PDB-7qsf: Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-12...

ID or keywords:

Entry

Database: PDB / ID: 7qsf

Title

Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-12 (G206C, R207T, D210A, S211A)

Components

Isoaspartyl peptidase
Isoaspartyl peptidase subunit beta

Keywords

HYDROLASE / L-asparaginase / Ntn-hydrolase / EcAIII

Function / homology

Function and homology information

beta-aspartyl-peptidase / asparagine catabolic process via L-aspartate / asparaginase activity / beta-aspartyl-peptidase activity / protein autoprocessing / hydrolase activity / cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Loch, J.I. / Kadziolka, K. / Jaskolski, M.

Funding support

Poland, 1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structural and biophysical studies of new L-asparaginase variants: lessons from random mutagenesis of the prototypic Escherichia coli Ntn-amidohydrolase.
Authors: Loch, J.I. / Klonecka, A. / Kadziolka, K. / Bonarek, P. / Barciszewski, J. / Imiolczyk, B. / Brzezinski, K. / Gilski, M. / Jaskolski, M.

History

Deposition	Jan 13, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 13, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	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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PDBx/mmCIF format	7qsf.cif.gz	214.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7qsf.ent.gz		Display	PDB format
PDBx/mmJSON format	7qsf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7qsf_validation.pdf.gz	439.3 KB	Display	wwPDB validaton report
Full document	7qsf_full_validation.pdf.gz	440.1 KB	Display
Data in XML	7qsf_validation.xml.gz	27.6 KB	Display
Data in CIF	7qsf_validation.cif.gz	41.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qs/7qsf ftp://data.pdbj.org/pub/pdb/validation_reports/qs/7qsf	HTTPS FTP

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Related structure data

Related structure data	7qq8C 7qtcC 7qvrC 7qy6C 7qymC 7qyxC 7r1gC 7r5cC 2zalS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.18150/T0WC49 / Data set type: diffraction image data

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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

AAA: Isoaspartyl peptidase

BBB: Isoaspartyl peptidase subunit beta

CCC: Isoaspartyl peptidase

DDD: Isoaspartyl peptidase subunit beta

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	51.623, 75.052, 149.137
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Isoaspartyl peptidase / Beta-aspartyl-peptidase / EcAIII / Isoaspartyl dipeptidase Mass: 19013.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: iaaA, spt, ybiK, b0828, JW0812 / Plasmid: pET11d / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Gold / References: UniProt: P37595, beta-aspartyl-peptidase
#2: Protein	Isoaspartyl peptidase subunit beta Mass: 14358.137 Da / Num. of mol.: 2 / Mutation: G206C, R207T, D210A, S211A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: iaaA, spt, ybiK, b0828, JW0812 / Plasmid: pET11d / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Gold / References: UniProt: P37595
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 597 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.16 Å³/Da / Density % sol: 43.17 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% PEG 6000, 0.2 M MgCl2 in 0.1M Tris-HCl pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.54056 Å
Detector	Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 16, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54056 Å / Relative weight: 1
Reflection	Resolution: 1.6→19.05 Å / Num. obs: 69731 / % possible obs: 90.7 % / Redundancy: 2.3 % / CC_1/2: 0.995 / R_merge(I) obs: 0.056 / R_rim(I) all: 0.07 / Net I/σ(I): 9.8
Reflection shell	Resolution: 1.6→1.63 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.22 / Num. unique obs: 3274 / CC_1/2: 0.883 / R_rim(I) all: 0.293 / % possible all: 86.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
CrysalisPro		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2ZAL

2zal

Resolution: 1.6→19.05 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.928 / SU B: 3.741 / SU ML: 0.067 / Cross valid method: FREE R-VALUE / ESU R: 0.091 / ESU R Free: 0.093

	R_factor	Num. reflection	% reflection
R_free	0.2109	1039	1.491 %
R_work	0.1737	68661	-
all	0.174	-	-
obs	-	69700	90.157 %

Solvent computation

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

Displacement parameters

B_iso mean: 16.778 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.082 Å²	-0 Å²	-0 Å²
2-	-	0.022 Å²	-0 Å²
3-	-	-	0.06 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→19.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4198	0	4	597	4799

