PDB-8c23: Structure of E. coli Class 2 L-asparaginase EcAIII, mutant M200T ...

ID or keywords:

Entry

Database: PDB / ID: 8c23

Title

Structure of E. coli Class 2 L-asparaginase EcAIII, mutant M200T (monoclinic form M200T#m)

Components

(Isoaspartyl peptidase subunit ...) x 2

Keywords

HYDROLASE / L-asparaginase / isoaspartylpeptidase / mutation / Ntn-hydrolase

Function / homology

Function and homology information

beta-aspartyl-peptidase / asparaginase activity / beta-aspartyl-peptidase activity / protein autoprocessing / hydrolase activity
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.842 Å

Authors

Sciuk, A. / Ruszkowski, M. / Jaskolski, M. / Loch, J.I.

Funding support

Poland, 1items

Citation

Journal: Protein Sci. / Year: 2023
Title: The effects of nature-inspired amino acid substitutions on structural and biochemical properties of the E. coli L-asparaginase EcAIII.
Authors: Janicki, M. / Sciuk, A. / Zielezinski, A. / Ruszkowski, M. / Ludwikow, A. / Karlowski, W.M. / Jaskolski, M. / Loch, J.I.

History

Deposition	Dec 21, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 3, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jun 7, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2	Jun 19, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8c23.cif.gz	423.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8c23.ent.gz		Display	PDB format
PDBx/mmJSON format	8c23.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8c23_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	8c23_full_validation.pdf.gz	1.4 MB	Display
Data in XML	8c23_validation.xml.gz	46 KB	Display
Data in CIF	8c23_validation.cif.gz	66.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c2/8c23 ftp://data.pdbj.org/pub/pdb/validation_reports/c2/8c23	HTTPS FTP

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Related structure data

Related structure data	8bi3C 8bkfC 8bp9C 8bqoC 8c0iC C: citing same article (ref.)
Similar structure data	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) #235 - Jul 2019 AMPA Receptor similarity (1) #176 - Aug 2014 Dynein similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

AAA: Isoaspartyl peptidase subunit alpha

BBB: Isoaspartyl peptidase subunit beta

CCC: Isoaspartyl peptidase subunit alpha

DDD: Isoaspartyl peptidase subunit beta

EEE: Isoaspartyl peptidase subunit alpha

FFF: Isoaspartyl peptidase subunit beta

GGG: Isoaspartyl peptidase subunit alpha

HHH: Isoaspartyl peptidase subunit beta

hetero molecules

134 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Isoaspartyl peptidase subunit alpha

BBB: Isoaspartyl peptidase subunit beta

CCC: Isoaspartyl peptidase subunit alpha

DDD: Isoaspartyl peptidase subunit beta

hetero molecules

defined by author&software
Evidence: gel filtration
67.3 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

EEE: Isoaspartyl peptidase subunit alpha

FFF: Isoaspartyl peptidase subunit beta

GGG: Isoaspartyl peptidase subunit alpha

HHH: Isoaspartyl peptidase subunit beta

hetero molecules

defined by author&software
67 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	127.461, 149.649, 105.130
Angle α, β, γ (deg.)	90.000, 126.718, 90.000
Int Tables number	5
Space group name H-M	C121

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Isoaspartyl peptidase subunit ... , 2 types, 8 molecules AAACCCEEEGGGBBBDDDFFFHHH

#1: Protein	Isoaspartyl peptidase subunit alpha Mass: 19013.773 Da / Num. of mol.: 4 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 (E. coli) / Strain (production host): BL21 Gold / References: UniProt: P37595
#2: Protein	Isoaspartyl peptidase subunit beta Mass: 14398.055 Da / Num. of mol.: 4 / Mutation: M200T 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 (E. coli) / Strain (production host): BL21 Gold / References: UniProt: P37595

#1: Protein

Isoaspartyl peptidase subunit alpha

Mass: 19013.773 Da / Num. of mol.: 4
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 (E. coli) / Strain (production host): BL21 Gold / References: UniProt: P37595

#2: Protein

Isoaspartyl peptidase subunit beta

Mass: 14398.055 Da / Num. of mol.: 4 / Mutation: M200T
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 (E. coli) / Strain (production host): BL21 Gold / References: UniProt: P37595

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Non-polymers , 6 types, 523 molecules

#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₅NO₂ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 507 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 3.3 Å³/Da / Density % sol: 62.7 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20-30% PEG4000,10-15% PEG 400,0.2M CaCl2 in 100 mM Tris-HCl pH 8.5, 100mM glycine

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.84→84.38 Å / Num. obs: 133092 / % possible obs: 98 % / Redundancy: 7 % / CC_1/2: 0.999 / R_merge(I) obs: 0.071 / R_rim(I) all: 0.077 / Net I/σ(I): 13.9
Reflection shell	Resolution: 1.84→1.84 Å / Num. unique obs: 6430 / CC_1/2: 0.564

