PDB-2ocd: Crystal structure of L-asparaginase I from Vibrio cholerae O1 bio...

ID or keywords:

Entry

Database: PDB / ID: 2ocd

Title

Crystal structure of L-asparaginase I from Vibrio cholerae O1 biovar eltor str. N16961

Components

L-asparaginase I

Asparaginase

Keywords

HYDROLASE /

L-asparaginase I / SAD / MCSG / PSI-2 /

Structural Genomics /

Protein Structure Initiative / Midwest Center for Structural Genomics

Function / homology

Function and homology information

asparaginase /

asparaginase activity / amino acid metabolic process /

cytosol
Similarity search - Function

Biological species

Vibrio cholerae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.45 Å

Authors

Nocek, B. / Wu, R. / Osipiuk, J. / Moy, S. / Kim, Y. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of L-asparaginase I from Vibrio cholerae O1 biovar eltor str. N16961
Authors: Nocek, B. / Wu, R. / Moy, S. / Joachimiak, A.

History

Deposition	Dec 20, 2006	Deposition site: RCSB / Processing site: RCSB
Supersession	Jan 30, 2007	ID: 2H7K
Revision 1.0	Jan 30, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Dec 27, 2023	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 300

BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S) ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2ocd.cif.gz	273.8 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	2ocd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oc/2ocd ftp://data.pdbj.org/pub/pdb/validation_reports/oc/2ocd	HTTPS FTP

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Related structure data

Similar structure data	2p2d-d 4lsx-2 3kq4-1 3kq4-3 5akh-1 2jd7-d 1ewr-d 6g26-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC26686

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: L-asparaginase I

B: L-asparaginase I

C: L-asparaginase I

D: L-asparaginase I

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	53.235, 117.838, 121.431
Angle α, β, γ (deg.)	90.00, 91.44, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	L-asparaginase I / Asparaginase Mass: 37491.375 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: N16961 / Gene: O1 biovar eltor / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9KQK3
#2: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 524 / 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: 2.54 Å³/Da / Density % sol: 51.53 %
Crystal grow	Temperature: 291 K / pH: 7 Details: 2M Ammonium Acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 7.00

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2004
Radiation	Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.45→40 Å / Num. obs: 55186 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / R_merge(I) obs: 0.131 / Net I/σ(I): 10.3
Reflection shell	Resolution: 2.45→2.49 Å / Redundancy: 3 % / R_merge(I) obs: 0.51 / Mean I/σ(I) obs: 2.2 / % possible all: 93.1

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-3000		data reduction
HKL-3000		data scaling
SHARP		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.45→33.3 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.901 / SU B: 17.687 / SU ML: 0.207 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.51 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.246	2739	5.1 %	RANDOM
R_work	0.176	-	-	-
obs	0.179	50838	97.4 %	-
all	-	50838	-	-

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: 15.51 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.14 Å²	0 Å²	0.12 Å²
2-	-	0.26 Å²	0 Å²
3-	-	-	-0.11 Å²

Refinement step

Cycle: LAST / Resolution: 2.45→33.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10089	0	22	524	10635

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	10389
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	6891
X-RAY DIFFRACTION	r_angle_refined_deg	1.822	1.977	14109
X-RAY DIFFRACTION	r_angle_other_deg	1.159	3	16972
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.262	5	1328
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.056	25.081	431
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.026	15	1745
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.373	15	41
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	1606
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	11578
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1915
X-RAY DIFFRACTION	r_nbd_refined	0.232	0.2	2439
X-RAY DIFFRACTION	r_nbd_other	0.212	0.2	7254
X-RAY DIFFRACTION	r_nbtor_refined	0.189	0.2	5078
X-RAY DIFFRACTION	r_nbtor_other	0.093	0.2	5714
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.192	0.2	571
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.012	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.125	0.2	19
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.178	0.2	42
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.201	0.2	3
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	1.065	1.5	7779
X-RAY DIFFRACTION	r_mcbond_other	0.151	1.5	2668
X-RAY DIFFRACTION	r_mcangle_it	1.328	2	10700
X-RAY DIFFRACTION	r_scbond_it	2.333	3	4153
X-RAY DIFFRACTION	r_scangle_it	3.329	4.5	3407
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.45→2.51 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.347	218	-
R_work	0.245	3517	-
obs	-	-	93.05 %

