PDB-7qq8: Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-8 ...

ID or keywords:

Entry

Database: PDB / ID: 7qq8

Title

Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-8 (G206Y, R207Q, D210P, S211T)

Components

(Beta-aspartyl-peptidase) x 2

Keywords

HYDROLASE / L-asparaginase / Ntn-hydrolase / EcAIII

Function / homology

beta-aspartyl-peptidase / Peptidase T2, asparaginase 2 / Asparaginase / asparaginase / asparaginase activity / beta-aspartyl-peptidase activity / Nucleophile aminohydrolases, N-terminal / : / Beta-aspartyl-peptidase

Function and homology information

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.8 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 6, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7qq8.cif.gz	222.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7qq8_validation.pdf.gz	451.1 KB	Display	wwPDB validaton report
Full document	7qq8_full_validation.pdf.gz	453.5 KB	Display
Data in XML	7qq8_validation.xml.gz	26 KB	Display
Data in CIF	7qq8_validation.cif.gz	38 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qq/7qq8 ftp://data.pdbj.org/pub/pdb/validation_reports/qq/7qq8	HTTPS FTP

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Related structure data

Related structure data	7qsfC 7qtcC 7qvrC 7qy6C 7qymC 7qyxC 7r1gC 7r5cC 2zalS S: Starting model for refinement C: citing same article (ref.)
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/VAZZ2F / Data set type: diffraction image data / Details: MX-RDR https://mxrdr.icm.edu.pl/

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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: Beta-aspartyl-peptidase

BBB: Beta-aspartyl-peptidase

CCC: Beta-aspartyl-peptidase

DDD: Beta-aspartyl-peptidase

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	50.005, 74.885, 147.835
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	CCC
3	2	BBB
4	2	DDD

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ALA	ALA	ALA	ALA	AAA	A	4 - 156	4 - 156
2	2	1	ALA	ALA	ALA	ALA	CCC	C	4 - 156	4 - 156
3	3	2	THR	THR	TYR	TYR	BBB	B	179 - 311	1 - 133
4	4	2	THR	THR	TYR	TYR	DDD	D	179 - 311	1 - 133

