PDB-2nuy: 2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius i...

ID or keywords:

Entry

Database: PDB / ID: 2nuy

Title

2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius in complex with pyruvate

Components

2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho gluconate aldolase

Keywords

LYASE / TIM barrel

Function / homology

Function and homology information

2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase / 2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity / 2-dehydro-3-deoxy-phosphogluconate aldolase activity
Similarity search - Function

Biological species

Sulfolobus acidocaldarius DSM 639 (acidophilic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

van Eerde, A. / Dijkstra, B.W.

Citation

Journal: Biochem.J. / Year: 2007
Title: Biochemical and structural exploration of the catalytic capacity of Sulfolobus KDG aldolases
Authors: Wolterink-van Loo, S. / van Eerde, A. / Siemerink, M.A.J. / Akerboom, J. / Dijkstra, B.W. / van der Oost, J.

History

Deposition	Nov 10, 2006	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Apr 10, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 2.0	Nov 15, 2023	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2nuy.cif.gz	130.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2nuy.ent.gz	103.2 KB	Display	PDB format
PDBx/mmJSON format	2nuy.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2nuy_validation.pdf.gz	437.6 KB	Display	wwPDB validaton report
Full document	2nuy_full_validation.pdf.gz	439.4 KB	Display
Data in XML	2nuy_validation.xml.gz	22.6 KB	Display
Data in CIF	2nuy_validation.cif.gz	32 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nu/2nuy ftp://data.pdbj.org/pub/pdb/validation_reports/nu/2nuy	HTTPS FTP

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Related structure data

Related structure data	2nuwC 2nuxC C: citing same article (ref.)
Similar structure data	2nux-1 2nuw-1 6h2r-d 5lky-d 5kze-1 3s5n-1 6g3z-1 1w3t-d 4ah7-d 3eb2-d Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#102 - Jun 2008 Lactate Dehydrogenase similarity (1) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1)

Deposited unit

A: 2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho gluconate aldolase

B: 2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho gluconate aldolase

hetero molecules

65.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho gluconate aldolase

B: 2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho gluconate aldolase

hetero molecules

A: 2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho gluconate aldolase

B: 2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho gluconate aldolase

hetero molecules

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

Unit cell

Length a, b, c (Å)	109.090, 109.090, 171.290
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Details

The biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operation: x-y,-y,-z+2/3 + (0 1 0)

#1: Protein	2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho gluconate aldolase Mass: 32554.482 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic) Species: Sulfolobus acidocaldarius / Strain: DSM639 / Gene: saci_0225 / Plasmid: pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q4JC35, 2-dehydro-3-deoxy-phosphogluconate aldolase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-PYR / PYRUVIC ACID Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₄O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 4.47 Å³/Da / Density % sol: 72.5 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% PEG400, 0.1M HEPES, 0.2M Magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 19, 2005
Radiation	Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 2.5→50 Å / Num. obs: 41289 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / B_iso Wilson estimate: 52.971 Å² / R_sym value: 0.056 / Net I/σ(I): 17.6
Reflection shell	Resolution: 2.5→2.65 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.348 / Mean I/σ(I) obs: 5.3 / Num. unique all: 6379 / % possible all: 97.1

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Processing

Software

Name	Version	Classification
REFMAC		refinement
PDB_EXTRACT	2	data extraction
ProDC		data collection
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: native structure of KDGA

Resolution: 2.5→47.25 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.954 / SU B: 10.899 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: isotropic B factor refinement in combination with TLS refinement
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.191	2131	5.2 %	RANDOM
R_work	0.159	-	-	-
obs	0.16	41249	99.6 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 29.73 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.58 Å²	1.79 Å²	0 Å²
2-	-	3.58 Å²	0 Å²
3-	-	-	-5.38 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→47.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4598	0	11	162	4771