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	4303
X-RAY DIFFRACTION	r_bond_other_d	0.015	0.015	4148
X-RAY DIFFRACTION	r_angle_refined_deg	1.672	1.631	5845
X-RAY DIFFRACTION	r_angle_other_deg	1.65	1.569	9523
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.82	5	590
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.119	22.143	196
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.632	15	686
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.511	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	581
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	4995
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	933
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	754
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.182	0.2	3691
X-RAY DIFFRACTION	r_nbtor_refined	0.153	0.2	2034
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.07	0.2	1816
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.2	367
X-RAY DIFFRACTION	r_metal_ion_refined	0.121	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.245	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.217	0.2	52
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.209	0.2	33
X-RAY DIFFRACTION	r_mcbond_it	1.871	0.332	2327
X-RAY DIFFRACTION	r_mcbond_other	1.863	0.331	2326
X-RAY DIFFRACTION	r_mcangle_it	2.322	0.485	2904
X-RAY DIFFRACTION	r_mcangle_other	2.322	0.485	2905
X-RAY DIFFRACTION	r_scbond_it	4.46	0.663	1976
X-RAY DIFFRACTION	r_scbond_other	4.459	0.663	1977
X-RAY DIFFRACTION	r_scangle_it	5.7	0.852	2933
X-RAY DIFFRACTION	r_scangle_other	5.699	0.852	2934
X-RAY DIFFRACTION	r_lrange_it	7.31	6.453	4684
X-RAY DIFFRACTION	r_lrange_other	7.278	6.238	4658

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 (%)
1.6-1.642	0.28	87	0.255	4865	X-RAY DIFFRACTION	88.2709
1.642-1.687	0.279	78	0.23	5073	X-RAY DIFFRACTION	93.1633
1.687-1.735	0.236	64	0.222	4952	X-RAY DIFFRACTION	94.1441
1.735-1.789	0.259	81	0.207	4867	X-RAY DIFFRACTION	94.4635
1.789-1.847	0.236	78	0.21	4688	X-RAY DIFFRACTION	94.5823
1.847-1.912	0.274	60	0.213	4610	X-RAY DIFFRACTION	95.209
1.912-1.984	0.294	64	0.201	4439	X-RAY DIFFRACTION	95.2613
1.984-2.065	0.181	56	0.184	4228	X-RAY DIFFRACTION	94.1953
2.065-2.157	0.214	59	0.179	3953	X-RAY DIFFRACTION	91.9972
2.157-2.262	0.219	72	0.168	3724	X-RAY DIFFRACTION	90.77
2.262-2.384	0.171	51	0.153	3507	X-RAY DIFFRACTION	89.3745
2.384-2.529	0.21	52	0.151	3285	X-RAY DIFFRACTION	88.0475
2.529-2.703	0.173	50	0.151	3028	X-RAY DIFFRACTION	86.4121
2.703-2.92	0.22	34	0.149	2838	X-RAY DIFFRACTION	86.1428
2.92-3.198	0.163	33	0.149	2537	X-RAY DIFFRACTION	83.7952
3.198-3.574	0.151	27	0.151	2281	X-RAY DIFFRACTION	82.3697
3.574-4.126	0.208	27	0.142	1985	X-RAY DIFFRACTION	81.031
4.126-5.049	0.191	32	0.134	1738	X-RAY DIFFRACTION	82.7489
5.049-7.124	0.204	20	0.175	1370	X-RAY DIFFRACTION	82.8367
7.124-19.05	0.121	14	0.158	693	X-RAY DIFFRACTION	70.2783

