PDB-4d9k: Crystal structure of Escherichia coli Diaminopropionate ammonia l...

ID or keywords:

Entry

Database: PDB / ID: 4d9k

Title

Crystal structure of Escherichia coli Diaminopropionate ammonia lyase in apo form

Components

Diaminopropionate ammonia-lyase

Keywords

LYASE / Fold type II PLP-dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzymes superfamily / S-hydroxyethylation of cysteine

Function / homology

Function and homology information

diaminopropionate ammonia-lyase / diaminopropionate ammonia-lyase activity / pyridoxal phosphate binding / protein homodimerization activity
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.19 Å

Authors

Bisht, S. / Rajaram, V. / Bharath, S.R. / Murthy, M.R.N.

Citation

Journal: J.Biol.Chem. / Year: 2012
Title: Crystal Structure of Escherichia coli Diaminopropionate Ammonia-lyase Reveals Mechanism of Enzyme Activation and Catalysis
Authors: Bisht, S. / Rajaram, V. / Bharath, S.R. / Kalyani, J.N. / Khan, F. / Rao, A.N. / Savithri, H.S. / Murthy, M.R.N.

History

Deposition	Jan 11, 2012	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Apr 25, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jul 11, 2012	Group: Database references
Revision 1.2	Nov 8, 2023	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 1.3	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4d9k.cif.gz	559.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4d9k_validation.pdf.gz	490.9 KB	Display	wwPDB validaton report
Full document	4d9k_full_validation.pdf.gz	498 KB	Display
Data in XML	4d9k_validation.xml.gz	54.9 KB	Display
Data in CIF	4d9k_validation.cif.gz	76.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d9/4d9k ftp://data.pdbj.org/pub/pdb/validation_reports/d9/4d9k	HTTPS FTP

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Related structure data

Related structure data	4d9gC 4d9iSC 4d9mC 4d9nC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3pfr-1 4d9g-d 1s39-1 4q8m-1 6fv5-d 2pwu-1 4q4o-1 4p7o-d 4gd0-1 2qii-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (3)

Deposited unit

A: Diaminopropionate ammonia-lyase

D: Diaminopropionate ammonia-lyase

B: Diaminopropionate ammonia-lyase

C: Diaminopropionate ammonia-lyase

hetero molecules

174 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Diaminopropionate ammonia-lyase

B: Diaminopropionate ammonia-lyase

hetero molecules

defined by author&software
87.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Diaminopropionate ammonia-lyase

C: Diaminopropionate ammonia-lyase

hetero molecules

defined by author&software
87.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	85.778, 94.145, 94.687
Angle α, β, γ (deg.)	90.00, 110.01, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Diaminopropionate ammonia-lyase / Diaminopropionatase / Alpha / beta-diaminopropionate ammonia-lyase Mass: 43448.531 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2871, JW2839, ygeX / Plasmid: pRSET-C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: P66899, diaminopropionate ammonia-lyase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.07 Å³/Da / Density % sol: 40.5 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 20% PEG 3350, 70mM magnesium chloride, 50mM lithium sulfate, 6mM sodium citrate, 5mM beta mercaptoethanol, 40mM tris HCl pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1
Detector	Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 14, 2006 / Details: bending magnet
Radiation	Monochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Relative weight: 1
Reflection	Resolution: 2.19→50 Å / Num. obs: 71324 / % possible obs: 98.3 % / Redundancy: 3.6 % / B_iso Wilson estimate: 36.3 Å² / R_merge(I) obs: 0.078 / Net I/σ(I): 18.9
Reflection shell	Resolution: 2.2→2.28 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.357 / Mean I/σ(I) obs: 2.48 / Num. unique all: 7006 / % possible all: 97.5

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.6.0117	refinement
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D9I

4d9i

Resolution: 2.19→40.65 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.923 / SU B: 14.508 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.351 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26065	3590	5 %	RANDOM
R_work	0.21338	-	-	-
obs	0.21574	67710	98.03 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 42.953 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.06 Å²	0 Å²	-0.04 Å²
2-	-	-0.01 Å²	0 Å²
3-	-	-	-0.08 Å²