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.842→84.38 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.956 / SU B: 8.611 / SU ML: 0.106 / Cross valid method: FREE R-VALUE / ESU R: 0.106 / ESU R Free: 0.106

	R_factor	Num. reflection	% reflection
R_free	0.216	1088	0.818 %
R_work	0.1848	131995	-
all	0.185	-	-
obs	-	133083	97.911 %

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: 39.318 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.775 Å²	0 Å²	-1.24 Å²
2-	-	-1.543 Å²	0 Å²
3-	-	-	1.239 Å²

Refinement step

Cycle: LAST / Resolution: 1.842→84.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8484	0	39	507	9030

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	8753
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	8391
X-RAY DIFFRACTION	r_angle_refined_deg	1.564	1.633	11871
X-RAY DIFFRACTION	r_angle_other_deg	1.4	1.572	19261
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.545	5	1189
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.291	21.957	414
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.923	15	1401
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.041	15	62
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	1164
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	10212
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1920
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	1740
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.185	0.2	7944
X-RAY DIFFRACTION	r_nbtor_refined	0.156	0.2	4276
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	3960
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.172	0.2	424
X-RAY DIFFRACTION	r_metal_ion_refined	0.161	0.2	13
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.294	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.367	0.2	55
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.213	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	1.947	3.108	4720
X-RAY DIFFRACTION	r_mcbond_other	1.947	3.107	4718
X-RAY DIFFRACTION	r_mcangle_it	3.01	4.639	5900
X-RAY DIFFRACTION	r_mcangle_other	3.01	4.639	5900
X-RAY DIFFRACTION	r_scbond_it	2.353	3.521	4033
X-RAY DIFFRACTION	r_scbond_other	2.345	3.521	4033
X-RAY DIFFRACTION	r_scangle_it	3.765	5.139	5964
X-RAY DIFFRACTION	r_scangle_other	3.763	5.139	5964
X-RAY DIFFRACTION	r_lrange_it	5.49	37.777	9490
X-RAY DIFFRACTION	r_lrange_other	5.49	37.775	9489

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.842-1.89	0.322	75	0.345	9575	0.345	10028	0.467	0.394	96.2306	0.338
1.89-1.942	0.356	76	0.321	9416	0.321	9784	0.456	0.508	97.0155	0.305
1.942-1.998	0.286	59	0.294	9164	0.294	9496	0.676	0.666	97.1251	0.276
1.998-2.059	0.266	68	0.256	8921	0.256	9227	0.806	0.801	97.4206	0.233
2.059-2.127	0.264	67	0.229	8658	0.229	8948	0.864	0.873	97.5078	0.209
2.127-2.202	0.262	72	0.209	8361	0.21	8638	0.88	0.905	97.6268	0.189
2.202-2.285	0.237	73	0.201	8150	0.201	8395	0.893	0.91	97.9512	0.18
2.285-2.378	0.212	61	0.174	7762	0.174	7992	0.919	0.942	97.8854	0.155
2.378-2.483	0.267	58	0.177	7513	0.178	7707	0.924	0.941	98.2354	0.16
2.483-2.605	0.194	47	0.173	7224	0.173	7399	0.942	0.947	98.27	0.156
2.605-2.745	0.211	74	0.171	6847	0.171	7030	0.94	0.951	98.4495	0.159
2.745-2.912	0.201	64	0.169	6483	0.169	6638	0.948	0.954	98.6291	0.16
2.912-3.112	0.208	68	0.173	6111	0.173	6260	0.927	0.952	98.7061	0.167
3.112-3.361	0.205	42	0.189	5694	0.189	5788	0.942	0.945	99.1016	0.187
3.361-3.682	0.154	34	0.171	5279	0.171	5365	0.958	0.961	99.0308	0.174
3.682-4.115	0.197	52	0.157	4773	0.157	4861	0.954	0.96	99.2594	0.165
4.115-4.75	0.196	42	0.153	4200	0.153	4285	0.958	0.962	98.9965	0.166
4.75-5.813	0.237	27	0.176	3570	0.177	3630	0.928	0.944	99.0909	0.191
5.813-8.201	0.27	13	0.174	2801	0.175	2833	0.883	0.94	99.3293	0.191
8.201-84.38	0.191	16	0.192	1493	0.192	1588	0.953	0.947	95.0252	0.214

