PDB-8sng: Crystal Structure of ArnB Transferase from Klebsiella aerogenes (...

ID or keywords:

Entry

Database: PDB / ID: 8sng

Title

Crystal Structure of ArnB Transferase from Klebsiella aerogenes (Lattice Translocation Disorder, P21 form)

Components

UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase

Keywords

TRANSFERASE / SSGCID /

STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE /

OXIDOREDUCTASE / ArnB Transferase

Function / homology

Function and homology information

UDP-4-amino-4-deoxy-L-arabinose aminotransferase /

UDP-4-amino-4-deoxy-L-arabinose aminotransferase / lipopolysaccharide biosynthetic process / lipid A biosynthetic process / response to antibiotic
Similarity search - Function

Biological species

Klebsiella aerogenes KCTC 2190 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	HHSN272201700059C	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal Structure of ArnB Transferase from Klebsiella aerogenes (Lattice Translocation Disorder, P21 form)
Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Cooper, A.

History

Deposition	Apr 27, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 10, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8sng.cif.gz	303.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8sng.ent.gz	247.1 KB	Display	PDB format
PDBx/mmJSON format	8sng.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

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
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

A: UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase

B: UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase

hetero molecules

86 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

Unit cell

Length a, b, c (Å)	60.084, 101.351, 68.483
Angle α, β, γ (deg.)	90.00, 101.78, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase Mass: 42563.484 Da / Num. of mol.: 2 / Mutation: E3D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella aerogenes KCTC 2190 (bacteria) Strain: ATCC 13048 / DSM 30053 / CCUG 1429 / JCM 1235 / KCTC 2190 / NBRC 13534 / NCIMB 10102 / NCTC 10006 / CDC 819-56 Gene: arnB / Plasmid: KlaeA.17333.b.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3FL22

#1: Protein

UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase

Mass: 42563.484 Da / Num. of mol.: 2 / Mutation: E3D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Klebsiella aerogenes KCTC 2190 (bacteria)
Strain: ATCC 13048 / DSM 30053 / CCUG 1429 / JCM 1235 / KCTC 2190 / NBRC 13534 / NCIMB 10102 / NCTC 10006 / CDC 819-56
Gene: arnB / Plasmid: KlaeA.17333.b.B1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3FL22

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Non-polymers , 6 types, 558 molecules

#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-EOH / ETHANOL / Ethanol Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.4 Å³/Da / Density % sol: 48.7 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Proplex H12: 15% Ethanol, 5% MPD, 0.1M Tris pH 8.5, 0.1 M NaCl, KlaeA.17333.b.B1.PW39179 at 27 mg/mL. Plate: 13222, well H12 drop 2. Puck: PSL-1014, Cryo: CRYO: 50% Crystallant + 50% MPD. ...Details: Proplex H12: 15% Ethanol, 5% MPD, 0.1M Tris pH 8.5, 0.1 M NaCl, KlaeA.17333.b.B1.PW39179 at 27 mg/mL. Plate: 13222, well H12 drop 2. Puck: PSL-1014, Cryo: CRYO: 50% Crystallant + 50% MPD. 2mM PLP and 2-oxoglutaric acidadded prior to crystallization. Partial occupanyc of PLP-Lys182 adduct and PLP-Tris adduct. The structure factors were corrected for lattice translocation disorder which caused initial high Rfactors (~25%) PH range: '

Crystal

Density Matthews: 2.4 Å³/Da / Density % sol: 48.7 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Proplex H12: 15% Ethanol, 5% MPD, 0.1M Tris pH 8.5, 0.1 M NaCl, KlaeA.17333.b.B1.PW39179 at 27 mg/mL. Plate: 13222, well H12 drop 2. Puck: PSL-1014, Cryo: CRYO: 50% Crystallant + 50% MPD. ...
PH range: '

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 14, 2022
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.55→101.35 Å / Num. obs: 116036 / % possible obs: 99.9 % / Redundancy: 5.9 % / CC_1/2: 0.998 / R_merge(I) obs: 0.12 / R_pim(I) all: 0.053 / R_rim(I) all: 0.132 / Χ²: 0.98 / Net I/σ(I): 6.1 / Num. measured all: 686630
Reflection shell	Resolution: 1.55→1.59 Å / % possible obs: 99.9 % / Redundancy: 5.6 % / R_merge(I) obs: 0.971 / Num. measured all: 47760 / Num. unique obs: 8576 / CC_1/2: 0.868 / R_pim(I) all: 0.449 / R_rim(I) all: 1.072 / Χ²: 0.99 / Net I/σ(I) obs: 1.6

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.55→58.82 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.82 / Stereochemistry target values: ML
Details: Lattice-translocation disorder correction notes: Native Patterson shows three off-origin peaks. Strongest one with vector (0.4029 0.50000.618), second one (0.1953 0.000 0.7638), and third ...