Refinement step

Cycle: LAST / Resolution: 2.19→40.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11015	0	35	503	11553

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.02	11280
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.022	1.948	15332
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.853	5	1444
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.904	24.949	489
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.879	15	1769
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.318	15	43
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	1731
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	8535
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.191→2.248 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.382	237	-
R_work	0.35	4709	-
obs	-	-	93.78 %

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	1.4461	-0.2424	0.0698	0.5188	-0.0846	0.5829	0.0351	-0.0246	0.0595	-0.0298	-0.0267	-0.1529	0.0553	0.1283	-0.0085	0.1351	-0.0093	-0.0123	0.0769	0.0111	0.1406	20.023	-3.185	44.823
2	1.6975	0.3817	-0.2755	1.2918	-0.1637	0.0616	0.0048	-0.0479	0.2671	0.0591	0.0463	-0.0501	0.0053	-0.022	-0.0511	0.2096	-0.0126	-0.0172	0.1135	0.0001	0.1343	10.465	4.655	44.795
3	2.4769	1.8	0.9661	2.8296	1.3935	1.6803	-0.0612	0.3924	0.2836	-0.1882	0.1484	-0.2878	-0.1461	0.0756	-0.0872	0.1437	-0.0153	0.0226	0.0836	0.0697	0.2746	24.989	17.331	31.631
4	9.731	-0.296	-0.5903	0.0712	0.44	3.4134	0.0703	1.2162	0.4229	-0.0493	-0.0727	-0.0347	-0.1942	-0.1347	0.0024	0.1839	0.0486	0.0477	0.2842	0.1919	0.1751	14.052	9.54	22.737
5	6.4622	0.199	0.4503	3.8719	0.1764	1.9393	-0.022	1.4371	-0.0205	-0.3337	-0.0973	-0.4595	0.175	0.4719	0.1193	0.108	0.0662	0.1006	0.4452	0.0754	0.1108	23.835	3.984	20.21
6	1.6808	0.1191	-0.6032	0.7825	-0.7795	1.0132	0.0275	-0.045	0.0535	0.0211	-0.0445	-0.1265	0.0217	0.0372	0.017	0.2056	-0.0112	-0.028	0.1081	0.0077	0.1084	19.994	-1.208	46.501
7	1.4236	-0.1312	0.2946	0.509	-0.0335	0.2471	0.0297	0.1005	-0.1597	0.0005	-0.008	-0.1288	0.0364	-0.0675	-0.0218	0.2427	-0.0036	-0.0087	0.095	-0.0114	0.1162	8.348	-10.484	42.893
8	1.6775	-0.3699	0.4613	0.4431	-0.4552	0.7807	-0.0045	0.1095	-0.0004	-0.0404	-0.0506	-0.081	0.0295	-0.0553	0.0552	0.2273	-0.0011	-0.0009	0.1332	-0.0217	0.056	2.082	-5.172	38.375
9	1.8907	-0.0044	0.7157	0.2606	-0.4385	1.2607	-0.071	0.1941	0.2361	-0.0532	0.1045	0.1379	0.0245	-0.3008	-0.0335	0.1391	0.0152	-0.0385	0.2159	-0.0033	0.1595	-34.72	2.778	35.06
10	0.8333	0.283	-1.0261	0.427	-0.4031	1.5781	0.1056	-0.0038	0.1872	0.0597	-0.0389	0.0865	-0.0774	-0.033	-0.0667	0.2213	0.0057	-0.0014	0.1356	-0.0185	0.1538	-26.376	4.295	46.141
11	3.1385	-4.4229	-4.1514	16.5439	0.694	8.0738	-0.1204	-0.0715	-0.0013	1.1383	0.1818	0.0914	-0.3108	0.0275	-0.0614	0.1885	-0.0431	-0.015	0.2417	0.0599	0.2632	-45.684	-1.146	62.926
12	4.8744	0.4689	-1.6989	1.4484	-0.2295	0.6536	-0.0324	-0.1205	-0.4308	0.0304	-0.0869	0.0261	-0.0644	0.0846	0.1194	0.2057	-0.0258	-0.0077	0.1087	0.0237	0.1039	-29.951	-13.017	54.797
13	3.8689	-0.07	-0.3379	3.7757	-0.4322	1.0791	-0.0216	0.2651	-0.3302	-0.1977	-0.0366	0.2845	0.1397	-0.0784	0.0582	0.1857	-0.0651	0.0207	0.0574	-0.0674	0.1735	-38.789	-19.33	49.524
14	2.2086	0.8707	-1.0598	1.3041	-1.0811	1.1064	0.0005	0.0801	0.1348	-0.0268	0.0215	0.0738	-0.0456	-0.1968	-0.022	0.2029	0.064	-0.0157	0.2126	-0.0298	0.116	-33.95	5.159	40.916
