PDB-7os6: Crystal structure of Rhizobium etli inducible L-asparaginase ReAV...

ID or keywords:

Entry

Database: PDB / ID: 7os6

Title

Crystal structure of Rhizobium etli inducible L-asparaginase ReAV (monoclinic form MP1)

Components

L-asparaginase

Keywords

HYDROLASE / L-asparaginase / amidohydrolase / Rhizobium etli

Function / homology

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

Function and homology information

Biological species

Rhizobium etli (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.43 Å

Authors

Loch, J.I. / Imiolczyk, B. / 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 7, 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	Nov 6, 2024	Group: Data collection / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _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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Download

PDBx/mmCIF format	7os6.cif.gz	523.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7os6.ent.gz		Display	PDB format
PDBx/mmJSON format	7os6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7os6_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	7os6_full_validation.pdf.gz	2.7 MB	Display
Data in XML	7os6_validation.xml.gz	64 KB	Display
Data in CIF	7os6_validation.cif.gz	98.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/os/7os6 ftp://data.pdbj.org/pub/pdb/validation_reports/os/7os6	HTTPS FTP

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Related structure data

Related structure data	7os3C 7os5C 7ou1C 7oz6C C: citing same article (ref.)
Similar structure data	1nai-1 6k0g-1 7ou1-2 1a9y-1 2vxy-1 2c20-3 1udc-1 7ou1-1 7os6-2 1kvr-1 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/XBX6JE / Data set type: diffraction image data / Metadata reference: 10.18150/XBX6JE

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#13 - Jan 2001 Alcohol Dehydrogenase similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #44 - Aug 2003 Calmodulin similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

AAA: L-asparaginase

DDD: L-asparaginase

BBB: L-asparaginase

CCC: L-asparaginase

hetero molecules

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

1

DDD: L-asparaginase

CCC: L-asparaginase

hetero molecules

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

2

AAA: L-asparaginase

BBB: L-asparaginase

hetero molecules

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

Unit cell

Length a, b, c (Å)	77.812, 91.044, 113.662
Angle α, β, γ (deg.)	90.000, 97.075, 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	DDD
3	2	AAA
4	2	BBB
5	3	AAA
6	3	CCC
7	4	DDD
8	4	BBB
9	5	DDD
10	5	CCC
11	6	BBB
12	6	CCC

NCS domain segments:

End auth comp-ID: GLY / End label comp-ID: GLY

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	SER	SER	1	AAA	A	4 - 352	10 - 358
2	1	1	SER	SER	1	DDD	B	4 - 352	10 - 358
3	2	2	SER	SER	2	AAA	A	4 - 352	10 - 358
4	2	2	SER	SER	2	BBB	C	4 - 352	10 - 358
5	3	3	SER	SER	3	AAA	A	4 - 352	10 - 358
6	3	3	SER	SER	3	CCC	D	4 - 352	10 - 358
7	4	4	PRO	PRO	4	DDD	B	3 - 352	9 - 358
8	4	4	PRO	PRO	4	BBB	C	3 - 352	9 - 358
9	5	5	PRO	PRO	5	DDD	B	3 - 352	9 - 358
10	5	5	PRO	PRO	5	CCC	D	3 - 352	9 - 358
11	6	6	PRO	PRO	6	BBB	C	3 - 352	9 - 358
12	6	6	PRO	PRO	6	CCC	D	3 - 352	9 - 358

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

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Protein , 1 types, 4 molecules AAADDDBBBCCC

#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: pET151D-TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Magic / References: UniProt: Q2K0Z2

#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: pET151D-TOPO / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Magic / References: UniProt: Q2K0Z2

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Non-polymers , 6 types, 1560 molecules

#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-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-EOH / ETHANOL Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1543 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.6 Å³/Da / Density % sol: 52.1 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 25% PEG3350, 0.2 M Li2SO4, 0.1 M Tris pH 8.0, 20 mM n-octyl-beta-D-thioglucoside

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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 PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.43→77.22 Å / Num. obs: 287575 / % possible obs: 99.3 % / Redundancy: 4.1 % / B_iso Wilson estimate: 22.93 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.073 / R_rim(I) all: 0.084 / Net I/σ(I): 10.2
Reflection shell	Resolution: 1.43→1.52 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.818 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 45258 / CC_1/2: 0.671 / R_rim(I) all: 0.952 / % possible all: 96.8

