PDB-8su6: Crystal Structure of ArnB Transferase from Klebsiella aerogenes (...

ID or keywords:

Entry

Database: PDB / ID: 8su6

Title

Crystal Structure of ArnB Transferase from Klebsiella aerogenes (Lattice Translocation Disorder, P1 form2)

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 / pyridoxal phosphate binding / response to antibiotic / metal ion binding
Similarity search - Function

Biological species

Klebsiella aerogenes KCTC 2190 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 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, P1 form2 )
Authors: Seibold, S. / Lovell, S. / Battaile, K.P. / Cooper, A. / Liu, L.

History

Deposition	May 11, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 24, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8su6.cif.gz	301.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8su6.ent.gz	245.9 KB	Display	PDB format
PDBx/mmJSON format	8su6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8su6_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	8su6_full_validation.pdf.gz	2.1 MB	Display
Data in XML	8su6_validation.xml.gz	32.9 KB	Display
Data in CIF	8su6_validation.cif.gz	49.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/su/8su6 ftp://data.pdbj.org/pub/pdb/validation_reports/su/8su6	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

86.1 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)	60.172, 64.131, 67.252
Angle α, β, γ (deg.)	62.96, 76.67, 62.43
Int Tables number	1
Space group name H-M	P1

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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) 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)
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 , 5 types, 627 molecules

#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 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 Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Chemical	ChemComp-EOH / ETHANOL Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O
#5: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 620 / 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: 2.41 Å³/Da / Density % sol: 48.88 %
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 3. Puck: PSL-1013, 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 3. Puck: PSL-1013, Cryo: CRYO: 50% Crystallant + 50% MPD. 2mM PLP added prior to crystallization. Partial occupancy of PLP-Lys182 adduct and PLP-Tris adduct. The structure factors were corrected for lattice translocation disorder which caused initial high R factors (~25%)

Crystal

Density Matthews: 2.41 Å³/Da / Density % sol: 48.88 %

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 3. Puck: PSL-1013, Cryo: CRYO: 50% Crystallant + 50% MPD. ...

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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: 1.5→59.88 Å / Num. obs: 122421 / % possible obs: 96.3 % / Redundancy: 3.5 % / CC_1/2: 0.996 / R_merge(I) obs: 0.087 / R_pim(I) all: 0.055 / R_rim(I) all: 0.103 / Χ²: 0.95 / Net I/σ(I): 7.1 / Num. measured all: 423449
Reflection shell	Resolution: 1.5→1.54 Å / % possible obs: 94.7 % / Redundancy: 3.5 % / R_merge(I) obs: 0.872 / Num. measured all: 30836 / Num. unique obs: 8868 / CC_1/2: 0.59 / R_pim(I) all: 0.544 / R_rim(I) all: 1.03 / Χ²: 1.08 / Net I/σ(I) obs: 1.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.21rc1_4933: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→29.94 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 18.62 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1751	5967	4.88 %
R_work	0.154	-	-
obs	0.155	122304	96.25 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.5→29.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5611	0	60	620	6291

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5920
X-RAY DIFFRACTION	f_angle_d	0.988	8075
X-RAY DIFFRACTION	f_dihedral_angle_d	12.789	2146
X-RAY DIFFRACTION	f_chiral_restr	0.06	913
X-RAY DIFFRACTION	f_plane_restr	0.009	1038

