PDB-4jmd: Enduracididine biosynthesis enzyme MppR complexed with the conden...

ID or keywords:

Entry

Database: PDB / ID: 4jmd

Title

Enduracididine biosynthesis enzyme MppR complexed with the condensation product of pyruvate and imidazole 4-carboxaldehyde

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: 1.67 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	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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4jmd.cif.gz	311 KB	Display	PDBx/mmCIF format
PDB format	pdb4jmd.ent.gz	261.6 KB	Display	PDB format
PDBx/mmJSON format	4jmd.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4jmd_validation.pdf.gz	442.3 KB	Display	wwPDB validaton report
Full document	4jmd_full_validation.pdf.gz	444.1 KB	Display
Data in XML	4jmd_validation.xml.gz	27.1 KB	Display
Data in CIF	4jmd_validation.cif.gz	41.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jm/4jmd ftp://data.pdbj.org/pub/pdb/validation_reports/jm/4jmd	HTTPS FTP

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Related structure data

Related structure data	4jm3C 4jmcC 4jmeC C: citing same article (ref.)
Similar structure data	4jm3-1 4jmc-1 4jme-1 4r1d-d 5b4m-d 6di8-d 5j5q-1 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

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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)	110.000, 110.000, 87.800
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-4IC / (3E)-4-(1H-imidazol-4-yl)but-3-enoic acid Mass: 152.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₈N₂O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 611 / 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: 2.38 Å³/Da / Density % sol: 48.25 %
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

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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: Mar 8, 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: 1.67→41.87 Å / Num. all: 71991 / Num. obs: 71343 / % possible obs: 99.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 9 % / R_merge(I) obs: 0.062 / Net I/σ(I): 26.3
Reflection shell	Resolution: 1.67→1.73 Å / Redundancy: 6.6 % / R_merge(I) obs: 0.475 / Mean I/σ(I) obs: 3.5 / % possible all: 91.8

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Processing

Software

Name	Version	Classification
MAR345		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

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

Resolution: 1.67→41.867 Å / SU ML: 0.13 / σ(F): 1.42 / Phase error: 15.51 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1691	3547	5.01 %
R_work	0.147	-	-
obs	0.1482	70788	98.97 %
all	-	71527	-

Solvent computation

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

Displacement parameters

B_iso mean: 26.8 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.7243 Å²	0 Å²	0 Å²
2-	-	2.7243 Å²	-0 Å²
3-	-	-	3.3504 Å²

Refinement step

Cycle: LAST / Resolution: 1.67→41.867 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3931	0	22	611	4564

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4301
X-RAY DIFFRACTION	f_angle_d	1.313	5905
X-RAY DIFFRACTION	f_dihedral_angle_d	13.03	1562
X-RAY DIFFRACTION	f_chiral_restr	0.083	604
X-RAY DIFFRACTION	f_plane_restr	0.007	808

