PDB-7oz6: Crystal structure of Rhizobium etli inducible L-asparaginase ReAV...

ID or keywords:

Entry

Database: PDB / ID: 7oz6

Title

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

Components

L-asparaginase

Keywords

HYDROLASE / L-asparaginase / amidohydrolase / Rhizobium etli

Function / homology

L-asparaginase II / L-asparaginase II / metal ion binding / DI(HYDROXYETHYL)ETHER / L-asparaginase II protein

Function and homology information

Biological species

Rhizobium etli (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.757 Å

Authors

Gilski, M. / Loch, J.I. / Imiolczyk, B. / 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 25, 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.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _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 / pdbx_initial_refinement_model
Revision 1.4	Nov 20, 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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PDBx/mmCIF format	7oz6.cif.gz	262.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7oz6_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	7oz6_full_validation.pdf.gz	1.6 MB	Display
Data in XML	7oz6_validation.xml.gz	29.8 KB	Display
Data in CIF	7oz6_validation.cif.gz	43.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oz/7oz6 ftp://data.pdbj.org/pub/pdb/validation_reports/oz/7oz6	HTTPS FTP

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Related structure data

Related structure data	7os3SC 7os5C 7os6C 7ou1C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7os5-d 6ii2-3 7os3-d 5yt3-1 6cqf-1 6qh8-d 4gjc-d 3a65-1 5tmk-d 5kot-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
Experimental dataset #1	Data reference: 10.18150/6W9HGI / Data set type: diffraction image data / Metadata reference: 10.18150/6W9HGI

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

AAA: L-asparaginase

BBB: L-asparaginase

hetero molecules

79.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

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

Unit cell

Length a, b, c (Å)	130.289, 87.283, 93.925
Angle α, β, γ (deg.)	90.000, 130.154, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	L-asparaginase Mass: 39570.867 Da / Num. of mol.: 2 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: pET151D-TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2K0Z2
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.61 Å³/Da / Density % sol: 52.96 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 25% PEG3350, 0.2 M Li2SO4, 0.01% (w/v) heptane-1,2,3-triol, 0.1 M Tris pH 8.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.757→46.732 Å / Num. obs: 78980 / % possible obs: 98.3 % / Redundancy: 6.74 % / B_iso Wilson estimate: 36.405 Å² / CC_1/2: 1 / R_sym value: 0.042 / Net I/σ(I): 22.04
Reflection shell	Resolution: 1.76→1.86 Å / Redundancy: 6.59 % / R_merge(I) obs: 0.556 / Mean I/σ(I) obs: 2.69 / Num. unique obs: 12374 / CC_1/2: 0.925 / % possible all: 95.7

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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: 1.757→46.732 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.954 / SU B: 5.692 / SU ML: 0.088 / Cross valid method: FREE R-VALUE / ESU R: 0.105 / ESU R Free: 0.109 / Details: Hydrogen atoms were added at riding positions.

	R_factor	Num. reflection	% reflection
R_free	0.2271	1000	1.266 %
R_work	0.1832	77974	-
all	0.184	-	-
obs	-	78974	98.682 %

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: 32.962 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.872 Å²	0 Å²	-0.701 Å²
2-	-	-0.931 Å²	-0 Å²
3-	-	-	1.645 Å²

Refinement step

Cycle: LAST / Resolution: 1.757→46.732 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5359	0	16	333	5708

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.013	5512
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	5221
X-RAY DIFFRACTION	r_angle_refined_deg	1.652	1.638	7454
X-RAY DIFFRACTION	r_angle_other_deg	1.483	1.581	12012
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.096	5	737
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.004	20.207	290
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.868	15	898
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.189	15	56
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	718
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	6366
X-RAY DIFFRACTION	r_gen_planes_other	0	0.02	1258
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	1301
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.192	0.2	5200
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	2776
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	2804
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.187	0.2	365
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.201	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.208	0.2	60
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.085	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	2.041	2.788	2906
X-RAY DIFFRACTION	r_mcbond_other	2.036	2.788	2905
X-RAY DIFFRACTION	r_mcangle_it	2.797	4.171	3633
X-RAY DIFFRACTION	r_mcangle_other	2.797	4.171	3634
X-RAY DIFFRACTION	r_scbond_it	2.77	3.065	2606
X-RAY DIFFRACTION	r_scbond_other	2.77	3.066	2607
X-RAY DIFFRACTION	r_scangle_it	4.196	4.478	3813
X-RAY DIFFRACTION	r_scangle_other	4.195	4.479	3814
X-RAY DIFFRACTION	r_lrange_it	5.535	34.561	6353
X-RAY DIFFRACTION	r_lrange_other	5.535	34.567	6354

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
1.757-1.802	0.329	68	0.297	5314	0.297	5887	0.742	0.745	91.4218	0.266
1.802-1.852	0.267	72	0.252	5642	0.252	5726	0.854	0.83	99.7904	0.217
1.852-1.905	0.259	71	0.236	5507	0.236	5589	0.886	0.869	99.8032	0.201
1.905-1.964	0.244	69	0.223	5379	0.224	5462	0.903	0.895	99.7437	0.188
1.964-2.028	0.226	65	0.219	5117	0.219	5206	0.906	0.904	99.539	0.187
2.028-2.099	0.27	64	0.208	5008	0.209	5119	0.88	0.917	99.0818	0.175
2.099-2.178	0.285	61	0.196	4747	0.197	4920	0.905	0.929	97.7236	0.163
2.178-2.267	0.192	60	0.177	4623	0.178	4689	0.946	0.946	99.872	0.147
2.267-2.368	0.231	57	0.168	4504	0.169	4569	0.942	0.954	99.8249	0.141
2.368-2.483	0.214	55	0.167	4263	0.167	4331	0.938	0.957	99.6998	0.14
2.483-2.617	0.218	52	0.171	4081	0.171	4158	0.93	0.956	99.3988	0.147
2.617-2.775	0.22	48	0.185	3741	0.185	3878	0.953	0.953	97.705	0.163
2.775-2.966	0.196	46	0.186	3587	0.187	3663	0.934	0.943	99.181	0.172
2.966-3.202	0.28	44	0.201	3368	0.202	3432	0.898	0.928	99.4173	0.194
3.202-3.506	0.222	40	0.197	3119	0.197	3180	0.938	0.942	99.3396	0.199
3.506-3.917	0.272	36	0.176	2805	0.177	2869	0.942	0.955	99.024	0.187
3.917-4.518	0.213	31	0.155	2454	0.155	2528	0.938	0.967	98.299	0.179
4.518-5.521	0.156	27	0.153	2119	0.153	2158	0.978	0.973	99.4439	0.182
5.521-7.754	0.246	21	0.157	1646	0.158	1686	0.929	0.972	98.8731	0.196
7.754-46.732	0.172	13	0.156	949	0.157	973	0.989	0.98	98.8695	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	0.5225	0.0376	0.0644	0.2971	-0.2537	0.4649	0.0155	0.0673	-0.0608	0.0097	-0.0644	-0.1332	-0.0621	0.0657	0.0488	0.025	-0.0132	0.0141	0.0436	0.0153	0.0806	-30.6476	-21.7476	10.3537
2	0.3263	0.038	0.0189	0.2335	-0.1039	0.3965	0.0236	-0.0333	-0.0356	0.0629	0.0324	0.0152	-0.046	-0.0849	-0.056	0.048	-0.0109	0.018	0.0411	0.0054	0.0171	-64.9374	-22.655	25.5445

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	3 - 363
2	X-RAY DIFFRACTION	2	ALL	BBB	2 - 363

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