PDB-8wou: The crystal structure of aspartate aminotransferases Lpg0070 from...

ID or keywords:

Entry

Database: PDB / ID: 8wou

Title

The crystal structure of aspartate aminotransferases Lpg0070 from Legionella pneumophila

Components

Aminotransferase

Keywords

TRANSFERASE / Aspartate aminotransferase / Legionella pneumophila

Function / homology

Function and homology information

Transferases; Transferring nitrogenous groups; Transaminases / amino acid metabolic process / transaminase activity / biosynthetic process / pyridoxal phosphate binding
Similarity search - Function

Biological species

Legionella pneumophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.14 Å

Authors

Gao, Y.S. / Hua, L. / Xie, R.

Funding support

China, 2items

Citation

Journal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Crystal structure of an aspartate aminotransferase Lpg0070 from Legionella pneumophila.
Authors: Gao, Y. / Yang, X. / Hua, L. / Wang, M. / Ge, Q. / Wang, W. / Wang, N. / Ma, J. / Ge, H.

History

Deposition	Oct 7, 2023	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Dec 6, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8wou.cif.gz	171.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8wou.ent.gz	129 KB	Display	PDB format
PDBx/mmJSON format	8wou.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8wou_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	8wou_full_validation.pdf.gz	1.9 MB	Display
Data in XML	8wou_validation.xml.gz	29.9 KB	Display
Data in CIF	8wou_validation.cif.gz	41.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wo/8wou ftp://data.pdbj.org/pub/pdb/validation_reports/wo/8wou	HTTPS FTP

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Related structure data

Related structure data	8wkjC 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

A: Aminotransferase

B: Aminotransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	65.160, 201.020, 151.490
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Aminotransferase Mass: 43822.891 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) Gene: C3927_15565, DIZ43_09905, ERS253283_01083, NCTC12000_00087 Production host: Escherichia coli (E. coli) References: UniProt: A0A130QXX8, Transferases; Transferring nitrogenous groups; Transaminases
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.89 Å³/Da / Density % sol: 57.49 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium sulfate 20% w/v PEG 3350 10% v/v Ethylene glycol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.987 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2023
Radiation	Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 2.14→75.86 Å / Num. obs: 55245 / % possible obs: 99.9 % / Redundancy: 12.3 % / B_iso Wilson estimate: 45.06 Å² / CC_1/2: 0.991 / Net I/σ(I): 8.4
Reflection shell	Resolution: 2.14→2.2 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4077 / CC_1/2: 0.579 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
Aimless	0.7.7	data scaling
PDB_EXTRACT	3.27	data extraction
XDS	0.7.7	data reduction
PHASER	2.7.0	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.14→75.86 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.932 / WR_factor R_free: 0.303 / WR_factor R_work: 0.256 / Average fsc free: 0.9137 / Average fsc work: 0.9295 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.211
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2816	2715	4.92 %
R_work	0.2357	52464	-
all	0.238	-	-
obs	-	55179	99.751 %

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: 53.81 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.673 Å²	0 Å²	-0 Å²
2-	-	-4 Å²	-0 Å²
3-	-	-	-0.672 Å²

Refinement step

Cycle: LAST / Resolution: 2.14→75.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6022	0	20	185	6227

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	6154
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	5916
X-RAY DIFFRACTION	r_angle_refined_deg	1.496	1.649	8370
X-RAY DIFFRACTION	r_angle_other_deg	0.741	1.568	13638
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.252	5	782
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	0.59	5	26
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.931	10	1042
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	18.137	10	264
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	962
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	7210
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	1322
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	1342
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.233	0.2	5723
X-RAY DIFFRACTION	r_nbtor_refined	0.188	0.2	3197
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	3450
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.175	0.2	220
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.08	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.085	0.2	5
X-RAY DIFFRACTION	r_nbd_other	0.219	0.2	69
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.12	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	5.386	5.455	3134
X-RAY DIFFRACTION	r_mcbond_other	5.385	5.455	3134
X-RAY DIFFRACTION	r_mcangle_it	7.203	9.772	3914
X-RAY DIFFRACTION	r_mcangle_other	7.202	9.774	3915
X-RAY DIFFRACTION	r_scbond_it	6.51	5.795	3020
X-RAY DIFFRACTION	r_scbond_other	6.494	5.788	3005
X-RAY DIFFRACTION	r_scangle_it	9.309	10.454	4456
X-RAY DIFFRACTION	r_scangle_other	9.299	10.442	4433
X-RAY DIFFRACTION	r_lrange_it	10.563	49.757	6942
X-RAY DIFFRACTION	r_lrange_other	10.567	49.771	6921

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
2.14-2.196	0.365	197	0.335	3871	0.336	4069	0.881	0.892	99.9754	0.326
2.196-2.256	0.538	200	0.456	3716	0.461	3936	0.813	0.798	99.4919	0.456
2.256-2.321	0.507	175	0.414	3605	0.418	3817	0.781	0.829	99.0306	0.406
2.321-2.392	0.351	167	0.303	3563	0.305	3733	0.915	0.924	99.9196	0.283
2.392-2.471	0.336	173	0.27	3431	0.273	3605	0.912	0.941	99.9723	0.252
2.471-2.557	0.326	183	0.269	3288	0.272	3478	0.937	0.947	99.7987	0.252
2.557-2.654	0.322	184	0.261	3210	0.265	3400	0.928	0.95	99.8235	0.244
2.654-2.762	0.352	158	0.274	3081	0.278	3243	0.916	0.948	99.8767	0.256
2.762-2.885	0.343	155	0.281	2968	0.284	3125	0.929	0.947	99.936	0.262
2.885-3.025	0.355	141	0.271	2872	0.275	3016	0.924	0.948	99.9005	0.259
3.025-3.189	0.33	143	0.283	2691	0.286	2839	0.926	0.947	99.8239	0.277
3.189-3.382	0.332	115	0.273	2588	0.276	2706	0.918	0.951	99.8891	0.27
3.382-3.615	0.299	127	0.256	2425	0.258	2558	0.943	0.956	99.7654	0.257
3.615-3.903	0.269	122	0.232	2244	0.233	2375	0.955	0.964	99.621	0.244
3.903-4.275	0.236	118	0.185	2066	0.188	2190	0.966	0.978	99.726	0.214
4.275-4.778	0.188	93	0.161	1915	0.162	2010	0.979	0.984	99.9005	0.2
4.778-5.513	0.218	81	0.179	1689	0.181	1770	0.973	0.982	100	0.225
5.513-6.743	0.214	95	0.205	1425	0.205	1522	0.97	0.975	99.8686	0.258
6.743-9.499	0.201	60	0.164	1144	0.166	1207	0.975	0.983	99.7514	0.208
9.499-75.86	0.204	28	0.199	673	0.199	717	0.978	0.977	97.7685	0.237

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