PDB-4imd: Crystal Structure of Pasteurella multocida N-Acetyl-D-Neuraminic ...

ID or keywords:

Entry

Database: PDB / ID: 4imd

Title

Crystal Structure of Pasteurella multocida N-Acetyl-D-Neuraminic acid lyase trapped with pyruvate covalently bound through a Schiff base to Lys164

Components

N-acetylneuraminate lyase

Keywords

LYASE / Tim barrel / Schiff base

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

Pasteurella multocida subsp. gallicida (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.1 Å

Authors

Fisher, A.J. / Huynh, N.

Citation

Journal: Biochemistry / Year: 2013
Title: Structural Basis for Substrate Specificity and Mechanism of N-Acetyl-d-neuraminic Acid Lyase from Pasteurella multocida.
Authors: Huynh, N. / Aye, A. / Li, Y. / Yu, H. / Cao, H. / Tiwari, V.K. / Shin, D.W. / Chen, X. / Fisher, A.J.

History

Deposition	Jan 2, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 6, 2013	Provider: repository / Type: Initial release
Revision 1.1	Dec 11, 2013	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4imd.cif.gz	474.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4imd.ent.gz	407.9 KB	Display	PDB format
PDBx/mmJSON format	4imd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4imd_validation.pdf.gz	481.5 KB	Display	wwPDB validaton report
Full document	4imd_full_validation.pdf.gz	500.7 KB	Display
Data in XML	4imd_validation.xml.gz	53.6 KB	Display
Data in CIF	4imd_validation.cif.gz	76.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/im/4imd ftp://data.pdbj.org/pub/pdb/validation_reports/im/4imd	HTTPS FTP

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Related structure data

Related structure data	4imcC 4imeC 4imfC 4imgC C: citing same article (ref.)
Similar structure data	1f7b-1 3lcl-d 1f6p-d 2wo5-d 4ime-1 4imc-d 1hl2-d 1fdz-d 1f73-d 2wnz-d Search similar-shape structures by Omokage search (details) 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

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	80.825, 114.057, 82.030
Angle α, β, γ (deg.)	90.00, 111.74, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D

#1: Protein	N-acetylneuraminate lyase / N-acetylneuraminate pyruvate-lyase / N-acetylneuraminic acid aldolase / Sialate lyase / Sialic acid ...N-acetylneuraminate pyruvate-lyase / N-acetylneuraminic acid aldolase / Sialate lyase / Sialic acid aldolase / Sialic acid lyase Mass: 32702.555 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pasteurella multocida subsp. gallicida (bacteria) Strain: P1059 / Gene: nanA, PM1715 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9CKB0, N-acetylneuraminate lyase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 799 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	UNIPROT SEQUENCE REFERENCE Q9CKB0 IS FOR A DIFFERENT STRAIN (PM70).

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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: 54.19 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 21% PEG1000, 0.15 M sodium chloride, 0.1 M sodium potassium phosphate, soaked in 0.05 M pyruvate for 24 hours, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 10, 2008
Radiation	Monochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. all: 79123 / Num. obs: 79123 / % possible obs: 98.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / R_merge(I) obs: 0.084 / Net I/σ(I): 14
Reflection shell	Resolution: 2.1→2.154 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.325 / Mean I/σ(I) obs: 3.4 / % possible all: 91.6

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHASER		phasing
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction
Blu-Ice		data collection
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→35.68 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.926 / Occupancy max: 1 / Occupancy min: 0.38 / SU B: 8.971 / SU ML: 0.122 / SU R Cruickshank DPI: 0.2084 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21847	4045	5.1 %	RANDOM
R_work	0.17949	-	-	-
obs	0.18146	75078	98.16 %	-
all	-	79123	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 29.191 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.05 Å²	0 Å²	0.32 Å²
2-	-	0.46 Å²	0 Å²
3-	-	-	-2 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→35.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9184	0	64	799	10047

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.019	9543
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.919	1.988	12864
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.363	5	1196
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.913	25.061	409
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.447	15	1722
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.729	15	29
X-RAY DIFFRACTION	r_chiral_restr	0.124	0.2	1424
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	7089
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 2276 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Dom-ID	Auth asym-ID	Rms dev position (Å)
1	A	1.87
2	B	1.79
3	C	2.4
4	D	1.9

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.257	267	-
R_work	0.21	5560	-
obs	-	-	97.69 %