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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: XXXX

Resolution: 1.43→77.22 Å / Cor.coef. F_o:F_c: 0.975 / Cor.coef. F_o:F_c free: 0.966 / SU B: 2.439 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.051 / ESU R Free: 0.053 / Details: Hydrogen atoms were added at riding positions

	R_factor	Num. reflection	% reflection
R_free	0.179	1000	0.348 %
R_work	0.1585	286572	-
all	0.159	-	-
obs	-	287572	99.291 %

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: 18.944 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.678 Å²	-0 Å²	0.703 Å²
2-	-	-0.705 Å²	0 Å²
3-	-	-	1.172 Å²

Refinement step

Cycle: LAST / Resolution: 1.43→77.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10352	0	47	1543	11942

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	10849
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	10318
X-RAY DIFFRACTION	r_angle_refined_deg	1.681	1.618	14706
X-RAY DIFFRACTION	r_angle_other_deg	1.521	1.58	23770
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.283	5	1484
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.099	20.215	558
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.628	15	1787
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.708	15	106
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	1417
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	12685
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2481
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	2330
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.18	0.2	9687
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.2	5307
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	4911
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.173	0.2	1054
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.122	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.198	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.217	0.2	124
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.204	0.2	73
X-RAY DIFFRACTION	r_mcbond_it	1.175	1.569	5701
X-RAY DIFFRACTION	r_mcbond_other	1.169	1.568	5699
X-RAY DIFFRACTION	r_mcangle_it	1.846	2.348	7151
X-RAY DIFFRACTION	r_mcangle_other	1.842	2.348	7151
X-RAY DIFFRACTION	r_scbond_it	1.927	1.8	5148
X-RAY DIFFRACTION	r_scbond_other	1.927	1.801	5149
X-RAY DIFFRACTION	r_scangle_it	2.977	2.608	7516
X-RAY DIFFRACTION	r_scangle_other	2.977	2.608	7517
X-RAY DIFFRACTION	r_lrange_it	4.817	20.558	12716
X-RAY DIFFRACTION	r_lrange_other	4.734	20.35	12619
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.058	0.05	11483
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.072	0.05	11343
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.073	0.05	11298
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.069	0.05	11421
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.073	0.05	11393
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.059	0.05	11508

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	0.05834	0.05009
1	2	DDD	X-RAY DIFFRACTION	Local ncs	0.05834	0.05009
2	3	AAA	X-RAY DIFFRACTION	Local ncs	0.07232	0.05008
2	4	BBB	X-RAY DIFFRACTION	Local ncs	0.07232	0.05008
3	5	AAA	X-RAY DIFFRACTION	Local ncs	0.07346	0.05008
3	6	CCC	X-RAY DIFFRACTION	Local ncs	0.07346	0.05008
4	7	DDD	X-RAY DIFFRACTION	Local ncs	0.06912	0.05008
4	8	BBB	X-RAY DIFFRACTION	Local ncs	0.06912	0.05008
5	9	DDD	X-RAY DIFFRACTION	Local ncs	0.07308	0.05008
5	10	CCC	X-RAY DIFFRACTION	Local ncs	0.07308	0.05008
6	11	BBB	X-RAY DIFFRACTION	Local ncs	0.0594	0.05009
6	12	CCC	X-RAY DIFFRACTION	Local ncs	0.0594	0.05009

