PDB-2zak: Orthorhombic crystal structure of precursor E. coli isoaspartyl p...

ID or keywords:

Entry

Database: PDB / ID: 2zak

Title

Orthorhombic crystal structure of precursor E. coli isoaspartyl peptidase/L-asparaginase (EcAIII) with active-site T179A mutation

Components

L-asparaginase precursor

Keywords

HYDROLASE / isoaspartyl peptidase / asparaginase / Ntn-hydrolase / autoproteolysis / precursor

Function / homology

beta-aspartyl-peptidase / Peptidase T2, asparaginase 2 / Asparaginase / asparaginase activity / beta-aspartyl-peptidase activity / protein autoprocessing / Nucleophile aminohydrolases, N-terminal / hydrolase activity / Isoaspartyl peptidase

Function and homology information

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.01 Å

Authors

Michalska, K. / Hernandez-Santoyo, A. / Jaskolski, M.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Crystal packing of plant-type L-asparaginase from Escherichia coli
Authors: Michalska, K. / Borek, D. / Hernandez-Santoyo, A. / Jaskolski, M.

History

Deposition	Oct 7, 2007	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 25, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Nov 10, 2021	Group: Data collection / Database references / Derived calculations Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Nov 1, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	2zak_validation.pdf.gz	454.5 KB	Display	wwPDB validaton report
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Data in XML	2zak_validation.xml.gz	23 KB	Display
Data in CIF	2zak_validation.cif.gz	32.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/za/2zak ftp://data.pdbj.org/pub/pdb/validation_reports/za/2zak	HTTPS FTP

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Related structure data

Related structure data	1jn9C 1k2xSC 1p4v 1t3m 2gac 2gez 2zal 9gaa 9gac 9gaf S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1jn9-d 2zal-d 2qvz-d 4et0-d 1t3m-d 1r9z-d 4pu6-d 4g81-5 4o0e-d 4lvu-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#166 - Oct 2013 Proteasome similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #176 - Aug 2014 Dynein similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: L-asparaginase precursor

B: L-asparaginase precursor

hetero molecules

66.8 kDa, 2 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)	51.350, 77.780, 147.930
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	L-asparaginase precursor / L-asparagine amidohydrolase Mass: 33262.676 Da / Num. of mol.: 2 / Mutation: T179A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 Description: The N-terminal methionine has been removed by an intracellular aminopeptidase (E. COLI). Gene: ybiK (iaaA) / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: P37595, beta-aspartyl-peptidase, asparaginase
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.22 Å³/Da / Density % sol: 44.6 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 200mM MgCl2, 100mM Tris/HCl, 15% PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 2, 2007
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→25 Å / Num. all: 38010 / Num. obs: 38010 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / R_merge(I) obs: 0.103 / Net I/σ(I): 9.2
Reflection shell	Resolution: 2→2.07 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.4 / Mean I/σ(I) obs: 2.1 / % possible all: 69.1

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MAR345dtb		data collection
DENZO		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1K2X

1k2x

Resolution: 2.01→25 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.913 / SU B: 10.862 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS. MAXIMUM LIKELIHOOD TARGET. THE REFINEMENT INCLUDED TLS PARAMETERS. THE RESIDUES 164-177 AND 314-321 FROM CHAIN A AS WELL AS 159-177 AND 314-321 ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25285	1524	4 %	RANDOM
R_work	0.19741	-	-	-
obs	0.19961	36439	93.72 %	-
all	-	36440	-	-

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: 23.628 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.84 Å²	0 Å²	0 Å²
2-	-	-2.37 Å²	0 Å²
3-	-	-	-2.47 Å²

Refinement step

Cycle: LAST / Resolution: 2.01→25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4286	0	12	140	4438

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	4366
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.548	1.972	5911
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.386	5	591
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.743	24.023	174
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.579	15	698
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.541	15	31
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	682
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3293
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	2269
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.298	0.2	3066
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.144	0.2	237
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.112	0.2	5
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.248	0.2	41
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.245	0.2	6
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	0.688	1.5	2906
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.099	2	4582
X-RAY DIFFRACTION	r_scbond_it	2.063	3	1486
X-RAY DIFFRACTION	r_scangle_it	3.085	4.5	1327
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.006→2.058 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.287	97	-
R_work	0.259	1802	-
obs	-	-	64.66 %

