PDB-7ou1: Crystal structure of Rhizobium etli inducible L-asparaginase ReAV...

ID or keywords:

Entry

Database: PDB / ID: 7ou1

Title

Crystal structure of Rhizobium etli inducible L-asparaginase ReAV (monoclinic form MP2)

Components

L-asparaginase

Keywords

HYDROLASE / L-asparaginase / amidohydrolase / Rhizobium etli

Function / homology

L-asparaginase II / L-asparaginase II / metal ion binding / L-asparaginase II protein

Function and homology information

Biological species

Rhizobium etli (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Imiolczyk, B. / Loch, J.I. / Gilski, M. / Jaskolski, M.

Funding support

Poland, 1items

Citation

Journal: Nat Commun / Year: 2021
Title: Crystal structures of the elusive Rhizobium etli L-asparaginase reveal a peculiar active site.
Authors: Loch, J.I. / Imiolczyk, B. / Sliwiak, J. / Wantuch, A. / Bejger, M. / Gilski, M. / Jaskolski, M.

History

Deposition	Jun 10, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 24, 2021	Provider: repository / Type: Initial release
Revision 1.1	Dec 1, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	Apr 26, 2023	Group: Derived calculations / Category: atom_type / Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.3	Feb 7, 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
Revision 1.4	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7ou1.cif.gz	498.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7ou1.ent.gz		Display	PDB format
PDBx/mmJSON format	7ou1.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/ou/7ou1 ftp://data.pdbj.org/pub/pdb/validation_reports/ou/7ou1	HTTPS FTP

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Related structure data

Related structure data	7os3SC 7os5C 7os6C 7oz6C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7os6-2 1ek6-d 1nah-1 1lrk-1 4gj5-d 1kvu-1 1n8s-d 1a9z-1 7ou1-2 1i3m-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.18150/VQQIHQ / Data set type: diffraction image data / Metadata reference: 10.18150/VQQIHQ

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

AAA: L-asparaginase

BBB: L-asparaginase

CCC: L-asparaginase

DDD: L-asparaginase

hetero molecules

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

1

AAA: L-asparaginase

BBB: L-asparaginase

hetero molecules

defined by author&software
Evidence: gel filtration
79.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

CCC: L-asparaginase

DDD: L-asparaginase

hetero molecules

defined by author&software
79.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	77.923, 91.308, 114.164
Angle α, β, γ (deg.)	90.000, 97.111, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	BBB
3	2	AAA
4	2	CCC
5	3	AAA
6	3	DDD
7	4	BBB
8	4	CCC
9	5	BBB
10	5	DDD
11	6	CCC
12	6	DDD

NCS domain segments:

Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 1 / Auth seq-ID: 3 - 352 / Label seq-ID: 9 - 358

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	1	AAA	A
2	1	1	BBB	B
3	2	2	AAA	A
4	2	2	CCC	C
5	3	3	AAA	A
6	3	3	DDD	D
7	4	4	BBB	B
8	4	4	CCC	C
9	5	5	BBB	B
10	5	5	DDD	D
11	6	6	CCC	C
12	6	6	DDD	D

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	L-asparaginase Mass: 39570.867 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Class 3 (R. etli) type L-asparaginase Source: (gene. exp.) Rhizobium etli (strain CFN 42 / ATCC 51251) (bacteria) Strain: CFN 42 / ATCC 51251 / Gene: ansA, RHE_PE00350 / Plasmid: pET-151D-TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Magic / References: UniProt: Q2K0Z2
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1403 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.55 Å³/Da / Density % sol: 51.69 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2% PEG8000, 20% PEG400, 5 mM Mg(CH3COO)2, 6 mM 3.0 mM sucrose monolaureate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.895 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 7, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.895 Å / Relative weight: 1
Reflection	Resolution: 1.65→45.65 Å / Num. obs: 189888 / % possible obs: 99 % / Redundancy: 4 % / B_iso Wilson estimate: 21.54 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.134 / Net I/σ(I): 10
Reflection shell	Resolution: 1.65→1.75 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.622 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 30255 / CC_1/2: 0.795 / % possible all: 98