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	0.5773	-0.0254	0.2202	1.7999	-0.1926	1.4668	0.0118	-0.135	0.0339	0.2888	-0.0666	0.0611	-0.1849	-0.1428	0.0548	0.0817	0.0223	0.0198	0.1275	-0.0769	0.1758	-14.621	3.995	0.188
2	1.2302	-0.6268	0.593	1.5498	-0.1016	1.3019	0.0608	-0.0239	-0.0547	0.2047	-0.0755	-0.0362	0.0208	-0.0294	0.0147	0.0564	-0.0309	0.0095	0.0791	-0.0226	0.1481	-7.804	-11.242	-0.048
3	0.352	0.0006	0.1523	1.2484	0.145	1.2567	0.0085	0.0186	0.0439	0.0822	-0.0331	0.0929	-0.1137	-0.1121	0.0246	0.0215	0.0217	-0.0081	0.0713	-0.0712	0.1598	-12.034	1.813	-14.726
4	8.7553	3.4065	4.3268	4.2665	0.7395	7.038	-0.033	0.0291	0.4012	-0.1473	-0.0648	0.0839	-0.6292	0.0601	0.0978	0.2028	0.0681	-0.0072	0.0536	-0.0541	0.2558	-10.097	20.348	-14.247
5	1.4416	0.2051	-0.1946	1.4193	-0.3797	0.9081	-0.0108	0.1855	-0.1285	-0.2321	-0.083	-0.0636	0.1068	-0.0202	0.0938	0.0843	0.0434	-0.0222	0.1437	-0.1005	0.1213	4.078	-16.085	-48.017
6	1.7056	0.3754	0.1145	1.2843	0.2669	0.8647	0.0857	0.101	0.0625	-0.1435	-0.1502	-0.1062	-0.036	0.0608	0.0645	0.0475	0.0542	-0.0137	0.1097	0.0155	0.0904	8.923	-0.821	-43.315
7	0.7854	0.0049	-0.2766	1.0764	0.0347	0.6192	0.0573	0.1461	-0.0672	-0.0905	-0.1123	0.0841	0.074	-0.111	0.055	0.0372	0.0257	-0.0365	0.0938	-0.0902	0.137	-4.094	-13.906	-35.255
8	9.8047	-2.6439	-1.1539	3.9444	-0.2174	1.6167	-0.2835	-0.1466	-0.5657	0.3392	0.0263	0.1685	0.3031	0.0334	0.2572	0.1599	0.0101	0.0087	0.0849	-0.1117	0.2761	-2.233	-32.437	-34.236
9	1.0519	-0.2869	-0.0221	1.3123	0.1304	1.2069	0.0724	0.1912	-0.0163	-0.1994	-0.169	-0.3933	-0.1135	0.3148	0.0966	0.043	-0.016	0.0339	0.2379	0.1745	0.3895	38.733	-1.331	-36.281
10	0.7309	0.4431	0.4702	1.96	-0.239	1.8665	0.0734	0.0509	-0.0459	-0.1875	-0.2324	-0.3014	0.2186	0.1232	0.159	0.0471	0.0511	0.0436	0.1353	0.0741	0.3068	30.922	-15.762	-33.34
11	0.5472	-0.2353	0.2248	0.9703	-0.1121	1.4355	-0.0117	0.0431	0.0261	0.0938	-0.1432	-0.3209	-0.1396	0.2629	0.1549	0.0269	-0.0559	-0.069	0.1417	0.1641	0.352	36.249	-0.56	-21.238
12	8.9556	-4.8138	9.9342	5.9738	-5.0547	11.8207	-0.5353	0.0819	0.4741	0.5257	0.1044	-0.5805	-1.1503	0.2588	0.4309	0.4861	-0.1477	-0.0732	0.1584	0.1938	0.4764	35.606	17.716	-25.068
13	1.2289	0.1888	0.4453	1.4619	0.2289	0.9613	-0.004	-0.2918	-0.0206	0.399	-0.1073	-0.1024	-0.1092	0.1135	0.1113	0.1695	-0.0886	-0.1201	0.1663	0.1117	0.1899	19.177	-10.805	14.52
14	1.5019	-0.2509	-0.3602	1.3512	-0.442	0.39	0.1018	-0.0528	0.1151	0.3217	-0.1799	-0.0565	-0.2339	0.046	0.0781	0.2071	-0.0811	-0.1227	0.1079	0.0092	0.1775	15.349	3.677	7.168
15	0.784	0.1889	-0.3556	1.1589	-0.0556	0.7208	0.0203	-0.1485	-0.042	0.1793	-0.1608	-0.2626	-0.067	0.2042	0.1405	0.0673	-0.0749	-0.1296	0.1294	0.1522	0.2603	27.406	-11.594	1.666
16	14.7579	3.8302	-1.2105	2.9267	0.012	0.8316	-0.2139	-0.0112	-0.8718	0.1015	-0.0163	-0.5657	0.3912	0.092	0.2302	0.2582	-0.0256	-0.0206	0.0946	0.1632	0.388	24.12	-29.912	3.986

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 57
2	X-RAY DIFFRACTION	2	A	58 - 167
3	X-RAY DIFFRACTION	3	A	168 - 277
4	X-RAY DIFFRACTION	4	A	278 - 293
5	X-RAY DIFFRACTION	5	B	2 - 57
6	X-RAY DIFFRACTION	6	B	58 - 167
7	X-RAY DIFFRACTION	7	B	168 - 277
8	X-RAY DIFFRACTION	8	B	278 - 293
9	X-RAY DIFFRACTION	9	C	2 - 57
10	X-RAY DIFFRACTION	10	C	58 - 167
11	X-RAY DIFFRACTION	11	C	168 - 277
12	X-RAY DIFFRACTION	12	C	278 - 293
13	X-RAY DIFFRACTION	13	D	2 - 57
14	X-RAY DIFFRACTION	14	D	58 - 167
15	X-RAY DIFFRACTION	15	D	168 - 277
16	X-RAY DIFFRACTION	16	D	278 - 293

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