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 (%)
1.43-1.467	0.313	70	0.318	19896	X-RAY DIFFRACTION	93.16
1.467-1.507	0.269	71	0.266	20605	X-RAY DIFFRACTION	99.8117
1.507-1.551	0.292	71	0.237	20194	X-RAY DIFFRACTION	99.8965
1.551-1.599	0.263	68	0.218	19601	X-RAY DIFFRACTION	99.7768
1.599-1.651	0.245	66	0.2	18915	X-RAY DIFFRACTION	99.7687
1.651-1.709	0.239	64	0.186	18315	X-RAY DIFFRACTION	99.913
1.709-1.773	0.181	62	0.17	17773	X-RAY DIFFRACTION	99.9328
1.773-1.846	0.186	59	0.165	17047	X-RAY DIFFRACTION	99.9066
1.846-1.928	0.174	57	0.153	16351	X-RAY DIFFRACTION	99.8054
1.928-2.022	0.132	55	0.136	15644	X-RAY DIFFRACTION	99.8156
2.022-2.131	0.148	52	0.134	14865	X-RAY DIFFRACTION	99.8394
2.131-2.26	0.138	49	0.134	14097	X-RAY DIFFRACTION	99.8729
2.26-2.416	0.178	46	0.131	13212	X-RAY DIFFRACTION	99.6093
2.416-2.61	0.146	43	0.131	12307	X-RAY DIFFRACTION	99.5005
2.61-2.858	0.16	40	0.136	11390	X-RAY DIFFRACTION	99.9388
2.858-3.195	0.21	35	0.148	10247	X-RAY DIFFRACTION	99.7865
3.195-3.688	0.153	32	0.146	9063	X-RAY DIFFRACTION	99.2254
3.688-4.515	0.189	27	0.138	7710	X-RAY DIFFRACTION	99.7679
4.515-6.374	0.16	21	0.167	5986	X-RAY DIFFRACTION	99.569
6.374-77.22	0.122	12	0.175	3353	X-RAY DIFFRACTION	99.0288

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	0.1197	-0.0932	-0.1378	0.2518	0.0976	0.184	-0.0083	-0.0268	0.0125	-0.0228	0.004	-0.0137	0.0228	0.0492	0.0043	0.0127	0.0175	0.0042	0.0298	0.0066	0.0127	29.5955	38.5123	51.1223
2	0.0964	0.1103	-0.073	0.2326	-0.0523	0.1747	-0.0033	0.006	0.0267	0.0169	-0.0125	0.0341	0.0275	-0.017	0.0158	0.0102	-0.0021	0.0036	0.013	-0.0046	0.0198	-36.4348	35.259	5.4428
3	0.0846	-0.1139	0.0378	0.2857	-0.0435	0.0994	0.0099	-0.0044	-0.0121	-0.0205	-0.0225	0.0097	-0.0064	-0.0226	0.0126	0.0144	0.01	-0.0021	0.0244	-0.0028	0.0063	-4.0373	55.1855	51.1522
4	0.0653	0.0947	0.0298	0.2951	0.0425	0.0611	0.0013	-0.0047	-0.0176	0.008	-0.0104	-0.0163	-0.0153	0.0145	0.0091	0.0184	-0.0052	-0.001	0.0191	0.0059	0.0119	-3.2155	52.9552	5.1951

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	4 - 352
2	X-RAY DIFFRACTION	1	ALL	AaA	354
3	X-RAY DIFFRACTION	1	ALL	AbA	355
4	X-RAY DIFFRACTION	1	ALL	AcA	358 - 738
5	X-RAY DIFFRACTION	2	ALL	DDD	3 - 352
6	X-RAY DIFFRACTION	2	ALL	DaD	353
7	X-RAY DIFFRACTION	2	ALL	DbD	354
8	X-RAY DIFFRACTION	2	ALL	DcD	355
9	X-RAY DIFFRACTION	2	ALL	DdD	356
10	X-RAY DIFFRACTION	2	ALL	DeD	362
11	X-RAY DIFFRACTION	2	ALL	DfD	363
12	X-RAY DIFFRACTION	2	ALL	DgD	365
13	X-RAY DIFFRACTION	2	ALL	DhD	366 - 769
14	X-RAY DIFFRACTION	3	ALL	BBB	3 - 352
15	X-RAY DIFFRACTION	3	ALL	BaB	353
16	X-RAY DIFFRACTION	3	ALL	BbB	354
17	X-RAY DIFFRACTION	3	ALL	BcB	355
18	X-RAY DIFFRACTION	3	ALL	BdB	356 - 752
19	X-RAY DIFFRACTION	4	ALL	CCC	3 - 352
20	X-RAY DIFFRACTION	4	ALL	CaC	353
21	X-RAY DIFFRACTION	4	ALL	CbC	354
22	X-RAY DIFFRACTION	4	ALL	CcC	355
23	X-RAY DIFFRACTION	4	ALL	CdC	356 - 760

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Protein , 1 types, 4 molecules AAADDDBBBCCC

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Non-polymers , 6 types, 1560 molecules

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Protein , 1 types, 4 molecules AAADDDBBBCCC

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Non-polymers , 6 types, 1560 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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

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