	R_factor	Num. reflection	% reflection
R_free	0.2199	5787	5 %
R_work	0.1981	-	-
obs	0.1992	115703	99.65 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.55→58.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5624	0	53	549	6226

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5918
X-RAY DIFFRACTION	f_angle_d	0.85	8069
X-RAY DIFFRACTION	f_dihedral_angle_d	12.092	2138
X-RAY DIFFRACTION	f_chiral_restr	0.053	905
X-RAY DIFFRACTION	f_plane_restr	0.007	1045

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 (%)
1.55-1.57	0.3109	218	0.3112	3628	X-RAY DIFFRACTION	100
1.57-1.59	0.3309	200	0.3109	3631	X-RAY DIFFRACTION	100
1.59-1.61	0.3437	185	0.3124	3622	X-RAY DIFFRACTION	100
1.61-1.63	0.3051	199	0.3048	3661	X-RAY DIFFRACTION	99
1.63-1.65	0.3109	183	0.2886	3621	X-RAY DIFFRACTION	100
1.65-1.67	0.2866	215	0.2874	3689	X-RAY DIFFRACTION	100
1.67-1.69	0.2868	194	0.272	3639	X-RAY DIFFRACTION	100
1.69-1.72	0.291	213	0.264	3627	X-RAY DIFFRACTION	100
1.72-1.75	0.3205	187	0.2601	3632	X-RAY DIFFRACTION	100
1.75-1.77	0.2914	186	0.2477	3704	X-RAY DIFFRACTION	100
1.77-1.8	0.255	195	0.2416	3662	X-RAY DIFFRACTION	100
1.8-1.84	0.281	194	0.2281	3606	X-RAY DIFFRACTION	100
1.84-1.87	0.2299	179	0.2254	3711	X-RAY DIFFRACTION	100
1.87-1.91	0.2615	196	0.2216	3651	X-RAY DIFFRACTION	100
1.91-1.95	0.2414	187	0.2187	3635	X-RAY DIFFRACTION	100
1.95-2	0.2438	206	0.2125	3690	X-RAY DIFFRACTION	100
2-2.05	0.2272	194	0.1995	3607	X-RAY DIFFRACTION	100
2.05-2.1	0.217	197	0.1941	3679	X-RAY DIFFRACTION	100
2.1-2.17	0.2264	169	0.1861	3691	X-RAY DIFFRACTION	100
2.17-2.24	0.2139	165	0.1821	3687	X-RAY DIFFRACTION	100
2.24-2.32	0.2165	211	0.178	3675	X-RAY DIFFRACTION	100
2.32-2.41	0.1941	201	0.1769	3666	X-RAY DIFFRACTION	100
2.41-2.52	0.1983	188	0.1758	3671	X-RAY DIFFRACTION	100
2.52-2.65	0.1672	171	0.1712	3676	X-RAY DIFFRACTION	100
2.65-2.82	0.2153	185	0.1798	3685	X-RAY DIFFRACTION	100
2.82-3.03	0.2057	182	0.1821	3700	X-RAY DIFFRACTION	100
3.03-3.34	0.1814	207	0.1751	3691	X-RAY DIFFRACTION	100
3.34-3.82	0.1818	191	0.153	3707	X-RAY DIFFRACTION	100
3.82-4.81	0.1559	204	0.1432	3672	X-RAY DIFFRACTION	100
4.82-58.82	0.2045	185	0.2021	3700	X-RAY DIFFRACTION	98