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	4726
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3226
X-RAY DIFFRACTION	r_angle_refined_deg	1.327	1.996	6407
X-RAY DIFFRACTION	r_angle_other_deg	0.846	3	7938
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.059	5	574
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.905	24.757	206
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.846	15	851
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.748	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	731
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	5140
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	888
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.3	993
X-RAY DIFFRACTION	r_nbd_other	0.179	0.3	3368
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.5	2345
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.5	2230
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.11	0.15	303
X-RAY DIFFRACTION	r_metal_ion_refined	0.06	0.5	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.154	0.3	15
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.197	0.3	22
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.131	0.15	15
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.07	0.5	2
X-RAY DIFFRACTION	r_mcbond_it	3.651	1.5	3768
X-RAY DIFFRACTION	r_mcbond_other	1.138	1.5	1148
X-RAY DIFFRACTION	r_mcangle_it	4.228	2	4699
X-RAY DIFFRACTION	r_scbond_it	8.145	3	2162
X-RAY DIFFRACTION	r_scangle_it	10.47	4.5	1708

LS refinement shell

Resolution: 2.5→2.565 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.246	129	-
R_work	0.231	2752	-
obs	-	2881	95.4 %

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	1.762	0.0595	-0.461	2.8277	0.3244	2.9258	0.0614	0.013	-0.1735	-0.251	-0.2204	0.1509	0.2051	-0.113	0.159	0.1631	0.0773	-0.006	0.1657	-0.0461	0.1593	-4.067	69.682	36.531
2	0.3534	0.5972	0.8573	1.2879	0.5826	4.769	0.1217	0.0537	-0.0786	-0.1779	-0.1259	-0.208	0.2158	0.2419	0.0043	0.1211	0.1234	0.0228	0.1453	0.0061	0.1332	7.537	68.15	41.079
3	0.8482	1.5016	2.4668	9.7275	7.4246	21.6323	0.2656	0.0421	-0.0826	0.1388	0.1781	-0.7745	-0.3822	0.5147	-0.4438	-0.0025	0.034	-0.0011	0.218	0.0741	0.2645	16.889	77.688	52.68
4	2.8137	-1.2272	-2.0701	3.773	1.721	4.7826	0.3794	0.1269	0.117	-0.253	-0.1746	-0.6457	-0.2768	0.2938	-0.2048	0.0336	0.042	0.0509	0.1848	0.0396	0.1313	12.281	78.423	43.607
5	1.8052	-2.7329	0.7351	5.1142	0.172	1.989	-0.0237	0.1806	0.4381	-0.5761	-0.1086	-0.8982	-0.1908	0.4375	0.1323	0.1192	0.0712	0.1033	0.1365	0.0425	0.1738	10.91	87.205	37.89
6	1.1204	2.1067	0.3781	4.3639	0.1177	1.0016	-0.1651	0.296	-0.0524	-0.9304	0.1293	0.0028	-0.1565	-0.0905	0.0357	0.2985	0.1304	-0.0078	0.1503	-0.021	0.0507	-2.867	87.849	27.285
7	9.6731	5.8476	-7.1509	6.0557	-5.5926	13.8655	0.018	0.3784	0.5932	-0.5079	0.1189	0.6664	-0.6134	-1.0143	-0.1369	0.2312	0.2235	-0.1278	0.0993	-0.0459	0.1087	-10.904	93.619	32.027