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 (%)
1.67-1.728	0.2173	335	0.1825	6394	X-RAY DIFFRACTION	95
1.728-1.7972	0.2012	356	0.1728	6621	X-RAY DIFFRACTION	98
1.7972-1.879	0.1921	349	0.1483	6640	X-RAY DIFFRACTION	99
1.879-1.9781	0.1685	350	0.1498	6673	X-RAY DIFFRACTION	99
1.9781-2.102	0.1709	352	0.1446	6730	X-RAY DIFFRACTION	100
2.102-2.2643	0.175	354	0.1407	6739	X-RAY DIFFRACTION	100
2.2643-2.4921	0.1652	358	0.1419	6789	X-RAY DIFFRACTION	100
2.4921-2.8527	0.1772	362	0.1564	6786	X-RAY DIFFRACTION	100
2.8527-3.5938	0.1785	351	0.1543	6861	X-RAY DIFFRACTION	100
3.5938-41.8805	0.1487	380	0.1359	7008	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	1.2137	-0.1429	-0.0775	0.6043	0.0837	0.7544	0.0542	-0.1064	-0.0605	0.0625	-0.0233	-0.0367	0.0644	0.1519	-0.0684	0.1157	0.0253	0.0031	0.0785	0.013	0.0868	44.3144	-68.4571	24.9734
2	3.2521	-1.5232	-1.2582	2.2362	-0.6529	2.1326	0.0076	0.106	-0.5294	0.1474	-0.1262	0.5084	0.6977	-0.2958	-0.0465	0.3133	-0.0761	0.0293	0.0481	0.0525	0.2311	24.8196	-88.4145	27.6855
3	1.3166	0.0408	0.1809	1.8567	0.0167	0.666	-0.0327	-0.1022	0.0325	0.1385	0.0494	0.0503	0.0861	0.0486	-0.0193	0.1296	0.0051	0.0229	0.0889	0.0044	0.0432	37.5988	-68.0615	29.457
4	1.0964	0.6024	-0.3612	1.2886	0.0043	0.4748	-0.0013	-0.0757	-0.1384	0.1975	0.0181	-0.0083	0.0784	0.0611	-0.0052	0.1504	0.0097	0.0147	0.0776	0.0191	0.0938	36.6015	-75.9254	24.679
5	1.0835	-1.2612	-1.2349	1.2236	1.2705	2.984	0.0704	-0.1017	0.0733	-0.0449	-0.0119	-0.0495	-0.2345	-0.0599	-0.1313	0.1507	-0.027	0.0285	0.1054	0.0014	0.1258	30.4314	-64.0979	26.2973
6	0.5127	0.3419	0.6193	1.9047	0.2881	2.1814	0.035	-0.1347	0.0483	0.3298	0.0052	0.1553	0.017	-0.1372	-0.0546	0.148	0.0205	0.0557	0.1446	0.0176	0.1421	21.8162	-57.8642	33.3774
7	0.9487	-0.2607	-0.4633	1.0431	0.1229	1.8986	-0.0553	-0.1271	-0.1516	0.1312	0.0466	0.1226	0.1529	0.0607	0.0035	0.1724	-0.0348	0.0195	0.0805	0.0268	0.136	30.6893	-74.6272	28.3125
8	0.9258	0.0017	0.0675	1.4074	0.3082	0.7498	-0.0059	-0.0699	-0.0391	0.1993	0.0059	0.1006	0.1826	-0.0245	0.0019	0.1822	-0.0125	0.0408	0.1117	0.0628	0.0896	30.6912	-75.3627	31.5291
9	0.8582	0.6673	-0.0083	0.9656	-0.0627	0.8552	0.0949	-0.0624	0.1981	0.1796	-0.2401	0.3038	-0.1065	-0.9727	0.0838	0.1445	0.0839	0.0217	0.3597	-0.077	0.2514	7.5917	-41.3226	18.2931
10	1.2132	-0.1269	0.2837	0.9207	0.3042	0.8013	-0.1893	-0.1794	0.3806	-0.0592	0.0702	-0.0761	-0.3712	0.0766	0.019	0.2857	-0.0281	-0.0461	0.1152	-0.0642	0.2139	36.8085	-29.2061	29.6586
11	1.375	0.222	-0.1925	1.5381	-0.0445	1.0878	-0.1148	-0.1444	0.1442	0.0477	0.0881	0.1137	-0.0925	-0.0957	0.024	0.1258	0.0135	0	0.0977	-0.0168	0.0878	26.8576	-42.8814	29.2291
12	1.5724	0.6625	0.7017	1.9148	0.0269	0.7581	-0.0649	-0.1448	0.2832	0.1475	-0.0188	0.1325	-0.2561	-0.1187	0.037	0.1783	0.0164	-0.0048	0.0933	-0.0217	0.1415	27.7626	-34.9263	23.9447
13	1.4635	-1.1073	1.8186	1.0723	-0.9062	2.8345	0.1566	-0.0943	0.014	-0.1304	0.0344	0.1472	0.2141	0.0709	-0.2347	0.1494	-0.0107	0.0057	0.1047	-0.0006	0.1275	34.4129	-46.626	26.0509
14	0.9948	0.1389	-0.4026	1.7626	0.0284	1.3353	-0.0307	-0.207	0.0592	0.19	0.0218	-0.1926	0.0178	0.0326	-0.0077	0.1038	0.0044	-0.0189	0.1218	-0.0258	0.1179	42.977	-51.8052	32.6263
15	1.1003	-0.0479	-0.1158	0.6146	-0.3221	4.7061	0.0248	-0.1017	0.1934	0.1896	0.1827	-0.5243	-0.0069	0.421	-0.2143	0.2643	-0.0076	-0.0593	0.1336	-0.0621	0.2047	45.1813	-44.0425	31.3633
16	0.6935	0.2073	-0.1576	1.5829	1.3886	1.3816	-0.2156	-0.0181	0.2629	0.0134	0.0846	0.1317	-0.8072	-0.172	0.1806	0.2708	0.022	-0.0098	0.1498	-0.0203	0.2659	26.5025	-29.4364	24.3803
17	1.8229	0.2547	0.3093	1.3379	0.0835	1.6946	-0.0987	-0.0187	0.2283	0.066	0.0755	-0.0169	-0.3872	-0.0435	0.0077	0.2476	0.0086	-0.0234	0.108	-0.063	0.152	34.0868	-34.2972	30.8451

Refinement TLS group

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

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