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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
Starting model: 7OS3

7os3

Resolution: 1.65→45.65 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.928 / SU B: 5.22 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.091 / ESU R Free: 0.092 / Details: Hydrogen atoms were added at riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2217	1000	0.527 %
R_work	0.1898	188888	-
all	0.19	-	-
obs	-	189888	99.048 %

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: 16.259 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.931 Å²	-0 Å²	0.344 Å²
2-	-	-0.671 Å²	0 Å²
3-	-	-	1.47 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→45.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10372	0	8	1403	11783

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	10744
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	10161
X-RAY DIFFRACTION	r_angle_refined_deg	1.645	1.597	14557
X-RAY DIFFRACTION	r_angle_other_deg	1.509	1.579	23390
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.404	5	1455
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.435	20.163	553
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.289	15	1752
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.74	15	106
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	1404
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	12587
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2463
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	2329
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.184	0.2	9465
X-RAY DIFFRACTION	r_nbtor_refined	0.16	0.2	5294
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	4795
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.156	0.2	1009
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.108	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.157	0.2	24
X-RAY DIFFRACTION	r_nbd_other	0.211	0.2	112
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.198	0.2	56
X-RAY DIFFRACTION	r_mcbond_it	1.079	1.29	5689
X-RAY DIFFRACTION	r_mcbond_other	1.068	1.289	5687
X-RAY DIFFRACTION	r_mcangle_it	1.697	1.928	7133
X-RAY DIFFRACTION	r_mcangle_other	1.687	1.928	7133
X-RAY DIFFRACTION	r_scbond_it	1.702	1.462	5055
X-RAY DIFFRACTION	r_scbond_other	1.702	1.462	5056
X-RAY DIFFRACTION	r_scangle_it	2.636	2.124	7405
X-RAY DIFFRACTION	r_scangle_other	2.636	2.125	7406
X-RAY DIFFRACTION	r_lrange_it	4.596	16.687	12547
X-RAY DIFFRACTION	r_lrange_other	4.545	16.33	12409
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.077	0.05	11236
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.074	0.05	11217
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.058	0.05	11305
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.077	0.05	11323
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.082	0.05	11230
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.079	0.05	11309

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	0.07696	0.05008
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.07696	0.05008
2	3	AAA	X-RAY DIFFRACTION	Local ncs	0.07361	0.05008
2	4	CCC	X-RAY DIFFRACTION	Local ncs	0.07361	0.05008
3	5	AAA	X-RAY DIFFRACTION	Local ncs	0.05758	0.05008
3	6	DDD	X-RAY DIFFRACTION	Local ncs	0.05758	0.05008
4	7	BBB	X-RAY DIFFRACTION	Local ncs	0.0769	0.05008
4	8	CCC	X-RAY DIFFRACTION	Local ncs	0.0769	0.05008
5	9	BBB	X-RAY DIFFRACTION	Local ncs	0.0819	0.05008
5	10	DDD	X-RAY DIFFRACTION	Local ncs	0.0819	0.05008
6	11	CCC	X-RAY DIFFRACTION	Local ncs	0.07944	0.05008
6	12	DDD	X-RAY DIFFRACTION	Local ncs	0.07944	0.05008