8	2.8296	-0.4072	-1.0413	2.7891	0.5025	5.5578	0.1159	0.0941	-0.0799	-0.1583	-0.1587	0.3863	-0.0855	-0.5831	0.0428	0.0407	0.0421	-0.052	0.1957	-0.0837	0.1622	-14.744	76.108	41.239
9	14.8223	0.5503	-0.0017	23.5745	-14.7017	14.1334	0.1209	-0.1853	-0.6153	0.2233	0.1282	1.5467	-0.1016	-1.5786	-0.2491	-0.1122	0.1465	-0.0724	0.4023	-0.1227	0.3125	-24.477	81.108	42.073
10	16.5162	5.9017	-13.5965	4.8327	-3.9509	19.0529	-0.3173	1.0878	0.0228	-0.8734	0.0661	0.9969	0.4431	-0.8037	0.2512	0.101	0.2255	-0.2191	0.2386	-0.0655	0.2416	-19.273	88.161	27.198
11	1.3958	-0.5405	-0.6419	1.9212	1.3575	4.335	0.0288	0.0908	-0.2324	0.2296	-0.1312	-0.1781	0.369	0.2362	0.1024	0.2031	-0.0351	-0.0167	0.1259	0.0525	0.1716	7.511	65.048	70.133
12	0.7189	-0.6501	0.6729	0.86	-0.9502	4.1295	0.0798	0.0247	-0.1893	0.2173	-0.1318	0.0957	0.2968	-0.2449	0.052	0.1704	-0.0963	0.0401	0.1022	-0.0173	0.1273	-4.349	64.027	66.537
13	20.112	-4.7119	-4.3727	12.0227	4.037	2.2196	0.3471	0.6337	0.3315	-0.5193	-0.3575	0.0817	-0.744	-0.681	0.0104	0.1687	0.0922	-0.0204	0.3142	0.0103	0.0796	-8.735	80.938	51.708
14	1.4514	0.8365	-0.0912	3.195	-0.0485	1.9141	0.2494	0.1537	-0.0074	0.1478	-0.2754	0.5275	-0.0118	-0.368	0.026	0.1174	-0.0387	0.0474	0.1726	-0.0258	0.1236	-9.837	75.411	64.08
15	5.841	1.2159	-0.9074	5.3184	2.4805	3.7225	-0.0835	-0.0259	0.1952	0.3926	-0.2592	0.8282	0.0843	-0.5133	0.3427	0.1356	-0.063	0.0455	0.1162	-0.0125	0.1279	-9.384	82.695	72.727
16	0.2755	0.3826	0.057	1.3246	1.1869	1.5589	0.0001	-0.1837	-0.1145	0.4854	-0.0314	-0.0567	0.0452	0.1517	0.0314	0.1963	-0.0883	-0.0338	0.1297	0.0762	0.0518	5.991	80.162	79.813
17	7.5232	-2.4193	-8.3234	3.6295	1.8194	15.9388	-0.1931	-0.5533	-0.1238	0.7229	0.104	-0.301	-0.384	0.9524	0.0892	0.2434	-0.068	-0.1759	0.1701	0.04	0.1509	12.6	85.53	83.699
18	5.3207	1.0073	-1.3687	8.5115	-6.4089	11.6756	0.1299	0.3145	0.1373	0.1147	-0.374	-0.5775	0.0161	0.7308	0.2441	0.156	-0.0089	-0.0757	0.2621	0.061	0.2682	18.561	75.329	68.541
19	2.8683	0.6754	-0.2715	2.9523	1.2462	1.9619	0.1456	0.1976	-0.118	0.1207	-0.1005	-0.6204	0.1561	0.8535	-0.0451	-0.0237	0.0686	-0.0987	0.2086	0.0915	0.2055	21.268	70.82	65.869
20	16.5004	0.4381	-12.083	2.2532	0.951	18.9866	-0.5682	-0.6364	-0.3017	0.6722	0.063	-1.0487	0.7923	0.7975	0.5051	0.0633	-0.0739	-0.2385	0.2692	0.0459	0.2079	24.175	80.53	81.668

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	1 - 56	1 - 56
2	2	A	A	57 - 104	57 - 104
3	3	A	A	105 - 117	105 - 117
4	4	A	A	118 - 142	118 - 142
5	5	A	A	143 - 181	143 - 181
6	6	A	A	182 - 216	182 - 216
7	7	A	A	217 - 232	217 - 232
8	8	A	A	233 - 265	233 - 265
9	9	A	A	266 - 275	266 - 275
10	10	A	A	276 - 288	276 - 288
11	11	B	B	1 - 56	1 - 56
12	12	B	B	57 - 101	57 - 101
13	13	B	B	102 - 110	102 - 110
14	14	B	B	111 - 142	111 - 142
15	15	B	B	143 - 173	143 - 173
16	16	B	B	174 - 208	174 - 208
17	17	B	B	209 - 233	209 - 233
18	18	B	B	234 - 248	234 - 248
19	19	B	B	249 - 273	249 - 273
20	20	B	B	274 - 288	274 - 288

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