PDB-8u92: Crystal structure of N-acetylneuraminate lyase (NanA) from Klebsi...

ID or keywords:

Entry

Database: PDB / ID: 8u92

Title

Crystal structure of N-acetylneuraminate lyase (NanA) from Klebsiella aerogenes (pyruvate bound, Orthorhombic P form)

Components

N-acetylneuraminate lyase

Keywords

LIPID TRANSPORT / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / N-acetylneuraminate lyase

Function / homology

Function and homology information

N-acetylneuraminate lyase / N-acetylneuraminate lyase activity / N-acetylneuraminate catabolic process / carbohydrate metabolic process / cytosol
Similarity search - Function

Biological species

Klebsiella aerogenes KCTC 2190 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 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)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of N-acetylneuraminate lyase (NanA) from Klebsiella aerogenes (pyruvate bound, Orthorhombic P form)
Authors: Lovell, S. / Liu, L. / Seibold, S. / Battaile, K.P.

History

Deposition	Sep 18, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 27, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8u92.cif.gz	713.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8u92.ent.gz	592.1 KB	Display	PDB format
PDBx/mmJSON format	8u92.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8u92_validation.pdf.gz	503.6 KB	Display	wwPDB validaton report
Full document	8u92_full_validation.pdf.gz	510.3 KB	Display
Data in XML	8u92_validation.xml.gz	71.6 KB	Display
Data in CIF	8u92_validation.cif.gz	101.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u9/8u92 ftp://data.pdbj.org/pub/pdb/validation_reports/u9/8u92	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

Deposited unit

A: N-acetylneuraminate lyase

B: N-acetylneuraminate lyase

C: N-acetylneuraminate lyase

D: N-acetylneuraminate lyase

E: N-acetylneuraminate lyase

F: N-acetylneuraminate lyase

hetero molecules

206 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: N-acetylneuraminate lyase

B: N-acetylneuraminate lyase

C: N-acetylneuraminate lyase

D: N-acetylneuraminate lyase

hetero molecules

defined by author&software
Evidence: gel filtration
137 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: N-acetylneuraminate lyase

F: N-acetylneuraminate lyase

hetero molecules

E: N-acetylneuraminate lyase

F: N-acetylneuraminate lyase

hetero molecules

defined by author&software
137 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	94.588, 145.738, 216.813
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	F-309- CL
2	1	E-543- HOH

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein	N-acetylneuraminate lyase Mass: 33738.566 Da / Num. of mol.: 6 / Mutation: V93A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella aerogenes KCTC 2190 (bacteria) Gene: nanA / Plasmid: KlaeA.01563.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3FJT8

#1: Protein

N-acetylneuraminate lyase

Mass: 33738.566 Da / Num. of mol.: 6 / Mutation: V93A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Klebsiella aerogenes KCTC 2190 (bacteria)
Gene: nanA / Plasmid: KlaeA.01563.a.B1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3FJT8

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Non-polymers , 5 types, 996 molecules

#2: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical	... ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 943 / 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: 3.69 Å³/Da / Density % sol: 66.68 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: JCSG+ B5: 0.1 M Na cacodylate pH 6.5, 40% MPD, 5% PEG 8000. KlaeA.01563.a.B1.PW39186 at 18.6 mg/mL. Plate 13190, well B5 drop 2. Puck: PSL-1402, Cryo: direct

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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 20, 2023
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: 2.1→48.58 Å / Num. obs: 174815 / % possible obs: 100 % / Redundancy: 13.7 % / CC_1/2: 0.999 / R_merge(I) obs: 0.139 / R_pim(I) all: 0.039 / R_rim(I) all: 0.144 / Χ²: 1.01 / Net I/σ(I): 15.3 / Num. measured all: 2398101
Reflection shell	Resolution: 2.1→2.14 Å / % possible obs: 100 % / Redundancy: 13.6 % / R_merge(I) obs: 1.332 / Num. measured all: 116082 / Num. unique obs: 8536 / CC_1/2: 0.862 / R_pim(I) all: 0.375 / R_rim(I) all: 1.385 / Χ²: 1.04 / Net I/σ(I) obs: 2.3

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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: 2.1→47.29 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.08 / Phase error: 19.64 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1927	8808	5.05 %
R_work	0.1533	-	-
obs	0.1553	174557	99.86 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1→47.29 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13861	0	172	943	14976

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	14286
X-RAY DIFFRACTION	f_angle_d	1.044	19356
X-RAY DIFFRACTION	f_dihedral_angle_d	14.564	5230
X-RAY DIFFRACTION	f_chiral_restr	0.053	2182
X-RAY DIFFRACTION	f_plane_restr	0.012	2518