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	0.3597	0.1618	-0.0191	0.3446	-0.0056	0.5166	-0.1053	-0.0019	-0.0017	0.0473	0.0544	0.005	-0.1385	-0.0116	0.0509	0.12	0.007	-0.0394	0.0456	0.0065	0.0654	24.3053	82.8047	5.6518
2	0.0432	-0.2003	0.0123	0.9822	-0.0339	0.1973	-0.0105	0.0144	0.0343	-0.0424	-0.0155	-0.1808	-0.0816	0.0934	0.026	0.048	-0.0598	-0.022	0.1058	0.0118	0.1083	38.838	78.0771	1.9702
3	0.2539	-0.2295	0.313	0.6276	0.0916	0.7286	0.0394	0.0156	-0.0762	-0.0482	0.0023	0.1168	0.0724	0.0379	-0.0417	0.097	0.013	0.0072	0.01	-0.0175	0.0946	21.6286	50.9829	-6.2625
4	0.0963	0.1685	0.1416	0.6747	0.0089	0.3677	0.0595	0.0365	-0.0384	0.0432	0.0076	-0.1049	0.1357	0.0916	-0.0671	0.0794	0.0659	-0.0105	0.0655	-0.0166	0.1217	35.8518	52.0177	0.0435
5	0.4051	-0.2626	0.4385	0.7534	-0.0311	0.5914	-0.0776	-0.1463	0.0375	-0.2045	0.0862	-0.0611	-0.1677	-0.1508	-0.0086	0.1447	0.0384	-0.038	0.0603	-0.0383	0.0875	-3.8017	98.706	30.831
6	0.0946	-0.1712	0.1011	1.3113	-0.457	0.1841	-0.1746	-0.0874	0.0521	0.2354	0.1344	-0.1275	-0.1474	-0.1007	0.0402	0.2246	0.1319	-0.0773	0.1112	-0.0722	0.0486	-1.0014	97.4298	46.3591
7	0.397	-0.1186	0.1925	0.3833	-0.0256	0.5059	0.0598	-0.0289	-0.0526	-0.0055	0.0565	-0.102	0.0499	-0.0345	-0.1162	0.0626	-0.0092	-0.0298	0.065	0.0146	0.0739	8.2223	67.1472	35.9154
8	0.4758	-0.3419	0.2979	1.2558	0.0591	0.2618	-0.0423	-0.161	-0.101	0.1898	0.1051	0.0973	0.0198	-0.1146	-0.0628	0.0823	-0.0005	-0.0015	0.1605	0.0594	0.0303	0.81	71.4304	49.1207
9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.0553	0	0	0.0553	0	0.0553	0	0	0

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	3 - 160
2	X-RAY DIFFRACTION	1	ALL	AaA	161
3	X-RAY DIFFRACTION	1	ALL	AbA	162
4	X-RAY DIFFRACTION	1	ALL	AcA	163
5	X-RAY DIFFRACTION	1	ALL	AdA	164 - 275
6	X-RAY DIFFRACTION	2	ALL	BBB	179 - 313
7	X-RAY DIFFRACTION	2	ALL	BaB	314
8	X-RAY DIFFRACTION	2	ALL	BbB	315
9	X-RAY DIFFRACTION	2	ALL	BcB	316 - 366
10	X-RAY DIFFRACTION	3	ALL	CCC	3 - 159
11	X-RAY DIFFRACTION	3	ALL	CaC	160
12	X-RAY DIFFRACTION	3	ALL	CbC	161
13	X-RAY DIFFRACTION	3	ALL	CcC	162 - 240
14	X-RAY DIFFRACTION	4	ALL	DDD	179 - 313
15	X-RAY DIFFRACTION	4	ALL	DaD	314
16	X-RAY DIFFRACTION	4	ALL	DbD	315
17	X-RAY DIFFRACTION	4	ALL	DcD	316 - 348
18	X-RAY DIFFRACTION	5	ALL	EEE	4 - 157
19	X-RAY DIFFRACTION	5	ALL	EaE	158
20	X-RAY DIFFRACTION	5	ALL	EbE	159 - 223
21	X-RAY DIFFRACTION	6	ALL	FFF	179 - 313
22	X-RAY DIFFRACTION	6	ALL	FaF	314
23	X-RAY DIFFRACTION	6	ALL	FbF	316 - 336
24	X-RAY DIFFRACTION	7	ALL	GGG	3 - 159
25	X-RAY DIFFRACTION	7	ALL	GaG	160
26	X-RAY DIFFRACTION	7	ALL	GbG	161
27	X-RAY DIFFRACTION	7	ALL	GcG	162
28	X-RAY DIFFRACTION	7	ALL	GdG	163 - 274
29	X-RAY DIFFRACTION	8	ALL	HHH	179 - 312
30	X-RAY DIFFRACTION	8	ALL	HaH	313 - 345

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Isoaspartyl peptidase subunit ... , 2 types, 8 molecules AAACCCEEEGGGBBBDDDFFFHHH

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Non-polymers , 6 types, 523 molecules

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-Isoaspartyl peptidase subunit ... , 2 types, 8 molecules AAACCCEEEGGGBBBDDDFFFHHH

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-Experimental details

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

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Isoaspartyl peptidase subunit ... , 2 types, 8 molecules AAACCCEEEGGGBBBDDDFFFHHH

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Non-polymers , 6 types, 523 molecules

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Experimental details

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Yorodumi