PDB-2nux: 2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius, ...

ID or keywords:

Entry

Database: PDB / ID: 2nux

Title

2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius, native structure in p6522 at 2.5 A resolution

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 / (R,S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-tetrahydrodipicolinate synthase activity / glyoxylate catabolic process / cytosol
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 / Derived calculations / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.4	Oct 25, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2nux.cif.gz	129.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2nux.ent.gz	101.6 KB	Display	PDB format
PDBx/mmJSON format	2nux.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2nux_validation.pdf.gz	430.3 KB	Display	wwPDB validaton report
Full document	2nux_full_validation.pdf.gz	434.8 KB	Display
Data in XML	2nux_validation.xml.gz	21.8 KB	Display
Data in CIF	2nux_validation.cif.gz	30.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nu/2nux ftp://data.pdbj.org/pub/pdb/validation_reports/nu/2nux	HTTPS FTP

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Related structure data

Related structure data	2nuwSC 2nuyC 1nuy S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2nuy-1 2nuw-1 6h2r-d 6g3z-1 6h7r-d 3s5n-1 1w3i-d 5lky-d 5kze-1 4ah7-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

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

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

Unit cell

Length a, b, c (Å)	109.509, 109.509, 319.559
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

Components on special symmetry positions

ID	Model	Components
1	1	A-1034- HOH
2	1	B-318- HOH

Details

The biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operation: x, x-y, -z+5/6 + (0 0 -1)

#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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.25 Å³/Da / Density % sol: 71.03 %
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: ID14-1 / Wavelength: 0.934 Å

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 11, 2004

Radiation

Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.934 Å / Relative weight: 1

Reflection

Resolution: 2.5→36 Å / Num. obs: 36273 / % possible obs: 90.1 % / Observed criterion σ(I): -3 / Redundancy: 33.1 % / B_iso Wilson estimate: 50.216 Å² / R_merge(I) obs: 0.155 / Net I/σ(I): 23.77

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique all	% possible all
2.5-2.55		19.8	0.39	8	23512	1194	53
2.55-2.6			0.367	8.7	24839	1241	58.8
2.6-2.7			0.34	9.4	52427	2574	69.5
2.7-2.8			0.292	10.6	59720	2913	89.6
2.8-3			0.449	13.5	139424	5120	97.5
3-4			0.248	22.7	496645	13107	98
4-5			0.122	36.6	195772	4799	98.3
5-6			0.102	41.2	87488	2154	98.4
	6		0.077	47.4	94847	2423	98.6

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Phasing

Phasing MR

R_factor: 0.339 / Cor.coef. F_o:F_c: 0.703

	Highest resolution	Lowest resolution
Rotation	4 Å	38.2 Å
Translation	4 Å	38.2 Å

Phasing dm

FOM : 0.59 / FOM acentric: 0.59 / FOM centric: 0.62 / Reflection: 36481 / Reflection acentric: 30905 / Reflection centric: 5576

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
2.5-2.7	0.13	0.14	0.12	4421	3999	422
2.7-3.1	0.36	0.37	0.35	11212	9935	1277
3.1-3.6	0.7	0.71	0.64	6658	5762	896
3.6-4.5	0.85	0.86	0.79	6723	5658	1065
4.5-7.1	0.86	0.88	0.79	5512	4325	1187
7.1-38.199	0.9	0.92	0.86	1955	1226	729

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
MOLREP		phasing
RESOLVE	2.1	phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction
ProDC		data collection
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2NUW

2nuw

Resolution: 2.5→36 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.943 / SU B: 13.789 / SU ML: 0.147 / 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: 0.253 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, Reported Average Isotropic B Value is without TLS contribution

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.216	1878	5.2 %	RANDOM
R_work	0.175	-	-	-
obs	0.177	36261	90.16 %	-
all	-	40218	-	-

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: 28.345 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.43 Å²	1.21 Å²	0 Å²
2-	-	2.43 Å²	0 Å²
3-	-	-	-3.64 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→36 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4598	0	1	94	4693