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 (%)
1.5-1.52	0.2924	205	0.2607	3734	X-RAY DIFFRACTION	94
1.52-1.53	0.2887	184	0.2524	3838	X-RAY DIFFRACTION	94
1.53-1.55	0.2654	179	0.2339	3807	X-RAY DIFFRACTION	95
1.55-1.57	0.2664	195	0.2348	3856	X-RAY DIFFRACTION	95
1.57-1.59	0.264	204	0.2231	3788	X-RAY DIFFRACTION	95
1.59-1.62	0.2368	196	0.226	3835	X-RAY DIFFRACTION	95
1.62-1.64	0.2183	195	0.2056	3790	X-RAY DIFFRACTION	95
1.64-1.66	0.2132	175	0.2026	3876	X-RAY DIFFRACTION	95
1.66-1.69	0.2403	172	0.2004	3879	X-RAY DIFFRACTION	95
1.69-1.72	0.2279	187	0.1868	3838	X-RAY DIFFRACTION	95
1.72-1.75	0.1848	227	0.1845	3818	X-RAY DIFFRACTION	96
1.75-1.78	0.2047	188	0.1805	3893	X-RAY DIFFRACTION	96
1.78-1.81	0.2125	183	0.1669	3897	X-RAY DIFFRACTION	96
1.81-1.85	0.1717	222	0.1576	3841	X-RAY DIFFRACTION	96
1.85-1.89	0.1718	191	0.1534	3912	X-RAY DIFFRACTION	96
1.89-1.93	0.1745	195	0.1516	3878	X-RAY DIFFRACTION	97
1.93-1.98	0.1711	204	0.1511	3875	X-RAY DIFFRACTION	97
1.98-2.04	0.1799	179	0.1494	3941	X-RAY DIFFRACTION	97
2.04-2.1	0.18	208	0.1485	3867	X-RAY DIFFRACTION	97
2.1-2.16	0.1851	178	0.1402	3929	X-RAY DIFFRACTION	97
2.16-2.24	0.1692	182	0.1392	3941	X-RAY DIFFRACTION	97
2.24-2.33	0.1622	185	0.1375	3938	X-RAY DIFFRACTION	97
2.33-2.44	0.1681	227	0.1417	3872	X-RAY DIFFRACTION	97
2.44-2.56	0.1587	212	0.1369	3918	X-RAY DIFFRACTION	97
2.56-2.73	0.1778	202	0.1433	3912	X-RAY DIFFRACTION	97
2.73-2.94	0.1668	204	0.1468	3885	X-RAY DIFFRACTION	96
2.94-3.23	0.1472	188	0.1484	3916	X-RAY DIFFRACTION	97
3.23-3.7	0.155	201	0.1334	3983	X-RAY DIFFRACTION	99
3.7-4.66	0.1354	268	0.1194	3936	X-RAY DIFFRACTION	99
4.66-29.94	0.1939	231	0.1689	3944	X-RAY DIFFRACTION	99