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 (%)
2.1-2.12	0.2487	306	0.2201	5448	X-RAY DIFFRACTION	100
2.12-2.15	0.2569	281	0.2117	5481	X-RAY DIFFRACTION	100
2.15-2.18	0.2516	298	0.2063	5440	X-RAY DIFFRACTION	100
2.18-2.2	0.2449	286	0.2034	5469	X-RAY DIFFRACTION	100
2.2-2.23	0.2515	282	0.1931	5484	X-RAY DIFFRACTION	100
2.23-2.26	0.2137	295	0.1812	5438	X-RAY DIFFRACTION	100
2.26-2.29	0.2253	266	0.1695	5482	X-RAY DIFFRACTION	100
2.29-2.33	0.2112	294	0.1655	5448	X-RAY DIFFRACTION	100
2.33-2.37	0.1985	290	0.1603	5525	X-RAY DIFFRACTION	100
2.37-2.4	0.2376	292	0.1643	5447	X-RAY DIFFRACTION	100
2.4-2.45	0.2143	290	0.1555	5476	X-RAY DIFFRACTION	100
2.45-2.49	0.1934	304	0.1548	5526	X-RAY DIFFRACTION	100
2.49-2.54	0.2112	283	0.1544	5465	X-RAY DIFFRACTION	100
2.54-2.59	0.2218	293	0.1562	5496	X-RAY DIFFRACTION	100
2.59-2.65	0.2148	320	0.155	5477	X-RAY DIFFRACTION	100
2.65-2.71	0.2238	297	0.165	5496	X-RAY DIFFRACTION	100
2.71-2.77	0.2041	296	0.1635	5506	X-RAY DIFFRACTION	100
2.78-2.85	0.2037	329	0.1574	5474	X-RAY DIFFRACTION	100
2.85-2.93	0.1826	280	0.1588	5506	X-RAY DIFFRACTION	100
2.93-3.03	0.2124	316	0.1519	5510	X-RAY DIFFRACTION	100
3.03-3.14	0.1998	297	0.1586	5516	X-RAY DIFFRACTION	100
3.14-3.26	0.2246	297	0.1635	5547	X-RAY DIFFRACTION	100
3.26-3.41	0.19	308	0.155	5528	X-RAY DIFFRACTION	100
3.41-3.59	0.161	303	0.1385	5530	X-RAY DIFFRACTION	100
3.59-3.82	0.1652	264	0.1374	5601	X-RAY DIFFRACTION	100
3.82-4.11	0.1631	255	0.1297	5632	X-RAY DIFFRACTION	100
4.11-4.52	0.1404	280	0.1144	5615	X-RAY DIFFRACTION	100
4.52-5.18	0.1636	300	0.1276	5617	X-RAY DIFFRACTION	100
5.18-6.52	0.2023	317	0.1769	5673	X-RAY DIFFRACTION	100
6.52-47.29	0.1877	289	0.1641	5896	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	4.1759	0.6865	-2.0744	6.6548	-3.5045	6.876	-0.0416	0.3008	-0.1038	-0.0615	-0.033	0.0305	0.3567	0.131	0.074	0.2903	0.0068	0.0259	0.3078	-0.0879	0.219	31.5257	19.9812	6.6152
2	2.2123	-0.2179	-0.1598	1.1834	-0.3224	1.282	-0.1292	0.0786	-0.2175	0.005	0.1012	0.0935	0.259	-0.0686	0.0347	0.3112	-0.0577	0.03	0.2516	-0.0374	0.2952	17.0418	22.1732	11.9436
3	6.9149	-0.0131	-2.6383	0.7579	-2.1791	7.7655	-0.0494	-0.2243	-0.3552	0.1297	-0.0402	0.0525	0.2128	-0.293	0.0662	0.3581	0.0049	0.0657	0.1713	0.0392	0.2499	18.3698	12.6351	27.2762
4	1.6733	0.5264	-0.5436	2.0411	-1.171	2.3839	-0.0863	-0.084	-0.1468	-0.0143	-0.071	-0.2048	0.2949	0.3656	0.1782	0.242	0.0503	0.0497	0.2771	-0.0241	0.2168	39.0847	21.4571	19.8123
5	3.9395	-0.9092	1.9647	4.0541	-0.7771	4.6368	-0.0068	-0.4249	0.0342	0.3573	-0.1121	0.1529	-0.2294	-0.2669	0.1294	0.2946	0.0011	0.0434	0.4283	-0.1063	0.2627	13.9565	55.5044	62.119
6	0.4526	0.6654	0.3477	2.7654	0.3356	1.6839	0.0449	-0.3723	0.031	0.1206	-0.0834	0.2783	-0.0846	-0.1774	0.0441	0.2172	0.0165	0.0185	0.4327	-0.0417	0.2903	8.2312	43.0298	60.5667
7	1.1316	0.343	0.446	0.9118	-0.1886	1.4119	-0.077	-0.1345	0.111	-0.0523	0.0183	0.0679	-0.1907	-0.0693	0.0674	0.3041	0.0675	-0.0149	0.347	-0.083	0.2912	13.4428	54.7343	47.702
8	4.9849	-1.5943	-2.2974	4.5137	0.1104	5.337	-0.08	-0.3575	-0.1533	0.3048	-0.0137	-0.0084	0.3706	0.125	0.0786	0.3869	0.0406	-0.0173	0.3675	0.1194	0.2271	22.5506	14.3162	60.8819
9	1.0082	0.5435	-0.5802	3.4073	-0.3959	1.7147	-0.0323	-0.317	-0.0427	0.063	-0.0593	-0.2104	0.1453	0.1701	0.0934	0.2484	0.0469	-0.0087	0.4316	0.0308	0.261	28.4741	26.8417	58.2971
