PDB-8col: Crystal structure of Rhizobium etli constitutive L-asparaginase R...

ID or keywords:

Entry

Database: PDB / ID: 8col

Title

Crystal structure of Rhizobium etli constitutive L-asparaginase ReAIV (orthorombic form R4oP-2)

Components

Putative L-asparaginase II protein

Keywords

HYDROLASE / L-asparaginase / Rhizobium etli / enzyme / amidohydrolase

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: 2 Å

Authors

Loch, J.I. / Worsztynowicz, P. / Sliwiak, J. / Imioloczyk, B. / Grzechowiak, M. / Gilski, M. / Jaskolski, M.

Funding support

Poland, 1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Rhizobium etli has two L-asparaginases with low sequence identity but similar structure and catalytic center.
Authors: Loch, J.I. / Worsztynowicz, P. / Sliwiak, J. / Grzechowiak, M. / Imiolczyk, B. / Pokrywka, K. / Chwastyk, M. / Gilski, M. / Jaskolski, M.

History

Deposition	Feb 28, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 9, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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	8col.cif.gz	456 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	8col.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8col_validation.pdf.gz	460.1 KB	Display	wwPDB validaton report
Full document	8col_full_validation.pdf.gz	464.5 KB	Display
Data in XML	8col_validation.xml.gz	55.5 KB	Display
Data in CIF	8col_validation.cif.gz	80.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/co/8col ftp://data.pdbj.org/pub/pdb/validation_reports/co/8col	HTTPS FTP

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Related structure data

Related structure data	8clyC 8clzC 8oriC 8oswC 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

Deposited unit

AAA: Putative L-asparaginase II protein

BBB: Putative L-asparaginase II protein

CCC: Putative L-asparaginase II protein

DDD: Putative L-asparaginase II protein

hetero molecules

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

1

AAA: Putative L-asparaginase II protein

BBB: Putative L-asparaginase II protein

hetero molecules

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

2

CCC: Putative L-asparaginase II protein

DDD: Putative L-asparaginase II protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	83.101, 89.749, 169.197
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 4 molecules AAABBBCCCDDD

#1: Protein	Putative L-asparaginase II protein Mass: 36116.391 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium etli (bacteria) / Gene: RHE_CH01144 / Plasmid: pET151D-topo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: Q2KB35

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Non-polymers , 5 types, 901 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 882 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
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: 2.18 Å³/Da / Density % sol: 43.68 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris pH 8.5, 0.2 M MgCl2, 17.5% PEG 8000, 0.3% dodecyl-beta-D-maltoside (DDM)

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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: 2→84.6 Å / Num. obs: 86068 / % possible obs: 99.7 % / Redundancy: 5.94 % / B_iso Wilson estimate: 34.76 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.135 / R_rim(I) all: 0.148 / Net I/σ(I): 10.22
Reflection shell	Resolution: 2→2.12 Å / Redundancy: 6.11 % / R_merge(I) obs: 1.115 / Mean I/σ(I) obs: 1.45 / Num. unique obs: 13748 / CC_1/2: 0.681 / R_rim(I) all: 1.22

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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: 2→84.599 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.944 / SU B: 12.409 / SU ML: 0.141 / Cross valid method: FREE R-VALUE / ESU R: 0.182 / ESU R Free: 0.168

	R_factor	Num. reflection	% reflection
R_free	0.2343	1000	1.162 %
R_work	0.1767	85052	-
all	0.177	-	-
obs	-	86052	99.711 %

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: 31.057 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.121 Å²	-0 Å²	0 Å²
2-	-	4.47 Å²	-0 Å²
3-	-	-	-2.349 Å²

Refinement step

Cycle: LAST / Resolution: 2→84.599 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9878	0	31	882	10791

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	10165
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.015	9648
X-RAY DIFFRACTION	r_angle_refined_deg	1.731	1.636	13762
X-RAY DIFFRACTION	r_angle_other_deg	1.48	1.573	22191
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.991	5	1371
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.233	20.664	497
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.74	15	1638
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	23.673	15	4
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.999	15	85
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	1352
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	13035
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	2387
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	2319
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	9492
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	4955
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	4610
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.185	0.2	710
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.041	0.2	3
X-RAY DIFFRACTION	r_metal_ion_refined	0.102	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.197	0.2	27
X-RAY DIFFRACTION	r_nbd_other	0.173	0.2	77
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.212	0.2	35
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.103	0.2	1
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.094	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	1.674	2.903	5382
X-RAY DIFFRACTION	r_mcbond_other	1.674	2.902	5381
X-RAY DIFFRACTION	r_mcangle_it	2.415	4.341	6730
X-RAY DIFFRACTION	r_mcangle_other	2.415	4.341	6731
X-RAY DIFFRACTION	r_scbond_it	2.152	3.175	4783
X-RAY DIFFRACTION	r_scbond_other	2.152	3.175	4784
X-RAY DIFFRACTION	r_scangle_it	3.333	4.657	7013
X-RAY DIFFRACTION	r_scangle_other	3.332	4.658	7014
X-RAY DIFFRACTION	r_lrange_it	4.909	35.801	11639
X-RAY DIFFRACTION	r_lrange_other	4.907	35.793	11636