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	2.5827	1.8119	0.77	1.5353	0.3325	2.4249	0.0163	-0.1554	-0.5207	0.0008	0.042	-0.1075	0.1868	0.0989	-0.0582	0.1383	0.0539	-0.0304	0.0436	0.0385	0.0748	2.6396	-16.9695	36.2566
2	6.3461	-6.3636	-5.0634	6.4035	5.2056	4.7728	0.1336	-0.2976	0.2043	0.123	0.1984	-0.1695	-0.064	0.8834	-0.332	0.1537	0.0788	-0.0679	0.2094	-0.0305	0.1768	9.9497	-18.7477	40.3396
3	0.5174	-0.1903	0.1814	0.4819	0.0463	1.4156	-0.0164	0.0156	-0.0255	0.0495	-0.0197	-0.0173	0.0588	0.0405	0.0361	0.1289	0.0055	-0.009	0.1068	0.0081	0.1042	-0.826	-12.9866	30.8949
4	0.5335	-0.481	0.2279	2.1526	-0.9435	5.068	0.1047	-0.0541	0.0324	0.0056	-0.2683	-0.2199	-0.329	0.403	0.1636	0.1327	-0.0263	-0.0124	0.1441	0.0021	0.1102	2.5515	0.5075	25.0152
5	1.377	0.2996	-1.0576	1.5004	1.0683	4.3204	0.0314	0.0196	0.0259	0.0127	-0.0222	0.144	-0.0602	-0.3525	-0.0092	0.0281	0.1004	-0.0655	0.0737	0.0421	0.0586	-10.3026	-7.1438	25.4441
6	0.8892	0.4941	0.5157	0.6592	-0.3263	1.2755	-0.0776	0.293	0.0061	-0.1521	0.2138	0.022	0.0371	0.0198	-0.1362	0.1295	0.0139	-0.0077	0.1735	-0.0436	0.1135	6.2132	-3.1818	-1.5111
7	1.8323	-0.3051	0.3385	2.7169	0.8043	2.8838	0.0205	0.0681	0.112	-0.2756	-0.2169	0.2677	-0.1889	0.0018	0.1965	0.1078	0.0128	-0.0288	0.1793	-0.0077	0.0468	-0.7686	2.3178	-1.4309
8	0.3826	0.1915	0.671	0.9276	0.5023	1.2102	0.0932	0.0012	-0.0542	-0.0199	-0.15	0.0379	-0.0956	-0.1409	0.0568	0.1198	0.0055	-0.0085	0.1435	-0.0299	0.121	-8.5209	-5.2341	8.0085
9	4.0063	-0.79	0.4461	2.7615	1.871	2.2991	0.2039	0.2195	0.0989	-0.2293	-0.2237	-0.1685	-0.0619	-0.1007	0.0199	0.1154	-0.0151	0.0228	0.0423	0.0741	0.0621	15.3036	30.0392	3.0552
10	0.5575	-0.4333	-0.4046	1.7849	-0.317	0.5691	0.2064	-0.4237	0.1332	-0.1404	-0.1501	0.1406	-0.2906	-0.5467	-0.0562	0.143	0.0556	0.0158	0.1626	0.0374	0.0918	9.1443	35.0939	3.4385
11	1.0672	-0.3733	0.0657	2.1833	0.5683	0.5121	0.048	0.0565	0.0251	0.0203	-0.0222	-0.0919	-0.009	-0.0036	-0.0258	0.0887	0.0027	0.0206	0.127	0.0582	0.0918	18.3354	22.8393	4.2181
12	0.9727	-0.692	1.2704	4.4595	0.6365	2.8535	0.0585	-0.1902	-0.0166	0.3652	0.0137	0.2511	0.0905	-0.1486	-0.0722	0.1359	-0.0037	0.047	0.1097	0.0432	0.0824	14.2461	14.8218	16.1724
13	0.6079	0.418	-0.049	3.1013	1.1799	3.6681	-0.0228	0.001	-0.0901	0.1602	-0.1333	-0.3582	-0.0717	0.3956	0.1561	-0.044	0.0443	-0.0598	0.1268	0.1083	0.1004	27.5463	17.1637	10.0776
14	1.0792	0.5638	-1.5629	1.5462	-0.4837	2.3519	-0.0206	0.2119	-0.0786	-0.0649	-0.017	-0.0711	0.1678	-0.1215	0.0376	0.0902	0.0508	0.0093	0.1909	-0.0174	0.094	13.1891	-10.538	4.5221
15	1.8355	0.7349	-0.1144	0.3589	0.4946	4.5265	-0.0792	-0.0963	-0.1325	0.0302	-0.012	-0.0982	0.3294	0.1294	0.0912	0.1343	0.0676	0.0361	0.1055	0.0165	0.128	20.0261	-11.7677	9.6817
16	0.8696	-0.3998	0.3639	0.6034	0.567	1.4376	0.0197	-0.0297	-0.0721	-0.0745	-0.003	-0.0526	-0.0391	0.059	-0.0167	0.1023	0.0221	0.0153	0.1333	0.0336	0.1252	26.7003	-1.2836	7.2065