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	0.2382	0.2615	0.9101	0.5271	0.1738	6.3126	-0.1812	0.0509	0.0952	-0.0529	-0.0902	0.0228	-0.6481	-0.0105	0.2076	0.1961	0.0435	-0.0418	0.1627	-0.0029	0.1929	-11.5253	18.0128	17.2825
2	0.4988	0.1426	0.1441	0.8025	-0.3847	0.8027	-0.0103	0.0094	-0.036	-0.0031	0.0133	-0.0445	0.0916	-0.0099	0.0015	0.1291	0.0249	0.0036	0.1453	-0.0376	0.1214	-1.0876	-7.6486	19.6032
3	1.1638	1.1753	0.8451	4.4704	0.4374	1.3709	-0.0282	-0.0153	-0.1468	-0.0595	0.0711	-0.322	0.0937	0.0986	-0.0389	0.1228	0.031	0.0194	0.1847	-0.0217	0.1178	7.6716	-5.4074	23.6846
4	1.8203	0.2186	0.1626	1.8151	0.6825	1.3086	-0.0915	-0.0176	-0.0452	-0.0808	0.09	-0.0128	-0.0393	0.1543	-0.0027	0.0912	0.0083	0.02	0.1438	-0.0018	0.0638	0.4983	0.776	14.8172
5	1.7929	-0.4663	0.128	3.6362	-0.1524	1.8717	0.0316	0.3949	0.023	-0.2249	0.0361	-0.4488	0.001	0.1417	-0.0797	0.092	0.0003	0.0215	0.1872	-0.0177	0.1566	-10.2612	-5.2709	0.2214
6	2.5085	0.2754	3.5661	0.4515	0.4056	7.3685	-0.1592	0.1042	0.1352	-0.002	0.0423	-0.001	-0.4008	0.2537	0.1132	0.1417	0.0083	-0.0205	0.1098	-0.0338	0.1263	0.4594	15.3077	26.5753
7	2.5598	-0.4744	-1.2319	1.3007	0.4261	3.8103	-0.1644	-0.2778	-0.0858	0.2067	0.0555	-0.0425	0.0104	0.1189	0.0834	0.1363	0.034	-0.0292	0.1404	-0.039	0.1115	2.711	3.858	40.848
8	0.5099	-1.1426	-0.9684	5.0933	2.1267	1.8399	-0.0801	-0.0728	-0.0869	0.0636	-0.0438	0.4919	-0.0037	-0.2051	0.1259	0.103	0.0338	0.0231	0.2135	-0.0254	0.1259	-12.4422	4.8063	41.6831
9	3.232	1.4375	2.5382	3.8994	0.2146	3.0941	0.175	-0.2039	-0.0879	0.0964	-0.1063	0.0194	0.7622	-0.234	-0.0712	0.2595	-0.0253	0.0497	0.1672	0.0127	0.1077	-9.2586	-14.457	35.3968
10	0.9858	0.6969	-0.267	3.9704	0.2962	2.4213	-0.0338	-0.1442	0.1551	0.1134	-0.0217	0.0643	-0.2834	-0.1665	0.06	0.1368	0.0503	-0.0181	0.178	-0.0451	0.1222	-5.2844	13.5888	41.8535
11	0.4707	-0.3777	0.9996	1.0422	0.5186	4.4826	-0.1868	0.0156	0.1157	-0.0328	-0.0127	-0.0758	-0.6115	0.1728	0.1792	0.1248	-0.011	-0.0343	0.1329	-0.021	0.2066	-18.5104	17.831	9.3462
12	0.7945	0.1146	0.1649	0.6109	0.0332	0.8803	-0.0098	-0.0736	-0.046	-0.0077	0.0208	0.0591	0.0204	-0.037	-0.0116	0.0685	0.0103	-0.0002	0.0724	-0.0174	0.103	-28.4875	-7.8484	5.9038
13	1.229	-1.1155	0.6038	3.0965	-1.2276	1.0931	-0.0551	-0.0735	-0.0953	0.0419	0.1222	0.2215	0.0973	-0.1308	-0.0653	0.0736	0.01	0.021	0.095	-0.0365	0.1014	-37.2281	-5.4099	1.9912
14	1.222	0.0413	0.3644	1.1133	-0.4517	1.3077	-0.0271	-0.1403	-0.0145	-0.034	-0.0093	0.0412	-0.0027	-0.126	0.0338	0.0986	0.0296	-0.0043	0.0954	-0.0483	0.1103	-30.0505	0.7637	10.854
15	1.3598	-0.6545	0.372	3.8027	0.2542	0.5687	0.0554	-0.4328	-0.0534	0.3959	-0.0424	0.2753	0.0292	-0.2743	-0.0464	0.1202	-0.0038	0.017	0.2425	-0.0189	0.1141	-19.0825	-4.9989	25.1519
16	0.6179	0.007	1.11	0.4996	0.6285	6.4178	-0.1268	-0.0678	0.1499	-0.0011	-0.0517	0.0866	-0.3007	-0.3506	0.1722	0.1302	0.0204	-0.0249	0.079	-0.0315	0.1395	-30.0704	15.2023	-0.8837
17	2.2386	0.0931	-0.2602	0.9018	-0.1609	2.2322	-0.0293	0.2341	-0.1082	-0.2949	0.0284	0.0474	0.0263	-0.0606	0.0337	0.169	0.0083	-0.0176	0.088	-0.0356	0.096	-32.2221	3.8642	-15.1958
18	0.6815	1.5298	-0.8466	6.2613	-4.1617	5.1176	-0.0257	0.1886	-0.1094	0.0598	-0.0744	-0.366	-0.1144	0.2499	0.1034	0.0905	0.0239	0.0021	0.1617	-0.0135	0.1442	-17.1049	4.8253	-15.9872
19	2.2309	-0.742	2.3372	1.9377	-0.6517	2.6152	0.2005	0.1026	-0.1996	-0.2287	-0.0409	0.0157	0.3178	0.1707	-0.1359	0.1642	0.0294	0.0066	0.141	-0.0689	0.1314	-20.6346	-14.5223	-9.9353
20	1.6908	-0.5065	0.0296	4.5618	1.2164	2.8552	-0.0663	0.1179	0.0653	-0.2527	-0.023	-0.0834	-0.1509	0.0423	0.0816	0.0748	-0.0056	-0.0134	0.0848	-0.0095	0.0825	-24.2816	13.6126	-16.153

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 32 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 33 through 126 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 127 through 164 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 165 through 206 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 207 through 239 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 240 through 270 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 271 through 305 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 306 through 326 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 327 through 349 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 350 through 377 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 3 through 32 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 33 through 126 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 127 through 164 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 165 through 206 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 207 through 239 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 240 through 270 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 271 through 305 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 306 through 326 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 327 through 349 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 350 through 377 )

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Protein , 1 types, 2 molecules AB

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Non-polymers , 6 types, 558 molecules

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 6 types, 558 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

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Yorodumi