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	4696
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3212
X-RAY DIFFRACTION	r_angle_refined_deg	1.34	1.995	6370
X-RAY DIFFRACTION	r_angle_other_deg	0.861	3	7904
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.951	5	574
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.77	24.804	204
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.74	15	848
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.534	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	728
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	5116
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	880
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.3	1028
X-RAY DIFFRACTION	r_nbd_other	0.183	0.3	3349
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.5	2345
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.5	2233
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.105	0.15	248
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.173	0.3	20
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.25	0.3	50
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.14	0.15	18
X-RAY DIFFRACTION	r_mcbond_it	3.684	1.5	3775
X-RAY DIFFRACTION	r_mcbond_other	1.155	1.5	1148
X-RAY DIFFRACTION	r_mcangle_it	4.42	2	4690
X-RAY DIFFRACTION	r_scbond_it	7.784	3	2121
X-RAY DIFFRACTION	r_scangle_it	9.896	4.5	1680

LS refinement shell

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

	R_factor	Num. reflection	% reflection
R_free	0.299	97	-
R_work	0.221	1461	-
obs	-	1558	53.71 %

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	1.752	0.0712	0.1173	2.2592	-0.4953	4.2898	0.0025	-0.216	-0.3471	0.0859	-0.0681	0.0423	0.1733	0.0317	0.0657	0.1037	0.0053	0.0151	0.2572	0.1463	0.2291	-28.0623	34.7996	-11.7714
2	1.3406	1.2388	-2.0064	3.6312	1.1489	6.6292	-0.0637	0.0329	0.0093	0.1317	0.1296	0.3509	0.1188	-0.0368	-0.0659	0.029	0.0235	0.0305	0.3474	0.1499	0.2167	-35.3274	38.6644	-8.2998
3	2.7692	1.4323	-1.1311	2.8246	-2.4608	3.5243	-0.1628	-0.3943	0.0643	0.1636	0.0412	0.1559	-0.0922	-0.1727	0.1215	0.0938	0.0425	-0.025	0.2398	0.0614	0.2104	-36.2862	48.8341	-16.3729
4	14.6387	7.5885	-3.8599	11.3725	-4.6039	13.1479	-0.2295	-0.1192	0.6001	0.3726	-0.2492	-0.0908	-1.0067	0.3843	0.4787	0.195	0.0404	-0.1154	0.0691	0.0477	0.1524	-30.2912	61.8142	-22.6603
5	4.6328	1.0272	-0.4867	2.7776	-1.1589	3.8704	-0.1278	-0.4598	0.4199	0.0323	0.1302	0.3639	-0.1625	0.0154	-0.0024	0.09	0.0074	-0.0604	0.1501	0.0628	0.0705	-30.5285	54.1597	-13.4781
6	2.9224	0.3776	0.853	1.1435	-0.8744	2.1966	0.0982	-0.633	0.0918	0.383	-0.1466	0.0986	-0.3041	0.0307	0.0484	0.0885	-0.023	0.0123	0.2911	0.093	0.0613	-18.1631	50.4052	-5.7059
7	2.9687	2.4111	3.1346	8.4889	2.4831	12.1561	0.1162	-0.5409	-0.6577	0.879	-0.2681	-0.3458	0.827	1.0335	0.1519	0.0655	0.0019	-0.0916	0.3415	0.3257	0.2198	-5.8178	39.9397	-0.6137
