PDB-8u91: Crystal structure of N-acetylneuraminate lyase (NanA) from Klebsi...

ID or keywords:

Entry

Database: PDB / ID: 8u91

Title

Crystal structure of N-acetylneuraminate lyase (NanA) from Klebsiella aerogenes (Apo, 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: 2.65 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 (Apo, 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8u91.cif.gz	714.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8u91.ent.gz	596.5 KB	Display	PDB format
PDBx/mmJSON format	8u91.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8u91_validation.pdf.gz	481 KB	Display	wwPDB validaton report
Full document	8u91_full_validation.pdf.gz	487.7 KB	Display
Data in XML	8u91_validation.xml.gz	61.4 KB	Display
Data in CIF	8u91_validation.cif.gz	85.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u9/8u91 ftp://data.pdbj.org/pub/pdb/validation_reports/u9/8u91	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

204 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
136 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
136 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	95.101, 146.566, 216.916
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	N-acetylneuraminate lyase Mass: 33669.527 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
#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-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.74 Å³/Da / Density % sol: 67.13 %
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, B5 drop 1. Puck: PSL-1401, 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: 2.65→48.86 Å / Num. obs: 88752 / % possible obs: 100 % / Redundancy: 13.9 % / CC_1/2: 0.998 / R_merge(I) obs: 0.189 / R_pim(I) all: 0.053 / R_rim(I) all: 0.196 / Χ²: 1.01 / Net I/σ(I): 12.4 / Num. measured all: 1230081
Reflection shell	Resolution: 2.65→2.7 Å / % possible obs: 100 % / Redundancy: 14.5 % / R_merge(I) obs: 1.892 / Num. measured all: 65115 / Num. unique obs: 4481 / CC_1/2: 0.796 / R_pim(I) all: 0.513 / R_rim(I) all: 1.961 / Χ²: 1.01 / Net I/σ(I) obs: 1.8

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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: 2.65→47.66 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.8 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2222	4393	4.96 %
R_work	0.1801	-	-
obs	0.1822	88593	99.84 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.65→47.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13751	0	117	309	14177

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	14591
X-RAY DIFFRACTION	f_angle_d	0.497	19805
X-RAY DIFFRACTION	f_dihedral_angle_d	12.375	5354
X-RAY DIFFRACTION	f_chiral_restr	0.038	2260
X-RAY DIFFRACTION	f_plane_restr	0.004	2574