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	3.666	2.6393	-1.4456	5.384	-0.1021	2.9392	-0.1798	-0.2664	-0.0679	0.5993	0.1574	-0.5882	-0.3004	0.2707	0.0224	0.0174	0.0012	-0.0488	0.0095	0.0096	-0.0595	13.8587	-6.3071	82.7353
2	18.5208	8.8145	-5.4114	8.9054	2.0214	6.0671	0.109	0.9105	0.4233	-0.7568	0.9232	-0.0121	-2.7195	-0.9945	-1.0322	0.8048	0.0584	-0.0323	0.2766	0.0486	0.4311	10.5317	10.0642	95.5701
3	4.8805	4.9028	2.569	8.9	4.7634	9.6031	0.0768	-0.6834	0.4881	1.3212	-0.2199	0.4612	0.0702	-0.7364	0.1431	0.1982	0.0076	0.0559	0.1337	0.0192	0.0626	5.5691	-0.1851	94.6473
4	3.4465	-5.6838	-1.2867	24.8099	5.1522	1.0752	-0.1289	-0.6505	-0.4689	1.3372	0.1894	-0.0412	0.1298	-0.0227	-0.0605	0.0907	0.0147	0.017	0.0414	0.0509	0.0751	7.7267	-16.4144	85.9634
5	1.6129	-0.896	0.104	2.2625	0.2149	1.2743	-0.0194	-0.0394	-0.0856	0.0787	0.0156	0.1196	0.0191	-0.1003	0.0038	-0.057	-0.0079	0.019	-0.0237	0.0085	0.0185	2.2337	-2.8125	75.5435
6	3.7424	0.0019	-0.9938	3.2508	0.6926	3.6397	-0.0401	0.1764	-0.2552	-0.0146	0.0439	0.3551	0.1378	-0.1097	-0.0039	-0.0869	-0.0182	-0.0045	-0.0119	0.007	0.0945	-2.9482	-5.0154	65.5546
7	1.3739	0.3772	-0.3011	8.6133	2.0983	1.2004	-0.1807	-0.1677	0.0767	0.1046	-0.0508	0.8618	0.0566	-0.2324	0.2315	-0.0277	0.0347	0.0089	0.086	0.0034	0.1398	-6.7487	7.2174	78.2028
8	40.9644	22.7292	-19.3939	14.331	-0.2145	73.858	0.5355	-0.4675	0.3059	0.1033	0.3892	-0.7712	-1.5469	3.86	-0.9247	0.1759	-0.0251	-0.0624	0.2327	-0.1008	0.3714	4.6375	26.7606	81.5015
9	5.2684	-2.7951	0.4881	1.7817	-1.2573	3.3808	-0.044	0.068	0.0683	0.2035	-0.0093	-0.3463	0.1736	0.0746	0.0533	-0.1106	-0.0063	0.0137	-0.0377	0.0022	0.0229	11.7645	-11.2886	76.1119
10	7.9984	-16.9666	0.9404	36.5298	-0.81	2.7127	0.0669	0.2299	0.2704	-0.4251	-0.1534	-0.5254	-0.3841	0.5064	0.0866	0.0405	-0.008	0.012	-0.0031	-0.0342	0.0347	2.5944	11.2951	74.5705
11	1.8926	-1.4868	0.0435	1.5241	-0.3203	1.2758	-0.0957	0.0638	-0.0002	0.0913	0.0456	-0.1039	-0.1028	0.1077	0.05	-0.0475	-0.0103	-0.0057	-0.0133	-0.0013	0.0282	14.5609	0.8689	68.9361
12	4.3469	-5.3408	0.1608	7.0194	-2.3897	10.5098	-0.0532	0.0526	0.0105	0.0532	-0.0502	-0.5415	-0.0635	0.5054	0.1034	-0.1153	-0.0358	-0.0031	0.0475	-0.0165	0.1729	28.3646	-3.6183	72.3457
13	6.0686	2.7538	1.1912	16.8643	-5.9156	6.1989	-0.4288	0.2638	-0.2173	0.616	0.3247	-0.4701	-0.5356	0.2487	0.1041	0.0075	-0.0508	-0.0148	0.0022	-0.022	0.1139	23.9863	8.7161	73.9947
14	0.3254	1.3194	0.5404	8.9337	1.1338	1.2089	0.0518	-0.1306	-0.1638	0.3512	-0.0693	-0.3784	-0.114	0.2067	0.0175	-0.0464	0.0033	-0.0041	0.0148	0.006	0.0887	20.3477	-4.0568	79.5055
15	9.1896	2.7229	-2.5367	8.3658	-2.9871	11.5082	0.0534	-0.8172	0.5858	0.2456	-0.3477	-0.2213	-0.6679	-0.6323	0.2943	-0.035	0.0337	-0.0703	0.0366	-0.0659	0.0425	13.8425	2.8331	86.9671
16	1.5349	2.644	0.6463	23.0722	9.7534	6.0222	0.3073	-0.3103	-0.3495	1.1047	0.0804	-1.2678	0.001	0.5262	-0.3877	0.2332	0.0449	-0.0567	0.1438	0.0272	0.0689	16.7232	-6.3168	90.3694
17	6.6839	3.8374	1.3867	10.4887	2.5647	8.2255	0.4768	0.1918	-0.4637	-0.0562	-0.124	-0.7558	-0.0687	0.3976	-0.3528	0.1755	-0.0424	0.0565	0.0762	-0.013	0.0186	20.8432	4.9934	42.4453