8	40.5755	-4.962	29.1806	9.7103	-8.0801	32.0378	-0.8355	0.2559	2.5089	-0.3165	-0.3844	-1.6956	-0.7243	1.8422	1.2199	-0.0034	0.0455	0.0511	0.0413	0.2066	0.3878	-7.5433	36.8265	-19.2547
9	3.7748	0.4606	-0.9272	2.6677	-0.8682	5.5717	-0.0449	-0.1893	-0.697	-0.089	-0.0971	-0.151	0.5239	0.2333	0.142	0.0754	0.0678	-0.0001	0.001	0.1565	0.2175	-19.0143	29.2161	-18.5958
10	4.7622	1.0481	7.5641	6.6634	2.28	22.4888	0.2326	-0.4094	-0.6937	0.2258	-0.3689	-0.7929	1.5021	0.1161	0.1363	0.1324	0.231	0.0111	0.1637	0.2715	0.3785	-6.4496	26.6882	-11.3461
11	2.1344	-0.3475	-0.6064	6.2285	-2.4251	3.3876	0.0062	-0.348	0.207	0.2196	-0.1417	-0.273	-0.4457	0.2071	0.1355	0.148	-0.0411	-0.1232	0.2413	0.0357	0.1917	11.6325	72.2083	-4.9946
12	0.6516	-0.9397	-0.1825	1.9127	-0.1475	4.2829	-0.1166	-0.1335	0.0863	0.0296	-0.0597	-0.2927	-0.0711	0.6146	0.1764	0.0317	-0.0069	-0.0818	0.2203	0.1559	0.1541	18.498	65.4248	-15.2468
13	4.7587	1.8592	-0.6599	7.2399	-0.7866	5.7781	-0.2229	0.0577	-0.2193	-0.7224	0.0841	-0.4022	0.5162	0.2014	0.1388	0.1858	0.0448	-0.0056	0.1544	0.0828	0.0524	7.8101	56.0152	-31.1364
14	3.6956	0.7155	1.4279	2.3634	-0.678	3.4189	0.0308	0.0793	-0.8079	-0.1518	0.0231	-0.2864	0.5327	0.2353	-0.0539	0.0899	0.0785	0.0007	0.1301	0.1403	0.1903	12.0495	53.1885	-19.7276
15	8.5815	1.0166	-1.0112	1.8073	-0.9285	3.2074	0.2073	0.0469	-0.89	0.0842	-0.2531	-0.2591	0.4117	0.0815	0.0459	0.1113	0.0173	-0.0833	0.1357	0.1335	0.1698	4.3121	49.2817	-11.6182
16	1.2837	-0.5085	-0.7657	2.6752	0.6679	2.6204	0.1198	-0.4941	-0.0128	0.3064	-0.118	-0.267	0.0149	-0.0936	-0.0018	0.044	0.0195	-0.0792	0.2908	0.1027	0.027	0.3738	60.3235	-1.8869
17	7.6597	0.2041	10.0267	16.6782	-2.1372	13.4718	0.44	-0.8922	-0.2862	1.7542	-0.0382	-0.1409	0.0633	-0.408	-0.4018	0.2916	-0.0933	-0.0563	0.378	0.1181	-0.0393	-5.5401	57.9902	7.8266
18	1.9647	-5.3727	2.1656	28.5362	-9.1162	24.4814	-0.5967	-0.2349	0.3675	0.7749	1.1222	1.0022	0.182	-1.8742	-0.5255	0.0721	0.0845	-0.0005	0.3812	0.0034	0.0461	-10.4885	67.7201	-3.5776
19	4.4773	0.3637	-0.0544	1.7204	-0.8739	5.3342	-0.2101	-0.4079	0.4778	0.2513	0.0077	0.1361	-0.7746	-0.4066	0.2023	0.2698	0.0686	-0.0914	0.0459	-0.0379	0.1649	-0.5268	79.4056	-9.3496
20	10.2385	-7.7332	5.272	25.0423	-11.1691	21.3456	-0.2108	-1.2336	1.1111	1.8892	-0.1087	0.3513	-1.3363	-0.4147	0.3194	0.1821	0.081	0.0999	0.2494	-0.111	0.1197	-8.6853	74.7266	4.7637

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 - 54	1 - 54
2	2	A	A	55 - 73	55 - 73
3	3	A	A	74 - 104	74 - 104
4	4	A	A	105 - 114	105 - 114
5	5	A	A	115 - 138	115 - 138
6	6	A	A	139 - 208	139 - 208
7	7	A	A	209 - 230	209 - 230
8	8	A	A	231 - 235	231 - 235
9	9	A	A	236 - 266	236 - 266
10	10	A	A	267 - 288	267 - 288
11	11	B	B	1 - 38	1 - 38
12	12	B	B	39 - 100	39 - 100
13	13	B	B	101 - 113	101 - 113
14	14	B	B	114 - 147	114 - 147
15	15	B	B	148 - 173	148 - 173
16	16	B	B	174 - 208	174 - 208
17	17	B	B	209 - 223	209 - 223
18	18	B	B	224 - 232	224 - 232
19	19	B	B	233 - 273	233 - 273
20	20	B	B	274 - 288	274 - 288

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