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4

#1: Protein	Beta-aspartyl-peptidase 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, JJT18_14590, JK375_14200 / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) / References: UniProt: A0A507WP93, beta-aspartyl-peptidase
#2: Protein	Beta-aspartyl-peptidase / IaaA protein / Isoaspartyl peptidase / isoaspartyl peptidase / Asparaginase / L-asparaginase / ...IaaA protein / Isoaspartyl peptidase / isoaspartyl peptidase / Asparaginase / L-asparaginase / Putative L-asparaginase / Putative asparaginase Mass: 14501.256 Da / Num. of mol.: 2 / Mutation: G206Y, R207Q, D210P, S211T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: ybiK, iaaA, iaaA_1, A6519_003716, A8W81_003313, ABE90_014520, ACN002_0860, ACN68_01690, ACN81_14685, ACU57_05935, AM270_18905, AM464_21585, AML23_23425, AT335_000572, AUQ29_12475, BANRA_01341, ...Gene: ybiK, iaaA, iaaA_1, A6519_003716, A8W81_003313, ABE90_014520, ACN002_0860, ACN68_01690, ACN81_14685, ACU57_05935, AM270_18905, AM464_21585, AML23_23425, AT335_000572, AUQ29_12475, BANRA_01341, BANRA_01555, BANRA_01783, BANRA_04872, BB545_05440, BG944_002984, BHF52_24110, BHS81_05055, BJI68_11585, BK292_21235, BMT50_00465, BMT91_20430, BN17_06281, BO068_000728, BOH76_20420, BON70_18240, BON72_22520, BON73_01295, BON76_25520, BON93_04325, BON94_25670, BON95_17475, BON98_19810, BTQ06_08955, BUE81_13890, BvCms2454_00926, BvCmsHHP019_05523, BvCmsKKP057_04358, BvCmsKKP061_03116, BvCmsKSNP073_02388, BvCmsKSP011_05390, BvCmsNSNP036_00638, BvCmsSIP082_02366, BVL39_24345, C5F72_1CFS32920, C5N07_02820, C5Y87_11355, C6B22_17135, C6N50_003302, C9114_12655, C9160_09270, CA593_24960, CCS08_19790, CF32_004569, CN875_002453, CO706_26955, COD50_05845, CV83915_00751, D0X26_04985, D3O91_06915, D4V09_05900, D6T60_26500, D9D77_09725, D9H13_07905, D9H94_11600, DAH18_23535, DAH34_00665, DAH37_00135, DB282_07105, DEN89_02655, DEN95_11270, DEO15_17945, DIV22_10390, DM968_05545, DS732_09125, DTL43_10625, DXT69_18875, DXT71_08810, E0I42_09220, E2119_12510, E2127_00560, E2128_05045, E2129_10495, E4K51_02720, E4K54_01015, E5S34_19335, E5S35_03615, E5S43_04770, E5S47_20155, E5S52_10740, EAI46_07630, EAN77_08435, EAX79_16315, EC3234A_14c00240, EC95NR1_05101, EHD79_04065, EHH55_13640, EI021_00645, EI041_07210, EIA13_17230, EIZ93_05000, EKI52_06310, EL79_3055, EL80_3016, ELT21_01570, ELV08_05385, ELY05_10390, ETECE36_04109, ETECE925_03147, F9V24_09900, FC554_12230, FOI11_009250, FOI11_10795, FTV92_09805, FV293_02290, FVB16_25145, FWK02_18715, FY127_05135, G9448_06620, GF646_11140, GIB53_03275, GKF86_16910, GKF89_13745, GNZ05_09030, GP650_11285, GP662_09655, GP946_16590, GP979_11145, GQE64_04115, GQF58_22125, GQF59_19085, GQM04_07810, GQM06_12705, GQM09_17025, GQM10_22525, GQR15_10775, GRW05_01460, GRW57_08990, GRW81_11185, GUC01_03155, H4P47_16170, H4P50_17220, H4P51_17070, HCF72_001403, HHH44_001163, HIE44_001059, HIR12_003510, HKA49_002523, HmCms184_01733, HMV95_02640, HNC52_00665, HNV65_21255, HPE39_07700, HVV53_24715, HVW11_02200, HX136_17405, I6H00_09890, I6H01_21700, I6H02_22440, JE86ST02C_09390, JE86ST05C_09930, NCTC10090_00399, NCTC10418_05023, NCTC11181_00590, NCTC13216_03372, NCTC4450_03859, NCTC8008_02934, NCTC8500_03679, NCTC8622_06405, NCTC8960_00506, NCTC9036_03423, NCTC9045_03895, NCTC9073_02377, NCTC9111_03436, NCTC9703_02658, ND22_003961, PGD_02506, RG28_00360, SAMEA3472043_03316, SAMEA3472080_01956, SAMEA3484427_01111, SAMEA3484429_00220, SAMEA3751407_00331, SAMEA3752386_00245, SAMEA3753300_01714, WP2S18E08_31210, WP4S18E08_29890, WQ89_23460, WR15_25260 Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) References: UniProt: J7QNS8, beta-aspartyl-peptidase, asparaginase
#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.: 412 / 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: 2.06 Å³/Da / Density % sol: 40.43 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG 4000; 15% PEG 400; 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 / Wavelength: 1.5406 Å
Detector	Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 24, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5406 Å / Relative weight: 1
Reflection	Resolution: 1.8→19.161 Å / Num. obs: 48975 / % possible obs: 93.6 % / Redundancy: 2.6 % / CC_1/2: 0.996 / R_merge(I) obs: 0.076 / R_rim(I) all: 0.092 / Net I/σ(I): 8
Reflection shell	Resolution: 1.8→1.84 Å / R_merge(I) obs: 0.519 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2945 / CC_1/2: 0.692 / R_rim(I) all: 0.631

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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: 1.8→19.161 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.921 / SU B: 8.88 / SU ML: 0.117 / Cross valid method: FREE R-VALUE / ESU R: 0.145 / ESU R Free: 0.137

	R_factor	Num. reflection	% reflection
R_free	0.2365	1001	2.046 %
R_work	0.1955	47923	-
all	0.196	-	-
obs	-	48924	93.436 %

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: 17.964 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.364 Å²	0 Å²	0 Å²
2-	-	0.11 Å²	-0 Å²
3-	-	-	-0.474 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→19.161 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4218	0	4	412	4634

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	4324
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.015	4143
X-RAY DIFFRACTION	r_angle_refined_deg	1.609	1.632	5877
X-RAY DIFFRACTION	r_angle_other_deg	1.473	1.569	9511
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.031	5	590
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.215	22.079	202
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.787	15	687
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.373	15	29
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	580
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	5031
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	951
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	985
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	0.2	4244
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	2183
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	1983
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.193	0.2	316
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.058	0.2	4
X-RAY DIFFRACTION	r_metal_ion_refined	0.158	0.2	6
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.297	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.272	0.2	60
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.233	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	1.07	1.342	2324
X-RAY DIFFRACTION	r_mcbond_other	1.069	1.341	2323
X-RAY DIFFRACTION	r_mcangle_it	1.864	2.004	2902
X-RAY DIFFRACTION	r_mcangle_other	1.863	2.006	2903
X-RAY DIFFRACTION	r_scbond_it	1.326	1.596	2000
X-RAY DIFFRACTION	r_scbond_other	1.321	1.593	1998
X-RAY DIFFRACTION	r_scangle_it	2.171	2.312	2967
X-RAY DIFFRACTION	r_scangle_other	2.17	2.312	2967
X-RAY DIFFRACTION	r_lrange_it	4.294	17.597	4988
X-RAY DIFFRACTION	r_lrange_other	4.272	17.541	4973
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.093	0.05	4506
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.057	0.05	3724