15	1.8521	0.2044	-0.1983	0.672	0.0602	0.7065	0.0228	0.2273	0.0145	-0.0036	-0.0182	0.059	0.0644	-0.0757	-0.0047	0.2117	0.0178	-0.0075	0.1732	0.0065	0.0404	-24.942	0.289	30.518
16	0.9248	-0.3155	0.014	0.7826	-0.6626	1.6431	0.0133	0.0554	-0.0683	-0.0737	0.0191	-0.0098	0.0948	-0.0834	-0.0325	0.1884	-0.0088	-0.0155	0.1228	-0.0111	0.087	-16.41	-4.062	36.646
17	2.5371	-0.4446	-0.9029	0.9695	0.6939	3.2322	-0.0313	0.4831	-0.1774	-0.0126	-0.1487	0.2529	-0.0857	-0.3458	0.1799	0.1121	0.1105	-0.0565	0.3172	-0.1042	0.0953	-18.743	-23.767	-3.419
18	2.162	-0.2213	-0.702	0.6984	-0.0716	1.0708	0.135	0.0527	-0.1472	0.0925	-0.2607	0.042	-0.1734	-0.0188	0.1257	0.25	0.0179	-0.0223	0.182	-0.0259	0.0202	-12.635	-20.877	13.465
19	1.3188	-5.0712	-0.4056	24.6023	-8.2054	20.0044	-0.2156	-0.2269	0.0785	1.049	0.0653	-0.4271	-0.0604	1.4796	0.1503	0.1258	-0.0939	-0.0242	0.4323	-0.1004	0.1973	-26.409	-22.796	29.62
20	3.1962	-2.0963	1.3736	4.5784	-0.5951	1.1979	-0.2005	-0.2273	-0.6308	0.1209	0.2232	0.7222	0.0352	-0.0173	-0.0227	0.1473	0.007	0.047	0.1116	0.0535	0.2649	-13.78	-38.047	20.912
21	6.7116	-5.2493	-0.3701	4.9852	0.8184	0.3807	0.2745	0.1249	-1.6943	0.074	-0.3185	1.1754	0.2419	-0.2187	0.044	0.2811	-0.2262	-0.0702	0.2062	-0.0633	0.6484	-22.375	-44.803	15.757
22	3.4857	-0.0998	-0.9593	0.4994	-0.7941	1.746	0.1819	0.5029	-0.2034	0.0504	-0.1538	0.0595	-0.2107	-0.0813	-0.0281	0.2249	0.1143	-0.0244	0.3672	-0.0672	0.0259	-18.382	-20.56	6.062
23	10.4582	-1.2097	-3.6749	0.6026	1.3497	3.2122	-0.0062	1.1511	-0.698	-0.0319	-0.2998	0.1322	-0.016	-0.6099	0.306	0.1519	0.1431	-0.0763	0.4461	-0.1785	0.0952	-19.983	-25.08	-3.139
24	1.7309	-0.5329	0.3704	0.3155	0.258	1.1063	0.0919	0.4854	-0.1903	-0.0638	-0.1894	0.078	-0.1124	-0.0174	0.0975	0.1981	0.0812	-0.0174	0.3274	-0.0489	0.1046	-1.607	-27.142	-2.055
25	1.4685	0.1375	-0.0534	1.7092	-0.5676	1.0503	0.0791	-0.0438	-0.1091	0.0796	-0.1732	-0.3734	-0.0366	0.1865	0.0941	0.0512	0.0154	0.0276	0.1246	0.0185	0.1702	37.171	-29.127	11.433
26	1.602	0.9984	-0.8412	1.0204	-0.7236	1.0226	0.0704	-0.0532	0.1334	0.0117	0.0333	0.0501	-0.1146	0.0043	-0.1038	0.2041	0.027	0.0208	0.1464	-0.0124	0.1223	29.591	-18.979	8.848
27	6.4309	-0.3686	1.8454	2.5365	-1.0095	4.1696	0.0036	-0.4736	0.462	0.2343	-0.1186	-0.0067	-0.4908	-0.004	0.1151	0.2679	-0.0804	-0.0003	0.1052	0.0119	0.1172	44.384	-3.398	0.169
28	4.4779	0.0885	-0.5726	0.0196	-0.1503	1.3215	-0.0444	0.4061	-0.099	0.0082	0.0389	-0.003	-0.013	-0.1828	0.0056	0.201	0.022	0.0455	0.1902	0.0243	0.1237	32.189	-16.497	-9.456
29	4.1617	-0.3998	-1.1128	4.051	0.9983	3.9076	-0.2417	0.4921	-0.7903	-0.1666	0.0776	-0.0884	0.2655	0.125	0.1641	0.1073	0.0113	0.0797	0.167	-0.0608	0.1769	40.381	-22.044	-14.194
30	1.8509	0.7639	-0.723	1.4539	-1.2985	1.1849	-0.0069	-0.0428	0.0145	0.0515	-0.1045	-0.1816	-0.012	0.0894	0.1115	0.1456	0.016	-0.0297	0.1509	-0.0084	0.1574	36.062	-26.795	12.576
31	1.4361	-0.5949	0.0372	1.5861	-0.1496	0.4284	0.0407	0.2242	-0.0918	-0.1285	-0.0491	-0.1281	0.0387	-0.0802	0.0084	0.199	0.0148	0.0181	0.1747	-0.014	0.085	24.285	-35.51	8.318
32	1.3962	-0.2259	0.1998	0.9874	-0.2615	0.9355	0.0234	0.2244	-0.1466	-0.0355	-0.0279	-0.0566	0.0285	-0.0185	0.0045	0.1709	0.0218	0.0197	0.2337	-0.0206	0.0501	19.158	-32.11	5.504