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	0.0317	-0.1985	-0.0879	1.3847	0.6235	0.3006	-0.0148	-0.0006	0.0355	0.2067	0.0224	-0.1287	0.0495	0.0188	-0.0076	0.1709	-0.0125	-0.0638	0.1328	0.0257	0.1712	17.9839	-5.7942	51.5948
2	0.0332	-0.2719	-0.2042	4.4015	3.203	2.3337	0.0927	0.0417	0.0351	0.188	0.1171	-0.33	0.1099	0.0409	-0.2097	0.3132	0.1902	0.0301	0.1576	0.0592	0.0848	8.8971	11.9995	60.8037
3	0.1771	-0.0479	0.0098	0.1191	0.0317	0.1095	-0.0211	-0.019	-0.0298	0.0532	0.0087	0.0281	-0.0028	0.001	0.0123	0.1486	0.0105	-0.0078	0.1399	0.0092	0.138	7.1177	-5.9791	54.5078
4	0.1793	-0.0644	-0.0005	0.2751	-0.1223	0.0663	-0.0401	-0.0124	0.0087	-0.0016	0.0372	0.0072	0.0279	0.0037	0.0029	0.1261	0.0033	-0.0057	0.1396	-0.0021	0.1551	3.3258	-9.2525	37.8006
5	1.4888	1.2111	-0.372	1.0325	-0.3236	0.5697	0.0066	0.0366	-0.0689	-0.0561	0.0272	-0.0039	-0.0424	-0.0502	-0.0338	0.1244	-0.009	-0.0054	0.1351	-0.0076	0.1633	-4.4178	-11.8215	34.1656
6	0.1673	-0.4533	0.0344	1.9785	-0.0377	0.013	-0.0758	0.0238	-0.0345	0.1264	0.089	0.1187	-0.0323	0.0065	-0.0132	0.1537	0.0112	0.0211	0.1332	0.005	0.1462	-8.811	5.8116	49.3705
7	1.6385	-1.045	-0.2002	1.0871	0.1107	0.1485	0.0264	-0.0053	0.0082	0.0106	-0.0444	-0.0392	-0.0331	0.0197	0.018	0.1202	0.0037	-0.0146	0.149	0.0086	0.1413	15.0513	-8.6766	45.0982
8	0.2774	-0.415	-0.0412	1.2154	0.7659	0.865	-0.0024	0.0576	0.0769	0.0917	-0.0343	-0.0704	0.0917	-0.0055	0.0367	0.1422	0.0007	0.0016	0.1552	0.0127	0.1437	-2.6089	7.985	38.7054
9	0.0887	-0.1175	0.0697	0.1597	-0.1152	0.3384	-0.0261	0.0087	-0.034	0.0335	-0.0085	0.0257	-0.0565	0.0545	0.0346	0.126	-0.0114	-0.0077	0.1564	0.0062	0.1524	19.1909	1.098	37.3877
10	0.4299	-0.272	-0.0409	0.5445	-0.2094	0.1955	0.0255	-0.0152	-0.016	0.0302	-0.0144	-0.0503	-0.0808	0.0514	-0.0111	0.1418	-0.0247	-0.0167	0.145	0.0012	0.149	22.2201	4.7665	43.2532
11	0.0256	0.112	0.1297	0.6896	0.5637	0.6678	-0.0025	0.0086	-0.0003	0.0905	0.0379	-0.0781	-0.0216	0.0458	-0.0354	0.1418	-0.0006	-0.0244	0.1412	0.0098	0.1536	18.027	-0.1069	55.3274
12	0.102	0.0426	0.6615	0.0208	0.2817	4.3351	0.0149	0.0274	-0.0147	0.0035	0.0399	0.0072	-0.0516	0.2213	-0.0548	0.1757	-0.0185	0.0068	0.1369	0.0279	0.1244	15.3371	8.6346	57.881
13	0.1461	0.5801	0.1014	2.3759	0.2019	0.7553	-0.0079	0.0028	-0.0053	-0.0886	-0.0015	-0.0272	0.0292	0.0405	0.0095	0.1267	-0.0124	0.019	0.1608	-0.0038	0.1403	16.8644	5.8679	9.7344
14	4.8251	5.5863	0.0578	6.4743	0.0484	0.0649	0.0827	-0.2192	-0.0983	-0.006	-0.1999	-0.1347	0.1813	-0.048	0.1172	0.5591	-0.131	0.2211	0.1263	-0.0293	0.1157	9.6628	-9.7494	-2.5258
15	0.1051	0.3992	0.2696	1.7301	0.6181	1.5192	-0.0048	0.0002	-0.0101	-0.0072	-0.0004	-0.0503	-0.0234	-0.0992	0.0052	0.141	-0.0064	0.0102	0.1839	-0.0153	0.1069	8.4421	-0.2676	-2.9946
16	0.6504	0.3583	-0.0033	0.2206	-0.0701	0.2657	-0.0342	0.0633	0.0189	-0.0099	0.0106	0.0148	-0.0274	-0.0142	0.0236	0.1427	-0.0138	-0.0054	0.1561	-0.0039	0.1307	6.5176	8.3133	9.3056
17	0.3146	-0.0036	-0.0194	0.0094	-0.0362	0.2433	-0.0102	0.0196	0.0157	0.0171	0.0145	0.0095	-0.0185	-0.0072	-0.0044	0.1311	-0.0084	-0.0026	0.1393	-0.0137	0.1537	1.8371	8.0848	22.9983
18	0.2744	-0.2545	-0.3336	1.3625	0.5983	0.6214	0.0046	0.0515	-0.0155	-0.0247	-0.0454	0.0187	0.0063	-0.1604	0.0408	0.121	-0.0182	-0.0081	0.1511	-0.0188	0.1367	-6.8454	0.187	15.1864
19	1.477	1.2225	0.3573	1.1161	0.1852	0.256	-0.0252	0.0272	0.0095	0.014	-0.0384	0.0175	-0.0061	0.0501	0.0636	0.1268	-0.0251	0.0003	0.1502	-0.0023	0.145	14.0502	9.9013	15.5049
20	0.7704	0.2512	0.8321	2.0194	0.9055	1.1091	0.0057	-0.0752	0.0467	-0.004	-0.0415	-0.0823	0.0181	-0.0913	0.0358	0.1423	-0.0441	0.0152	0.113	-0.0388	0.1885	-0.9828	-10.7092	20.188
21	0.4242	0.3315	0.0374	0.4811	-0.1864	0.2141	0.0077	0.0083	0.008	-0.0177	-0.0271	0.0017	0.0204	0.0341	0.0195	0.1292	-0.0064	0.0053	0.1515	-0.0016	0.1471	15.5907	-0.0082	24.0005
22	0.3963	0.3938	-0.566	0.4123	-0.3609	3.5823	-0.0483	-0.0122	-0.115	-0.0859	0.0024	-0.1027	-0.2132	0.1438	0.0459	0.0837	-0.0169	-0.0048	0.1719	0.0091	0.1512	29.5196	0.6096	21.5875
23	0.3496	0.206	0.1039	0.7703	-0.0882	0.0741	0.0225	0.031	-0.0192	-0.0085	-0.0236	-0.0066	0.0112	0.0553	0.0011	0.1267	-0.0073	0.0194	0.1648	-0.0041	0.1413	21.7707	-2.6741	16.4944
24	0.2082	-0.6618	-0.041	2.2386	0.3539	0.4085	0.0522	0.0396	0.0334	-0.1291	-0.0703	-0.1214	0.0096	0.1054	0.0181	0.1552	-0.0055	0.0267	0.164	0.0021	0.1301	18.3032	1.5908	3.6033