17	0.1743	0.4588	0.2647	1.4299	0.1329	1.8309	-0.0145	-0.4377	-0.1399	0.0832	-0.0063	-0.0084	0.0762	-0.0136	0.0208	0.0594	0.0016	-0.0194	0.1395	-0.0101	0.1002	13.0354	0.2951	59.2761
18	13.9819	-7.2148	-4.9634	10.7787	6.2117	3.6507	0.5369	0.285	-0.5872	0.3403	-0.6274	0.486	0.5231	-0.4589	0.0905	0.2232	-0.0692	-0.0275	0.1847	0.1875	0.1014	6.6402	-4.7226	59.4405
19	0.926	0.015	-0.1939	1.1703	0.3152	0.6415	0.0208	0.0133	-0.019	0.077	0.0401	-0.0113	0.0707	0.0147	-0.0609	0.0968	0.0015	-0.0186	0.1292	-0.002	0.1112	16.5524	6.4936	57.1639
20	2.3547	-2.3307	-1.6749	2.4036	1.5136	1.4063	0.0506	0.2523	-0.213	-0.2337	0.1318	0.2428	-0.0309	-0.2196	-0.1824	0.1103	-0.0227	-0.0295	0.1597	0.0227	0.138	14.0128	15.9379	45.6352
21	1.1794	-0.5	0.3217	1.7795	0.5039	1.2426	0.0105	0.0644	0.0537	0.0266	0.028	-0.2185	0.1481	0.0376	-0.0385	0.003	-0.0587	0.0283	0.1213	0.0047	0.0937	23.8351	16.3447	53.2479
22	1.0255	-1.0155	1.1099	1.1114	-1.6876	4.4789	-0.148	-0.0523	0.0843	0.0043	0.1917	-0.1605	-0.3497	0.0878	-0.0437	0.0752	-0.0408	-0.0116	0.188	-0.0197	0.0986	9.2637	40.9211	57.4785
23	1.6164	-0.2999	0.9309	2.9353	1.9151	3.9941	-0.0799	0.0003	0.1566	-0.3214	-0.092	-0.1767	-0.223	0.0278	0.1718	0.0687	-0.036	0.0145	0.1262	-0.0055	0.1378	17.2198	42.3478	51.4677
24	1.4159	0.8358	-0.1808	2.9862	0.9292	0.6167	0.0239	0.0075	0.0181	0.0329	0.0567	-0.1647	-0.0039	0.0985	-0.0805	0.0848	-0.0051	0.0037	0.1505	-0.0124	0.1017	24.0689	30.7663	56.489
25	2.0697	-0.6685	-0.3377	2.8336	0.4046	3.047	-0.0438	0.4899	0.5501	0.0469	0.0638	0.0089	-0.1983	0.3793	-0.0201	0.0891	-0.0729	0.0114	0.177	0.0386	-0.014	1.6762	46.0124	24.528
26	2.6172	1.1797	0.7802	1.0329	-0.0708	5.3132	-0.0422	0.2676	0.2031	-0.0908	0.0069	-0.2697	-0.0607	0.1101	0.0353	0.1486	-0.0497	0.0191	0.0644	0.0333	0.0602	3.3231	47.7694	23.1071
27	0.6118	0.1566	-0.065	0.6826	-0.0668	1.425	-0.0656	0.0547	-0.012	-0.0924	0.0281	-0.0249	-0.0175	-0.1339	0.0375	0.1407	-0.0072	0.0154	0.1371	-0.0067	0.0678	-3.8417	40.9922	31.0151
28	2.0011	1.1108	1.5259	1.3274	-0.3659	3.2334	-0.094	0.1467	-0.1777	-0.0795	0.0364	-0.211	0.367	0.2067	0.0576	0.1857	0.01	0.0425	0.1004	-0.0011	0.0981	1.1268	28.643	34.8072
29	0.9995	-0.3513	0.3871	0.8572	0.1553	2.2272	-0.0799	-0.0232	-0.1465	-0.147	0.1223	-0.0065	-0.0183	-0.2689	-0.0424	0.0537	-0.0785	0.0525	0.1061	-0.0061	0.098	-10.1955	34.8469	37.3356
30	0.7694	-1.2521	0.0737	2.4715	-0.3771	0.1595	-0.0532	-0.015	0.0878	0.2304	-0.0788	0.0111	0.0228	-0.0277	0.132	0.0777	0.0141	-0.0005	0.1608	-0.026	0.1341	2.4523	32.7881	63.1723
31	1.3473	-0.2101	0.2797	3.0797	0.4711	0.8548	-0.0952	-0.1182	-0.1685	0.1273	0.0833	0.1843	-0.0368	0.0742	0.012	0.0806	0.002	0.0312	0.1365	0.0168	0.1147	-4.1266	26.1773	61.6513
32	0.8405	0.2481	-0.513	1.0421	-0.6577	1.4534	0.0638	0.0592	-0.0186	0.0355	-0.142	0.0504	-0.0371	-0.2163	0.0782	0.0985	0.0007	0.0025	0.1488	-0.0094	0.1135	-11.3809	32.8094	52.9709