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.09254	0.05008
1	2	CCC	X-RAY DIFFRACTION	Local ncs	0.09254	0.05008
2	3	BBB	X-RAY DIFFRACTION	Local ncs	0.05673	0.05009
2	4	DDD	X-RAY DIFFRACTION	Local ncs	0.05673	0.05009

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
1.8-1.846	0.298	70	0.288	3551	0.288	3795	0.781	0.8	95.415	0.275
1.846-1.896	0.331	70	0.275	3443	0.276	3680	0.784	0.815	95.462	0.256
1.896-1.951	0.334	69	0.268	3363	0.27	3599	0.835	0.83	95.3598	0.244
1.951-2.01	0.251	66	0.256	3257	0.256	3474	0.855	0.851	95.6534	0.231
2.01-2.075	0.3	67	0.224	3210	0.226	3413	0.853	0.892	96.0152	0.203
2.075-2.147	0.277	66	0.225	3069	0.226	3268	0.866	0.889	95.9302	0.202
2.147-2.227	0.3	55	0.213	2974	0.214	3158	0.902	0.907	95.9151	0.194
2.227-2.317	0.257	75	0.201	2873	0.203	3073	0.913	0.922	95.9323	0.182
2.317-2.418	0.246	49	0.192	2761	0.193	2938	0.921	0.928	95.6433	0.177
2.418-2.534	0.282	65	0.204	2617	0.206	2815	0.899	0.923	95.2753	0.187
2.534-2.669	0.25	39	0.194	2535	0.195	2699	0.917	0.923	95.3687	0.182
2.669-2.827	0.244	54	0.185	2359	0.187	2554	0.919	0.942	94.4792	0.176
2.827-3.018	0.218	44	0.174	2192	0.175	2411	0.948	0.948	92.7416	0.168
3.018-3.253	0.23	48	0.182	2032	0.183	2258	0.934	0.939	92.1169	0.179
3.253-3.553	0.208	43	0.17	1822	0.171	2096	0.951	0.951	88.979	0.172
3.553-3.956	0.182	31	0.156	1609	0.157	1907	0.958	0.962	85.999	0.163
3.956-4.536	0.175	31	0.146	1404	0.146	1711	0.957	0.969	83.8691	0.156
4.536-5.479	0.11	25	0.151	1229	0.15	1469	0.981	0.972	85.3642	0.156
5.479-7.45	0.173	19	0.147	1012	0.148	1203	0.956	0.978	85.7024	0.151
7.45-19.161	0.165	15	0.165	611	0.165	782	0.96	0.976	80.0511	0.177

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	0.2909	0.1832	0.3018	0.2435	0.1601	0.8342	-0.0454	-0.095	-0.0479	-0.0366	-0.0539	0.0122	-0.0339	-0.1043	0.0993	0.0109	0.0188	0.0054	0.0374	0.0112	0.0744	1.6165	-4.6655	61.5636
2	0.1711	-0.1216	-0.2928	0.2785	0.0345	0.7618	0.0052	-0.0577	-0.0417	-0.0253	-0.0504	0.058	-0.044	0.1635	0.0452	0.0256	0.0137	-0.008	0.0628	0.0006	0.023	16.2556	-0.1832	58.1302
3	0.2819	-0.096	-0.2446	0.3514	0.0411	0.2735	-0.0232	0.0575	0.035	0.0038	0.0046	0.0458	0.0355	-0.0402	0.0186	0.0059	-0.0038	0.0104	0.0234	0.0204	0.0713	3.8356	6.0111	27.8501
4	0.3236	0.1318	0.1315	0.2513	-0.0219	0.3213	0.0172	0.0078	0.0329	-0.0016	-0.0367	-0.0209	0.0792	0.0446	0.0195	0.0288	0.0121	0.0163	0.0184	0.0054	0.0443	17.3207	-0.3592	32.2037

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	4 - 157
2	X-RAY DIFFRACTION	1	ALL	AaA	158
3	X-RAY DIFFRACTION	1	ALL	AbA	159 - 283
4	X-RAY DIFFRACTION	2	ALL	BBB	179 - 312
5	X-RAY DIFFRACTION	2	ALL	BaB	313
6	X-RAY DIFFRACTION	2	ALL	BbB	314 - 393
7	X-RAY DIFFRACTION	3	ALL	CCC	3 - 157
8	X-RAY DIFFRACTION	3	ALL	CaC	159
9	X-RAY DIFFRACTION	3	ALL	CbC	160 - 277
10	X-RAY DIFFRACTION	4	ALL	DDD	179 - 313
11	X-RAY DIFFRACTION	4	ALL	DaD	314
12	X-RAY DIFFRACTION	4	ALL	DbD	315 - 412

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About Yorodumi

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Yorodumi