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 (%)
2.65-2.68	0.3649	145	0.2891	2743	X-RAY DIFFRACTION	100
2.68-2.71	0.3281	120	0.2715	2812	X-RAY DIFFRACTION	100
2.71-2.74	0.3086	138	0.2616	2756	X-RAY DIFFRACTION	100
2.74-2.78	0.2739	148	0.2525	2779	X-RAY DIFFRACTION	100
2.78-2.82	0.3148	161	0.2428	2778	X-RAY DIFFRACTION	100
2.82-2.85	0.3514	152	0.2484	2758	X-RAY DIFFRACTION	100
2.85-2.9	0.3236	140	0.2525	2765	X-RAY DIFFRACTION	100
2.9-2.94	0.2791	154	0.236	2781	X-RAY DIFFRACTION	100
2.94-2.98	0.2927	149	0.2165	2760	X-RAY DIFFRACTION	100
2.98-3.03	0.2686	147	0.2088	2765	X-RAY DIFFRACTION	100
3.03-3.09	0.262	149	0.2154	2790	X-RAY DIFFRACTION	100
3.09-3.14	0.2738	156	0.223	2765	X-RAY DIFFRACTION	100
3.14-3.2	0.2966	140	0.2364	2804	X-RAY DIFFRACTION	100
3.2-3.27	0.26	138	0.2413	2792	X-RAY DIFFRACTION	100
3.27-3.34	0.2975	140	0.2058	2782	X-RAY DIFFRACTION	100
3.34-3.42	0.2402	137	0.1955	2807	X-RAY DIFFRACTION	100
3.42-3.5	0.2055	145	0.1747	2790	X-RAY DIFFRACTION	100
3.5-3.6	0.2272	155	0.164	2763	X-RAY DIFFRACTION	100
3.6-3.7	0.1944	139	0.1694	2824	X-RAY DIFFRACTION	100
3.7-3.82	0.1815	151	0.1621	2805	X-RAY DIFFRACTION	100
3.82-3.96	0.2088	156	0.1619	2818	X-RAY DIFFRACTION	100
3.96-4.12	0.1993	144	0.1488	2799	X-RAY DIFFRACTION	100
4.12-4.3	0.1888	140	0.1362	2821	X-RAY DIFFRACTION	100
4.3-4.53	0.1649	151	0.1308	2830	X-RAY DIFFRACTION	100
4.53-4.81	0.1865	137	0.1363	2832	X-RAY DIFFRACTION	100
4.81-5.18	0.1677	149	0.148	2821	X-RAY DIFFRACTION	100
5.19-5.71	0.2195	154	0.172	2874	X-RAY DIFFRACTION	100
5.71-6.53	0.2191	158	0.2009	2854	X-RAY DIFFRACTION	100
6.53-8.22	0.2064	155	0.1813	2908	X-RAY DIFFRACTION	100
8.22-47.66	0.1898	145	0.162	3024	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	4.0707	-1.1625	0.3485	6.8752	-2.5401	6.7805	-0.0545	0.5177	-0.1803	-0.0948	-0.1011	-0.0267	0.3965	0.3239	0.1572	0.317	-0.033	0.0493	0.4999	-0.092	0.3604	29.6877	22.1273	5.616
2	4.2705	-0.9624	-0.4317	3.095	-0.7229	1.7686	-0.3173	0.1015	-0.2688	0.2595	0.1758	0.2128	0.369	-0.4027	0.11	0.4447	-0.0491	0.0183	0.4413	-0.0142	0.4523	13.0681	22.461	14.4626
3	2.4912	0.2019	-0.4808	1.4067	-0.7333	1.895	-0.0488	-0.0803	-0.2039	0.0658	-0.0681	-0.1829	0.2188	0.2574	0.1285	0.4411	0.037	0.0493	0.4837	-0.0303	0.3849	34.3124	20.0626	21.1552
4	2.2175	0.8279	0.4834	2.6993	-0.0768	1.9875	0.0989	-0.4012	-0	0.095	-0.0758	0.1192	0.0103	-0.1191	-0.0031	0.3194	0.0349	0.0406	0.6039	-0.0418	0.3916	8.4735	45.369	57.836
5	2.6634	0.4757	1.5424	1.491	0.1249	1.9931	-0.1136	-0.236	0.2657	-0.013	-0.0203	0.0892	-0.3174	-0.0652	0.1414	0.3665	0.0333	0.0003	0.4935	-0.0917	0.4141	15.7468	58.0694	47.5739
6	2.2767	0.5847	-0.6305	3.3195	-0.5835	2.3365	0.0022	-0.3649	0.0176	-0.0177	-0.0791	-0.1818	0.2244	0.2538	0.0813	0.372	0.0705	-0.0121	0.5832	0.0543	0.3687	28.1368	24.809	56.8724
7	1.6031	0.2393	-1.1609	1.0404	0.156	1.861	-0.0873	-0.1288	-0.1926	-0.0237	-0.0371	0.0124	0.3602	0.0217	0.1448	0.5801	0.0482	0.0267	0.5693	0.1094	0.5113	19.9222	12.1618	46.3554
8	4.5777	-0.7468	0.8007	1.7096	0.1345	2.7133	-0.2911	0.1372	0.2623	-0.0356	0.1895	-0.2061	-0.2725	0.1335	0.1057	0.385	-0.0427	-0.021	0.4089	0.0254	0.4147	15.7132	50.3995	11.558
9	2.0644	0.0774	0.1378	1.4201	1.03	2.2078	-0.0887	-0.0897	0.1558	-0.0451	-0.0217	0.137	-0.2272	-0.3383	0.1436	0.3618	0.0435	-0.0533	0.4129	0.0236	0.3666	1.4769	51.9454	22.1658
10	5.6896	-1.9913	-2.6739	3.1521	1.3538	3.4056	-0.0205	0.2083	0.147	-0.4261	-0.0744	0.2314	-0.2033	-0.4891	0.1064	0.5185	-0.016	-0.0996	0.6047	-0.0097	0.3873	29.1216	72.2329	75.1446
11	4.7985	1.3457	-1.5365	3.7077	1.2548	2.6835	-0.0745	-0.3457	0.2094	-0.1078	-0.001	-0.1077	-0.4309	0.1076	0.0665	0.3749	0.0407	-0.0252	0.4544	0.0217	0.4064	39.2422	85.2715	83.845
12	1.0189	0.2922	-0.586	2.667	1.1133	1.7129	0.0491	-0.0009	0.1022	-0.1423	-0.1749	0.3815	-0.0871	-0.5356	0.1475	0.3779	0.0121	-0.0456	0.6705	-0.0536	0.3928	25.7545	71.7477	91.3848
13	4.1857	-5.6753	0.2971	9.4237	0.3751	3.9463	0.2613	-0.628	-1.0232	-0.2613	-0.1345	0.7811	0.4484	-1.0068	-0.0512	0.6165	-0.1935	-0.0481	0.8156	-0.0152	0.512	20.5455	55.1892	86.7357
14	2.4757	-1.3254	-0.4458	3.8148	0.7692	2.4473	0.084	-0.2857	-0.0399	0.5462	-0.1992	0.1069	0.0275	-0.3097	0.1147	0.5474	-0.1416	0.0386	0.6727	-0.0483	0.4148	32.9956	73.5714	129.9814
15	1.2538	-0.349	0.4962	1.3731	0.2329	1.7395	0.1129	-0.0083	0.0221	0.0105	-0.2261	0.2427	-0.1067	-0.3708	0.107	0.4649	-0.0487	0.0719	0.7339	-0.084	0.4129	29.3366	79.9092	115.9323

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 70 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 71 through 160 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 161 through 297 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 160 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 161 through 297 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 1 through 166 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 167 through 297 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 0 through 160 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 161 through 297 )
10	X-RAY DIFFRACTION	10	chain 'E' and (resid 1 through 70 )
11	X-RAY DIFFRACTION	11	chain 'E' and (resid 71 through 160 )
12	X-RAY DIFFRACTION	12	chain 'E' and (resid 161 through 278 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 279 through 297 )
14	X-RAY DIFFRACTION	14	chain 'F' and (resid 0 through 129 )
15	X-RAY DIFFRACTION	15	chain 'F' and (resid 130 through 296 )

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