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	2 - 19	2 - 19
2	X-RAY DIFFRACTION	2	A	A	20 - 41	20 - 41
3	X-RAY DIFFRACTION	3	A	A	42 - 154	42 - 154
4	X-RAY DIFFRACTION	4	A	A	155 - 182	155 - 182
5	X-RAY DIFFRACTION	5	A	A	183 - 213	183 - 213
6	X-RAY DIFFRACTION	6	A	A	214 - 245	214 - 245
7	X-RAY DIFFRACTION	7	A	A	246 - 290	246 - 290
8	X-RAY DIFFRACTION	8	A	A	291 - 337	291 - 337
9	X-RAY DIFFRACTION	9	B	B	2 - 19	2 - 19
10	X-RAY DIFFRACTION	10	B	B	20 - 45	20 - 45
11	X-RAY DIFFRACTION	11	B	B	46 - 150	46 - 150
12	X-RAY DIFFRACTION	12	B	B	151 - 182	151 - 182
13	X-RAY DIFFRACTION	13	B	B	183 - 213	183 - 213
14	X-RAY DIFFRACTION	14	B	B	214 - 247	214 - 247
15	X-RAY DIFFRACTION	15	B	B	248 - 284	248 - 284
16	X-RAY DIFFRACTION	16	B	B	286 - 337	286 - 337
17	X-RAY DIFFRACTION	17	C	C	2 - 20	2 - 20
18	X-RAY DIFFRACTION	18	C	C	25 - 41	25 - 41
19	X-RAY DIFFRACTION	19	C	C	42 - 153	42 - 153
20	X-RAY DIFFRACTION	20	C	C	154 - 182	154 - 182
21	X-RAY DIFFRACTION	21	C	C	183 - 218	183 - 218
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