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 41
2	X-RAY DIFFRACTION	2	A	42 - 88
3	X-RAY DIFFRACTION	3	A	89 - 131
4	X-RAY DIFFRACTION	4	A	132 - 155
5	X-RAY DIFFRACTION	5	A	156 - 194
6	X-RAY DIFFRACTION	6	A	195 - 261
7	X-RAY DIFFRACTION	7	A	262 - 363
8	X-RAY DIFFRACTION	8	A	364 - 398
9	X-RAY DIFFRACTION	9	B	1 - 37
10	X-RAY DIFFRACTION	10	B	38 - 91
11	X-RAY DIFFRACTION	11	B	92 - 113
12	X-RAY DIFFRACTION	12	B	114 - 157
13	X-RAY DIFFRACTION	13	B	158 - 195
14	X-RAY DIFFRACTION	14	B	196 - 243
15	X-RAY DIFFRACTION	15	B	244 - 362
16	X-RAY DIFFRACTION	16	B	363 - 398
17	X-RAY DIFFRACTION	17	C	2 - 32
18	X-RAY DIFFRACTION	18	C	33 - 95
19	X-RAY DIFFRACTION	19	C	96 - 110
20	X-RAY DIFFRACTION	20	C	112 - 158
21	X-RAY DIFFRACTION	21	C	159 - 194
22	X-RAY DIFFRACTION	22	C	195 - 246
23	X-RAY DIFFRACTION	23	C	247 - 303
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