10	1.6586	0.2469	-0.399	0.9791	0.1197	1.3764	-0.0639	-0.1319	-0.2549	-0.0651	0.0093	0.0216	0.3558	0.0295	0.0724	0.3992	0.0476	0.0286	0.3146	0.0924	0.2977	21.9244	13.8413	46.342
11	3.5289	-0.2188	1.2126	4.307	2.3233	6.2788	-0.0662	0.3264	0.1228	-0.0696	-0.0043	-0.0779	-0.2965	-0.165	0.0751	0.2559	-0.0186	-0.0515	0.2787	0.0842	0.2445	4.4094	52.3933	7.554
12	3.0884	-0.9509	0.5624	1.3307	0.0146	1.5375	-0.1513	0.182	0.2011	-0.0676	0.1107	-0.0708	-0.1687	0.0369	0.0534	0.2855	-0.0665	-0.0113	0.2614	0.0141	0.2752	18.1547	49.0539	10.5574
13	1.2863	0.0065	-0.0634	0.9662	0.4613	1.5348	-0.096	-0.009	0.1415	-0.0043	0.0596	0.0699	-0.1998	-0.151	0.0598	0.2639	0.0375	-0.0546	0.2314	0.0106	0.2387	3.6554	51.8719	22.2773
14	5.294	-1.9558	-1.1933	4.0269	2.7216	4.6197	0.0446	0.2808	0.1459	-0.1643	-0.1407	-0.0581	-0.1106	-0.536	0.1009	0.3658	0.0153	-0.0688	0.4206	-0.0008	0.2222	26.1373	71.3181	76.1737
15	2.7383	1.1842	0.2982	1.2339	0.3076	1.8121	-0.0044	0.0721	0.1882	-0.2516	-0.0447	0.1129	-0.2232	-0.1854	0.0555	0.3762	0.0472	-0.0337	0.2817	-0.0002	0.263	36.6242	80.2105	77.4851
16	0.8281	0.273	-0.1851	1.3235	0.2796	1.0997	0.0583	-0.0986	0.0775	0.018	-0.1442	0.1589	-0.0329	-0.2928	0.0938	0.3021	0.0204	-0.0401	0.412	-0.0557	0.2393	27.0487	71.9617	90.5724
17	6.0125	0.5866	1.689	4.0786	1.4953	6.8376	-0.0354	-0.1576	-0.0074	0.2976	0.0466	0.0412	-0.1686	-0.2249	-0.0225	0.383	-0.0596	0.1217	0.456	-0.0688	0.2386	27.9427	81.1048	130.4958
18	2.4358	-0.9064	-0.0575	1.8551	0.4746	0.9223	0.1181	-0.0907	-0.1051	0.2173	-0.2224	0.0761	0.0809	-0.2173	0.1084	0.4319	-0.1347	0.0391	0.4365	-0.0239	0.2766	34.8101	69.0852	127.6008
19	1.0206	-0.0085	0.2594	1.1729	0.2248	1.6992	0.0985	-0.0064	0.1177	0.0566	-0.1701	0.1404	-0.1541	-0.3522	0.0835	0.3721	-0.0208	0.0547	0.4878	-0.0857	0.2834	27.8086	82.0537	115.9379

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 36 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 170 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 171 through 190 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 191 through 297 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid -1 through 36 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 37 through 129 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 130 through 297 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid -1 through 36 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 37 through 148 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 149 through 297 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid -1 through 36 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 37 through 148 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 149 through 297 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid -1 through 36 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 37 through 129 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 130 through 297 )
17	X-RAY DIFFRACTION	17	chain 'F' and (resid -1 through 36 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 37 through 148 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 149 through 296 )

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Yorodumi