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

ID or keywords:

Entry

Database: PDB / ID: 8wkj

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: 1.7 Å

Authors

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

Funding support

China, 1items

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	Sep 27, 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	8wkj.cif.gz	105.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8wkj.ent.gz	74 KB	Display	PDB format
PDBx/mmJSON format	8wkj.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wk/8wkj ftp://data.pdbj.org/pub/pdb/validation_reports/wk/8wkj	HTTPS FTP

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Related structure data

Related structure data	8wouC 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

hetero molecules

44.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Aminotransferase

hetero molecules

A: Aminotransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	105.425, 105.425, 165.471
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	98
Space group name H-M	I4₁22
Symmetry operation	#1: x,y,z #2: -y+1/2,x,z+3/4 #3: y+1/2,-x,z+3/4 #4: x+1/2,-y,-z+3/4 #5: -x+1/2,y,-z+3/4 #6: -x,-y,z #7: y,x,-z #8: -y,-x,-z #9: x+1/2,y+1/2,z+1/2 #10: -y+1,x+1/2,z+5/4 #11: y+1,-x+1/2,z+5/4 #12: x+1,-y+1/2,-z+5/4 #13: -x+1,y+1/2,-z+5/4 #14: -x+1/2,-y+1/2,z+1/2 #15: y+1/2,x+1/2,-z+1/2 #16: -y+1/2,-x+1/2,-z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	A-661- HOH
2	1	A-811- HOH
3	1	A-824- HOH
4	1	A-880- HOH

#1: Protein	Aminotransferase Mass: 43822.891 Da / Num. of mol.: 1 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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.68 Å³/Da / Density % sol: 54.2 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Ammonium sulfate 0.05 M Magnesium sulfate heptahydrate 0.1 M Sodium citrate 5.5 22.5 % v/v PEG Smear Medium

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL18U1 / Wavelength: 0.978 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 19, 2023

Radiation

Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.978 Å / Relative weight: 1

Reflection

Resolution: 1.7→50 Å / Num. obs: 51188 / % possible obs: 99 % / Redundancy: 24.1 % / B_iso Wilson estimate: 23.29 Å² / CC_1/2: 0.996 / CC star: 0.999 / R_merge(I) obs: 0.135 / R_pim(I) all: 0.028 / R_rim(I) all: 0.138 / Χ²: 0.983 / Net I/σ(I): 6.2 / Num. measured all: 1236043

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.7-1.76	19.2	1.373	4639	0.707	0.91	0.311	1.411	0.892	90.7
1.76-1.83	22.3	1.011	5082	0.862	0.962	0.215	1.035	0.921	99.9
1.83-1.91	25.2	0.708	5075	0.945	0.986	0.142	0.722	0.947	99.9
1.91-2.02	24.3	0.472	5096	0.97	0.992	0.097	0.483	0.98	99.8
2.02-2.14	24.7	0.325	5149	0.985	0.996	0.066	0.332	1.013	100
2.14-2.31	25.7	0.24	5133	0.992	0.998	0.048	0.245	1.028	100
2.31-2.54	25.2	0.185	5143	0.995	0.999	0.037	0.188	1.01	100
2.54-2.91	25.8	0.144	5178	0.997	0.999	0.029	0.147	1.041	100
2.91-3.66	25	0.105	5242	0.998	0.999	0.021	0.107	1.012	100
3.66-50	23.7	0.079	5451	0.998	0.999	0.017	0.081	0.941	100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
HKL-3000	7.21	data scaling
PDB_EXTRACT	3.27	data extraction
HKL-3000	7.21	data reduction
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.7→48.92 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.968 / WR_factor R_free: 0.179 / WR_factor R_work: 0.166 / Average fsc free: 0.9761 / Average fsc work: 0.9817 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.08
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1717	2584	5.074 %
R_work	0.1554	48341	-
all	0.156	-	-
obs	-	50925	99.045 %

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: 23.945 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.016 Å²	0 Å²	0 Å²
2-	-	-0.016 Å²	0 Å²
3-	-	-	0.032 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→48.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3004	0	16	424	3444

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	3077
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	2957
X-RAY DIFFRACTION	r_angle_refined_deg	1.426	1.65	4181
X-RAY DIFFRACTION	r_angle_other_deg	0.705	1.568	6814
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.862	5	389
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	23.807	5	14
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.93	10	521
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.997	10	132
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	479
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	3603
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	662
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	659
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.208	0.2	2823
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	1640
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	1622
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.184	0.2	316
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.01	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.201	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.313	0.2	160
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.175	0.2	34
X-RAY DIFFRACTION	r_mcbond_it	2.763	2.392	1562
X-RAY DIFFRACTION	r_mcbond_other	2.763	2.392	1562
X-RAY DIFFRACTION	r_mcangle_it	3.819	4.267	1949
X-RAY DIFFRACTION	r_mcangle_other	3.818	4.267	1950
X-RAY DIFFRACTION	r_scbond_it	4.509	2.761	1515
X-RAY DIFFRACTION	r_scbond_other	4.513	2.763	1512
X-RAY DIFFRACTION	r_scangle_it	6.651	4.864	2232
X-RAY DIFFRACTION	r_scangle_other	6.649	4.864	2233
X-RAY DIFFRACTION	r_lrange_it	7.891	24.754	3739
X-RAY DIFFRACTION	r_lrange_other	7.627	23.603	3601

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
1.7-1.744	0.239	169	0.233	3152	0.233	3744	0.956	0.963	88.7019	0.209
1.744-1.792	0.271	166	0.208	3480	0.211	3652	0.951	0.971	99.8357	0.183
1.792-1.844	0.244	198	0.192	3348	0.195	3550	0.963	0.976	99.8873	0.167
1.844-1.9	0.197	159	0.183	3301	0.183	3460	0.976	0.979	100	0.159
1.9-1.963	0.201	196	0.17	3157	0.172	3360	0.973	0.981	99.7917	0.151
1.963-2.031	0.194	159	0.164	3079	0.166	3243	0.975	0.983	99.8458	0.147
2.031-2.108	0.169	173	0.155	2968	0.156	3141	0.98	0.985	100	0.142
2.108-2.194	0.161	155	0.153	2869	0.153	3024	0.985	0.985	100	0.142
2.194-2.291	0.143	169	0.144	2730	0.144	2899	0.987	0.987	100	0.139
2.291-2.403	0.152	145	0.143	2623	0.144	2768	0.985	0.987	100	0.14
2.403-2.532	0.192	108	0.141	2555	0.143	2665	0.979	0.987	99.9249	0.143
2.532-2.686	0.177	111	0.147	2384	0.148	2495	0.98	0.987	100	0.152
2.686-2.87	0.155	123	0.153	2261	0.154	2384	0.984	0.985	100	0.166
2.87-3.099	0.176	122	0.154	2105	0.156	2227	0.979	0.985	100	0.171
3.099-3.394	0.152	115	0.153	1928	0.153	2043	0.985	0.986	100	0.174
3.394-3.792	0.172	99	0.152	1765	0.153	1864	0.982	0.986	100	0.177
3.792-4.374	0.169	76	0.129	1570	0.131	1647	0.983	0.989	99.9393	0.162
4.374-5.347	0.139	62	0.141	1364	0.141	1430	0.989	0.989	99.7203	0.183
5.347-7.517	0.158	52	0.18	1067	0.179	1128	0.984	0.982	99.2021	0.233
7.517-48.92	0.189	27	0.168	635	0.169	688	0.984	0.98	96.2209	0.271

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