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 (%)
2-2.051	0.352	73	0.328	6185	X-RAY DIFFRACTION	99.3333
2.051-2.107	0.332	72	0.293	6094	X-RAY DIFFRACTION	99.919
2.107-2.168	0.331	69	0.263	5900	X-RAY DIFFRACTION	99.9163
2.168-2.235	0.244	67	0.249	5698	X-RAY DIFFRACTION	99.7577
2.235-2.308	0.237	66	0.209	5599	X-RAY DIFFRACTION	99.5257
2.308-2.389	0.221	62	0.192	5324	X-RAY DIFFRACTION	99.336
2.389-2.479	0.277	61	0.18	5194	X-RAY DIFFRACTION	99.602
2.479-2.58	0.322	59	0.171	5034	X-RAY DIFFRACTION	99.9607
2.58-2.695	0.247	57	0.172	4801	X-RAY DIFFRACTION	99.8356
2.695-2.826	0.21	54	0.154	4619	X-RAY DIFFRACTION	99.8504
2.826-2.979	0.193	52	0.15	4392	X-RAY DIFFRACTION	99.7755
2.979-3.159	0.218	48	0.149	4159	X-RAY DIFFRACTION	99.7865
3.159-3.377	0.254	46	0.148	3915	X-RAY DIFFRACTION	99.5977
3.377-3.647	0.206	43	0.146	3649	X-RAY DIFFRACTION	99.5954
3.647-3.994	0.198	40	0.152	3386	X-RAY DIFFRACTION	99.9417
3.994-4.465	0.204	36	0.147	3090	X-RAY DIFFRACTION	99.7447
4.465-5.153	0.211	33	0.151	2736	X-RAY DIFFRACTION	99.9278
5.153-6.305	0.291	27	0.198	2343	X-RAY DIFFRACTION	99.8315
6.305-8.892	0.195	22	0.156	1841	X-RAY DIFFRACTION	99.8392
8.892-84.599	0.112	13	0.177	1093	X-RAY DIFFRACTION	98.8382

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	0.0417	0.0217	-0.0195	0.0457	-0.0064	0.223	-0.0096	-0.0085	-0.0102	-0.0196	0.0007	-0.0077	-0.0051	0.0021	0.0089	0.0354	-0.0008	0.0044	0.0025	0.0009	0.0326	16.7033	24.4732	5.7436
2	0.0725	0.0086	-0.0071	0.027	0.0324	0.0698	-0.0056	-0.0033	-0.0037	0.0016	-0.0013	0.0065	-0.0051	-0.0041	0.0069	0.0313	0.0003	-0.0014	0.0098	0.001	0.032	-1.0405	25.8368	36.2437
3	0.0548	-0.0111	0.018	0.0224	0.0214	0.1246	-0.0052	0.0032	0.0103	-0.0086	0.0019	0.0049	0.0039	-0.0051	0.0033	0.0365	-0.0049	-0.0043	0.0016	0.0031	0.0372	24.8589	65.9268	5.9943
4	0.0327	0.0088	-0.0041	0.0284	-0.0192	0.0941	-0.0028	-0.0038	0.008	0.0025	-0.0013	0.0043	0.0043	0.0078	0.0041	0.035	0.002	-0.0012	0.0012	-0.002	0.0397	42.7469	67.4604	36.3528

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Selection details
1	X-RAY DIFFRACTION	1	ALL	{ A\|2-334 }
2	X-RAY DIFFRACTION	1	ALL	{ A\|335-335 }
3	X-RAY DIFFRACTION	1	ALL	{ A\|336-336 }
4	X-RAY DIFFRACTION	1	ALL	{ A\|337-337 }
5	X-RAY DIFFRACTION	1	ALL	{ A\|338-539 }
6	X-RAY DIFFRACTION	2	ALL	{ B\|1-335 }
7	X-RAY DIFFRACTION	2	ALL	{ B\|336-336 }
8	X-RAY DIFFRACTION	2	ALL	{ B\|337-337 }
9	X-RAY DIFFRACTION	2	ALL	{ B\|338-338 }
10	X-RAY DIFFRACTION	2	ALL	{ B\|339-565 }
11	X-RAY DIFFRACTION	3	ALL	{ C\|1-334 }
12	X-RAY DIFFRACTION	3	ALL	{ C\|335-335 }
13	X-RAY DIFFRACTION	3	ALL	{ C\|336-336 }
14	X-RAY DIFFRACTION	3	ALL	{ C\|337-337 }
15	X-RAY DIFFRACTION	3	ALL	{ C\|338-338 }
16	X-RAY DIFFRACTION	3	ALL	{ C\|339-577 }
17	X-RAY DIFFRACTION	4	ALL	{ D\|1-335 }
18	X-RAY DIFFRACTION	4	ALL	{ D\|336-336 }
19	X-RAY DIFFRACTION	4	ALL	{ D\|337-337 }
20	X-RAY DIFFRACTION	4	ALL	{ D\|338-338 }
21	X-RAY DIFFRACTION	4	ALL	{ D\|339-339 }
22	X-RAY DIFFRACTION	4	ALL	{ D\|340-340 }
23	X-RAY DIFFRACTION	4	ALL	{ D\|341-583 }

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