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	1.0839	-0.8727	-0.052	2.31	0.0613	0.7399	-0.0632	0.0179	-0.1145	0.0156	0.0194	0.234	0.1294	-0.1128	0.0491	0.1295	-0.0232	0.0155	0.1511	-0.001	0.1444	-67.0496	4.6345	-24.2209
2	1.094	-0.5505	0.3579	1.4459	-0.3933	0.8151	-0.0419	-0.0304	-0.1033	0.0539	0.0759	0.1085	0.0346	-0.1123	-0.0336	0.1214	-0.0045	0.0172	0.1501	-0.0066	0.112	-59.9717	6.0088	-13.4596
3	1.5042	-1.1662	0.5871	2.5631	0.9969	1.6424	-0.0174	-0.2601	-0.2182	0.2107	0.0027	0.2841	0.0836	-0.1645	-0.0041	0.1224	-0.0095	0.0207	0.1936	0.0147	0.1786	-48.9713	-5.4317	-3.6552
4	1.1177	-1.0351	1.5589	1.8527	-2.611	5.4662	-0.1382	-0.1192	0.096	0.1499	0.1377	0.0143	-0.2769	-0.3087	0.0133	0.1577	0.0086	-0.0138	0.1256	-0.0217	0.1549	-59.8654	24.2877	-17.3968
5	2.2576	0.8831	-0.3828	2.1822	-0.6387	1.8277	-0.0668	0.2957	0.0662	-0.2758	0.0783	0.0976	-0.0237	-0.0659	-0.0165	0.1542	0.0074	-0.0234	0.1324	0.0097	0.1184	-61.9594	20.7469	-35.4643
6	0.9555	1.4718	-0.3398	4.9251	-0.0878	1.2296	-0.0024	0.1439	0.0075	-0.022	0.029	-0.4011	-0.098	0.1807	-0.0344	0.1412	-0.0057	0.0225	0.2012	0.0328	0.2004	-46.8989	21.9632	-35.5971
7	0.5598	-0.5298	0.1508	2.0221	0.027	1.3836	0.0344	0.1081	0.0299	-0.2231	-0.0887	-0.0988	0.0382	0.0557	0.0487	0.1218	-0.0157	0.0254	0.1644	0.0141	0.1225	-52.1027	16.5328	-35.0708
8	0.2659	-0.2023	0.8952	1.4828	-1.6927	3.7672	-0.1646	-0.035	0.1053	0.2496	0.0487	-0.0653	-0.5389	-0.2092	0.0859	0.1993	0.0408	-0.0141	0.1842	-0.0162	0.2147	-41.4282	18.6048	0.0803
9	1.3192	-0.2239	0.0784	1.1232	0.4545	0.9411	-0.0208	0.077	0.1308	-0.0287	0.0271	-0.0636	-0.0864	0.1024	-0.0059	0.1287	-0.006	0.0023	0.1472	0.0157	0.1337	-30.4721	7.3696	-13.3281
10	0.6125	-0.1601	0.2155	0.9049	0.1676	0.7231	-0.0099	0.0389	-0.0461	-0.0199	0.0458	-0.0751	0.0573	0.0654	-0.0419	0.1074	-0.0052	0.0145	0.1264	-0.0034	0.1235	-28.0291	-6.8324	-5.7877
11	3.1236	-0.2979	1.2807	0.5988	0.4258	1.1993	-0.0301	0.5632	0.1014	-0.13	-0.0153	-0.0772	-0.0749	0.2623	0.0686	0.1519	-0.0246	0.0224	0.2147	0.0391	0.1674	-33.2726	4.4817	-23.5417
12	0.6608	-0.0778	0.6153	0.366	-0.2478	1.7726	-0.0967	0.0087	0.0881	0.0782	-0.0098	-0.0536	-0.1862	0.1123	0.1246	0.1391	0.003	-0.0066	0.1364	-0.0037	0.1605	-32.4327	10.2009	0.5832
13	1.7905	-0.5018	-0.5657	1.0521	-0.0556	2.3003	-0.0814	-0.2495	-0.1396	0.1914	0.0615	-0.0191	0.1782	0.1434	0.0331	0.1568	0.0221	-0.0207	0.147	0.0069	0.109	-27.1815	-4.772	14.7891
14	0.7065	-0.8809	-1.2156	3.1153	2.4549	4.6505	-0.0455	-0.0773	-0.1659	0.0565	-0.0847	0.3428	-0.056	-0.2118	0.1446	0.1366	0.003	0.0128	0.1948	0.0135	0.176	-42.3152	-4.2633	15.885
15	0.5132	-0.0193	0.4874	1.2032	0.4029	1.7412	0.0042	-0.0927	-0.0636	0.1162	0.0129	0.0246	0.1576	-0.0863	-0.0138	0.1279	-0.0046	0.0242	0.1457	0.0256	0.1532	-37.007	-7.0792	11.1498
16	0.4671	-0.7271	0.7259	1.1251	-1.1237	3.7165	-0.1772	-0.0371	0.1159	0.2888	0.0102	-0.1241	-0.5217	-0.02	0.1539	0.2034	-0.0132	-0.0458	0.1838	-0.0271	0.208	-48.5746	21.9871	-6.805
17	1.3645	-0.0724	0.244	1.5632	0.3498	0.9947	-0.0398	-0.1437	0.0048	0.0637	0.0228	0.1312	0.0008	-0.0629	0.0172	0.1258	-0.0037	0.0022	0.1459	0.0076	0.1227	-58.7568	5.0966	-9.0944
18	0.9813	-0.1976	0.3791	1.5977	-0.1835	0.9868	0.0313	0.0585	-0.0902	-0.0753	-0.0407	0.106	0.1086	0.0327	0.005	0.1459	-0.0003	0.014	0.1364	-0.0163	0.1356	-58.0793	-2.2042	-29.6483

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 127 through 164 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 165 through 206 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 207 through 246 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 247 through 277 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 278 through 312 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 313 through 333 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 334 through 384 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 1 through 32 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 33 through 67 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 68 through 189 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 190 through 236 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 237 through 277 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 278 through 312 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 313 through 333 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 334 through 384 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 3 through 32 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 33 through 67 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 68 through 126 )

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 627 molecules

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