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	2 - 13
2	X-RAY DIFFRACTION	2	ALL	AAA	14 - 20
3	X-RAY DIFFRACTION	3	ALL	AAA	21 - 76
4	X-RAY DIFFRACTION	4	ALL	AAA	77 - 120
5	X-RAY DIFFRACTION	5	ALL	AAA	121 - 137
6	X-RAY DIFFRACTION	6	ALL	AAA	138 - 160
7	X-RAY DIFFRACTION	7	ALL	BBB	179 - 199
8	X-RAY DIFFRACTION	8	ALL	BBB	200 - 208
9	X-RAY DIFFRACTION	9	ALL	BBB	209 - 259
10	X-RAY DIFFRACTION	10	ALL	BBB	260 - 287
11	X-RAY DIFFRACTION	11	ALL	BBB	288 - 309
12	X-RAY DIFFRACTION	12	ALL	BBB	310 - 312
13	X-RAY DIFFRACTION	13	ALL	CCC	3 - 14
14	X-RAY DIFFRACTION	14	ALL	CCC	15 - 22
15	X-RAY DIFFRACTION	15	ALL	CCC	23 - 34
16	X-RAY DIFFRACTION	16	ALL	CCC	35 - 76
17	X-RAY DIFFRACTION	17	ALL	CCC	77 - 124
18	X-RAY DIFFRACTION	18	ALL	CCC	125 - 157
19	X-RAY DIFFRACTION	19	ALL	DDD	179 - 199
20	X-RAY DIFFRACTION	20	ALL	DDD	200 - 206
21	X-RAY DIFFRACTION	21	ALL	DDD	207 - 248
22	X-RAY DIFFRACTION	22	ALL	DDD	249 - 262
23	X-RAY DIFFRACTION	23	ALL	DDD	263 - 292
24	X-RAY DIFFRACTION	24	ALL	DDD	293 - 312

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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi