.4558-34.2647	0.1661	152	0.1377	3769	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	2.1538	-0.0963	2.1452	0.425	-0.0652	3.4074	0.0727	0.0106	0.0386	-0.0147	-0.0728	-0.1458	-0.0603	0.1667	-0.0603	0.1286	-0.0312	-0.006	0.1348	0.0105	0.1384	50.4367	67.0932	-7.5796
2	2.4234	0.0855	1.1153	1.5879	-1.4351	1.8821	-0.0244	0.0114	0.3883	-0.2332	-0.0056	0.4995	-0.4154	-0.2813	0.0948	0.1816	0.0457	-0.0254	0.1493	0.0681	0.2615	21.1159	81.3458	-14.9422
3	0.2942	0.2399	-0.2175	0.7934	-0.0748	0.6433	-0.0418	0.1355	0.1621	-0.0961	0.0474	0.1706	-0.2331	0.0194	-0.0258	0.2014	-0.0038	-0.0452	0.093	0.0348	0.1593	31.578	76.954	-15.4349
4	7.9525	-2.1155	-2.2797	1.9495	1.0008	1.8553	-0.1031	0.0866	-0.0149	0.1105	0.0605	-0.1949	0.0897	0.2178	-0.0119	0.1285	0.0022	-0.0303	0.148	-0.0016	0.1273	42.9608	59.9151	-12.829
5	2.5587	1.1658	-0.6515	3.3959	-0.8738	1.4618	-0.0969	0.3345	0.2589	-0.4086	0.1418	-0.0167	-0.2849	0.0333	-0.0918	0.2617	-0.0171	-0.0243	0.1481	0.067	0.2063	32.1057	83.8712	-17.0793
6	0.7083	0.0409	0.2397	0.5149	0.0209	0.7486	0.0161	0.0465	0.0305	-0.0765	0.0143	0.0077	0.0361	-0.0233	-0.0312	0.1709	-0.0028	-0.0261	0.1177	0.0232	0.1285	32.4174	64.7423	-10.3328
7	0.7421	0.1404	0.3498	1.4585	0.2383	1.8363	0.017	0.1587	0.0851	-0.3355	0.002	0.2495	0.0626	-0.139	-0.0386	0.2086	0.0172	-0.0823	0.1484	0.0275	0.1753	22.9991	65.6737	-20.0708
8	0.9995	-0.4765	1.9005	0.2774	-0.6139	5.2904	0.0437	0.0495	0.132	0.1147	-0.0079	-0.2189	-0.2439	0.3129	-0.0576	0.2392	-0.082	-0.081	0.1409	0.0326	0.2522	40.9372	81.4296	-2.4374
9	0.5176	-0.6319	-1.7197	0.9827	2.1967	9.2792	-0.083	-0.1626	0.2863	0.0203	0.5135	-0.448	-0.3344	0.9461	-0.649	0.2654	-0.0345	-0.0386	0.222	0.024	0.2806	43.059	83.7215	-11.0953
10	0.8549	0.2252	-0.3016	1.4157	0.3973	2.3685	-0.0033	0.0888	0.0065	-0.246	-0.077	0.2487	-0.0278	-0.1393	0.0881	0.173	0.0273	-0.0672	0.1357	0.0662	0.1864	23.894	70.4207	-17.1082
11	0.7338	-0.3781	-0.0744	0.9611	-0.008	1.2904	0.1055	0.1969	0.1416	-0.2863	-0.0612	0.1324	-0.0937	-0.0576	0.0111	0.1787	0.0117	-0.0427	0.1124	0.0589	0.1391	29.7815	73.6787	-19.2341
12	0.9368	-0.4542	-0.5136	1.4459	0.0355	0.3194	-0.0997	-0.2158	0.4512	0.2625	0.1488	-0.8336	-0.3107	0.3465	-0.1863	0.3088	-0.0518	-0.0709	0.1579	0.0232	0.3899	43.4517	92.7037	-9.5021
13	0.7871	-0.0379	0.8508	0.2113	0.1144	1.0232	0.0679	-0.0006	-0.2104	-0.0516	-0.0626	0.1187	0.2322	-0.4847	0.039	0.2041	-0.0888	-0.0445	0.2008	-0.0002	0.1957	12.2445	40.9787	-7.6454
14	1.3964	-0.03	-0.1409	0.727	0.78	1.196	-0.0093	0.0669	-0.3353	-0.0266	0.1029	-0.1655	0.494	0.1372	-0.0386	0.3669	0.048	-0.0205	0.1406	-0.0524	0.1958	38.3856	28.5157	-13.9787
15	6.9566	-0.3149	0.9625	3.1035	-0.8446	2.249	-0.0295	0.0169	0.0817	-0.0188	0.0428	0.3071	0.0051	-0.2504	0.0313	0.1573	-0.0219	-0.0389	0.1476	0.0107	0.1385	18.6701	49.9973	-14.0715
16	1.5767	1.442	0.1481	3.4343	1.7593	1.2674	-0.031	0.2504	-0.2361	-0.3329	0.0724	0.6411	0.4591	0.0734	0.0788	0.4102	0.0203	-0.0851	0.1248	-0.0507	0.2794	32.7224	27.6436	-16.1486
17	1.4784	-0.0828	-0.3573	0.3797	0.1601	0.8362	0.0166	-0.0089	-0.233	-0.1037	0.0743	0.1225	0.321	-0.0802	-0.0404	0.2281	-0.0214	-0.0311	0.116	0.0009	0.1455	27.513	36.5791	-7.7751
18	2.5463	1.8584	-1.8501	5.2888	-2.384	3.036	-0.0083	0.0824	-0.0067	-0.0827	0.1301	0.2044	0.1168	0.0606	-0.1604	0.1699	0.0096	-0.0231	0.1335	-0.0045	0.1509	33.8406	44.7388	-8.7217
19	4.664	0.1213	1.0795	2.0493	-1.1387	6.3348	-0.2679	0.446	0.1202	-0.6979	0.0705	-0.0043	-0.2595	-0.0008	0.0753	0.2598	0.0173	0.032	0.2084	0.0139	0.1688	40.9188	60.1013	-24.8395
20	1.0231	0.4837	0.0528	1.7903	-0.5177	0.9648	-0.0412	0.2054	-0.152	-0.2239	0.0577	-0.1756	0.2391	0.0648	-0.0382	0.2112	0.0253	0.023	0.1485	-0.0457	0.1738	40.2	42.1357	-18.9229
21	1.3143	-0.4993	0.329	2.7433	0.5759	0.4855	-0.0253	-0.0795	-0.54	0.0343	-0.0733	0.4692	0.5252	-0.1677	-0.0378	0.3774	-0.101	-0.0076	0.1899	0.0444	0.3003	20.1776	27.6949	4.3592
22	2.6761	1.1129	-1.8299	2.4838	-3.0055	4.2312	0.0983	-0.216	-0.543	0.3044	0.0435	0.7715	0.427	-0.4532	-0.2803	0.5325	-0.1169	0.0323	0.2002	0.0356	0.3785	20.9295	25.3368	-10.7584
23	1.2358	0.1702	-0.1705	1.2102	-0.1603	1.4393	-0.004	0.0975	-0.0798	-0.0944	0.0476	-0.1786	0.2143	0.1725	-0.0185	0.2223	0.0427	-0.002	0.1364	-0.0662	0.1541	40.9265	37.4798	-15.3215
24	0.5599	-0.0744	-0.0912	0.7994	0.2296	0.6178	0.0557	0.079	-0.3536	-0.2098	-0.0084	0.0374	0.4381	-0.0673	-0.0118	0.3843	-0.0417	-0.0425	0.193	-0.0237	0.2243	28.5415	31.88	-18.1007

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 34:62)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 63:76)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 77:102)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 103:119)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 120:136)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 137:173)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 174:213)
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 214:225)
9	X-RAY DIFFRACTION	9	(CHAIN A AND RESID 231:241)
10	X-RAY DIFFRACTION	10	(CHAIN A AND RESID 242:265)
11	X-RAY DIFFRACTION	11	(CHAIN A AND RESID 266:289)
12	X-RAY DIFFRACTION	12	(CHAIN A AND RESID 290:296)
13	X-RAY DIFFRACTION	13	(CHAIN B AND RESID 25:64)
14	X-RAY DIFFRACTION	14	(CHAIN B AND RESID 65:99)
15	X-RAY DIFFRACTION	15	(CHAIN B AND RESID 100:117)
16	X-RAY DIFFRACTION	16	(CHAIN B AND RESID 118:130)
17	X-RAY DIFFRACTION	17	(CHAIN B AND RESID 131:153)
18	X-RAY DIFFRACTION	18	(CHAIN B AND RESID 154:165)
19	X-RAY DIFFRACTION	19	(CHAIN B AND RESID 166:172)
20	X-RAY DIFFRACTION	20	(CHAIN B AND RESID 173:218)
21	X-RAY DIFFRACTION	21	(CHAIN B AND RESID 219:231)
22	X-RAY DIFFRACTION	22	(CHAIN B AND RESID 232:240)
23	X-RAY DIFFRACTION	23	(CHAIN B AND RESID 241:271)
24	X-RAY DIFFRACTION	24	(CHAIN B AND RESID 272:295)

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