18	3.1485	0.6191	1.6243	6.9364	-8.2706	11.6657	0.8619	-1.3191	-0.9039	0.7514	-0.8687	-0.0657	0.521	-0.885	0.0067	0.7252	-0.2296	0.0648	0.4882	0.0436	0.1943	9.302	-7.2835	29.7117
19	0.8303	1.7902	3.1375	9.0361	7.2956	11.9104	-0.1426	0.2964	-0.1146	-1.0991	0.0323	-0.2943	-0.3974	0.301	0.1102	0.4262	-0.025	0.0619	0.1781	0.0272	0.0136	13.5101	6.1396	31.1833
20	8.0871	1.1574	-0.2767	4.6169	-0.8563	2.6486	-0.0818	0.7198	0.5847	-0.9242	0.3151	0.0453	-0.8787	0.2167	-0.2334	0.3224	-0.1226	0.0524	0.104	0.0142	0.1374	22.3713	17.8826	43.6616
21	3.0855	0.3541	0.0298	1.6681	0.3393	0.0696	-0.2	0.2455	0.0976	-0.5684	0.0376	-0.0183	-0.2828	-0.1596	0.1624	0.192	-0.0573	-0.0105	0.117	0.025	-0.0057	7.8549	10.3498	41.4482
22	1.7148	-0.5625	0.0526	1.9914	0.483	2.4503	-0.0175	0.0504	0.1306	-0.1203	0.0381	0.1315	-0.148	-0.2305	-0.0206	0.0214	-0.0052	-0.0164	0.0292	0.0112	0.0435	4.695	11.7302	55.2046
23	4.4297	3.9247	2.5596	17.453	11.4817	11.8409	-0.1077	0.1289	0.6818	-0.5418	-0.6322	1.2004	-0.1689	-0.8636	0.7399	0.2251	0.0668	-0.0779	0.1842	0.0752	0.124	-3.379	15.3858	47.512
24	13.0594	7.1715	-1.1186	15.3654	-6.4025	3.0278	0.2083	0.2937	-1.0098	-1.1432	0.3084	0.7734	1.2758	-0.218	-0.5167	0.72	-0.0937	-0.2379	0.2906	-0.0924	0.2751	-6.1276	-4.1827	38.8656
25	8.7911	-0.7346	-0.2523	0.1007	-0.3366	3.265	-0.0872	-0.0778	-0.1332	-0.4466	0.0272	-0.2275	-0.0632	0.1381	0.06	0.1027	-0.035	0.0681	0.0242	-0.0107	0.0126	18.1506	8.9278	48.7796
26	5.9104	-0.903	1.0543	0.9924	-1.377	1.9182	-0.2102	0.1128	0.1759	-0.4445	0.2072	0.1876	0.0797	-0.0389	0.003	0.0476	-0.0309	0.0039	0.0006	-0.0293	0.0093	4.5356	-0.8103	54.3795
27	1.747	0.2307	-0.0145	0.9294	0.8097	4.9275	-0.0727	0.2415	-0.1355	-0.27	0.2164	-0.0439	-0.0301	0.1688	-0.1436	-0.0335	0.006	0.0408	0.0427	-0.0154	0.0934	19.4127	2.4615	54.072
28	11.2128	0.7444	-0.1039	2.8972	-4.324	12.031	0.1271	-0.1816	-0.3847	-0.2732	0.1052	-0.1282	-0.0615	0.0729	-0.2324	0.0152	0.0401	-0.0031	-0.0158	-0.0216	-0.005	14.2521	-6.3614	57.3381
29	5.9315	-0.3446	-4.783	3.1043	2.5166	10.0222	0.0769	0.002	-0.1243	-0.3657	0.0066	-0.4154	0.0725	0.5278	-0.0836	-0.0365	-0.0131	0.027	0.0909	-0.0189	0.1052	28.0922	-4.078	56.0422
30	1.3741	1.5718	-0.566	6.6012	-0.6182	2.6819	0.1238	0.1645	-0.2745	0.1202	0.0757	-0.5632	0.191	0.2567	-0.1995	0.0834	-0.0044	0.0328	0.1103	-0.044	0.0824	23.1537	-4.3026	49.9767
31	3.9834	-4.422	2.8836	5.7735	-1.0659	7.3617	-0.0633	0.2212	-0.3995	-0.6046	0.0349	0.2804	0.3654	0.0654	0.0284	0.1633	-0.0261	0.069	0.1017	-0.0586	0.0115	17.5783	-4.4414	40.3914
32	13.1277	14.8537	6.2028	22.7869	10.5739	6.4932	0.0218	0.1673	-0.4535	-0.3875	0.426	-1.1956	-0.0543	0.7219	-0.4478	0.3796	-0.0734	0.1117	0.3267	0.0053	0.0846	24.0074	2.8468	35.1887

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 - 14	1 - 13
2	X-RAY DIFFRACTION	2	A	A	15 - 22	14 - 21
3	X-RAY DIFFRACTION	3	A	A	23 - 34	22 - 33
4	X-RAY DIFFRACTION	4	A	A	35 - 46	34 - 45
5	X-RAY DIFFRACTION	5	A	A	47 - 94	46 - 93
6	X-RAY DIFFRACTION	6	A	A	95 - 133	94 - 132
7	X-RAY DIFFRACTION	7	A	A	134 - 157	133 - 156
8	X-RAY DIFFRACTION	8	A	A	158 - 163	157 - 162
9	X-RAY DIFFRACTION	9	A	A	178 - 196	177 - 195
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