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
1.646-1.689	0.298	71	0.306	13489	0.306	14147	0.705	0.698	95.8507	0.278
1.689-1.735	0.283	72	0.284	13656	0.284	13744	0.738	0.757	99.8836	0.253
1.735-1.786	0.288	70	0.26	13267	0.26	13349	0.813	0.82	99.9101	0.226
1.786-1.84	0.21	69	0.238	12935	0.238	13019	0.892	0.868	99.8848	0.202
1.84-1.901	0.261	66	0.226	12546	0.226	12654	0.882	0.882	99.6681	0.191
1.901-1.967	0.239	64	0.213	12042	0.213	12161	0.905	0.901	99.5477	0.181
1.967-2.041	0.212	62	0.199	11626	0.199	11743	0.937	0.924	99.5316	0.169
2.041-2.125	0.242	59	0.189	11234	0.19	11348	0.914	0.938	99.5153	0.163
2.125-2.219	0.209	57	0.182	10752	0.182	10883	0.929	0.945	99.32	0.156
2.219-2.327	0.209	54	0.173	10246	0.173	10370	0.929	0.949	99.325	0.149
2.327-2.452	0.179	52	0.168	9777	0.168	9906	0.955	0.952	99.2227	0.146
2.452-2.601	0.205	49	0.16	9295	0.16	9415	0.941	0.958	99.2459	0.139
2.601-2.78	0.212	46	0.159	8694	0.16	8797	0.95	0.959	99.3521	0.141
2.78-3.001	0.214	43	0.17	8095	0.17	8213	0.94	0.954	99.0868	0.155
3.001-3.286	0.195	39	0.178	7426	0.178	7538	0.954	0.951	99.0316	0.168
3.286-3.672	0.231	36	0.177	6727	0.177	6866	0.935	0.952	98.4999	0.176
3.672-4.235	0.22	31	0.165	5899	0.165	6054	0.921	0.951	97.9518	0.169
4.235-5.176	0.161	27	0.164	5008	0.164	5166	0.957	0.97	97.4642	0.17
5.176-7.274	0.169	21	0.182	3949	0.182	4018	0.961	0.958	98.8054	0.183
7.274-45.654	0.44	12	0.173	2226	0.174	2313	0.688	0.951	96.7575	0.188

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	0.1242	0.1105	-0.0511	0.1795	-0.0587	0.1605	-0.0059	-0.0004	0.0317	0.0025	-0.0153	0.0243	0.026	-0.0211	0.0212	0.0063	-0.0043	0.0079	0.0192	-0.0115	0.0461	-36.4753	35.3605	5.2784
2	0.0961	0.0971	0	0.2162	0.0391	0.0376	0.0022	-0.0139	-0.0173	-0.0058	-0.0128	-0.0178	-0.0121	0.0033	0.0106	0.0115	-0.0039	0.0116	0.0146	0.0064	0.048	-3.2017	53.1679	5.3241
3	0.0944	-0.1454	0.0116	0.2396	-0.0487	0.1203	0.0064	0.0085	-0.0125	-0.0081	-0.0193	0.0131	-0.0052	-0.0071	0.0129	0.007	0.005	0.0087	0.0167	-0.0029	0.048	-4.0744	55.3438	51.3419
4	0.1251	-0.0827	-0.1483	0.2505	0.1224	0.1905	-0.0136	-0.041	0.0142	-0.0192	0.011	0.0004	0.0197	0.0617	0.0026	0.0104	0.0183	0.0043	0.0421	0.0091	0.0378	29.6152	38.5353	51.4278

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	3 - 352
2	X-RAY DIFFRACTION	1	ALL	AaA	353
3	X-RAY DIFFRACTION	1	ALL	AbA	354 - 506
4	X-RAY DIFFRACTION	2	ALL	BBB	3 - 352
5	X-RAY DIFFRACTION	2	ALL	BaB	353
6	X-RAY DIFFRACTION	2	ALL	BbB	354 - 533
7	X-RAY DIFFRACTION	3	ALL	CCC	3 - 352
8	X-RAY DIFFRACTION	3	ALL	CaC	353
9	X-RAY DIFFRACTION	3	ALL	CbC	354 - 538
10	X-RAY DIFFRACTION	4	ALL	DDD	3 - 352
11	X-RAY DIFFRACTION	4	ALL	DaD	353
12	X-RAY DIFFRACTION	4	ALL	DbD	354 - 516

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