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

ID or keywords:

Entry

Database: PDB / ID: 2nuw

Title

2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius, native structure at 1.8 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: 1.8 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	2nuw.cif.gz	137.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2nuw.ent.gz	107.5 KB	Display	PDB format
PDBx/mmJSON format	2nuw.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2nuw_validation.pdf.gz	425.4 KB	Display	wwPDB validaton report
Full document	2nuw_full_validation.pdf.gz	427.8 KB	Display
Data in XML	2nuw_validation.xml.gz	25.4 KB	Display
Data in CIF	2nuw_validation.cif.gz	37.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nu/2nuw ftp://data.pdbj.org/pub/pdb/validation_reports/nu/2nuw	HTTPS FTP

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Related structure data

Related structure data	2nuxC 2nuyC 1w3nS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2nuy-1 2nux-1 5lky-d 3lcx-d 5ud6-d 4woz-1 3flu-d 3lcw-d 3na8-d 4ama-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)	108.160, 108.160, 171.852
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 410 / 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: 4.45 Å³/Da / Density % sol: 72.39 %
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: 1.8→30 Å / Num. obs: 107995 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.9 % / B_iso Wilson estimate: 30.218 Å² / R_sym value: 0.096 / Net I/σ(I): 14.14
Reflection shell	Resolution: 1.8→1.88 Å / Redundancy: 4 % / R_merge(I) obs: 0.559 / Mean I/σ(I) obs: 2.3 / Num. measured obs: 52511 / Num. unique all: 13009 / % possible all: 99.8

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Phasing

Phasing MR

R_factor: 0.523 / Cor.coef. F_o:F_c: 0.445

	Highest resolution	Lowest resolution
Rotation	3 Å	27.1 Å
Translation	3 Å	27.1 Å

Phasing dm

FOM : 0.55 / FOM acentric: 0.55 / FOM centric: 0.54 / Reflection: 41108 / Reflection acentric: 38250 / Reflection centric: 2858

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
2.4-2.6	0.15	0.15	0.11	7396	6965	431
2.6-3	0.38	0.38	0.34	12924	12172	752
3-3.4	0.68	0.69	0.6	7171	6713	458
3.4-4.3	0.84	0.84	0.77	6958	6443	515
4.3-6.9	0.87	0.88	0.79	5190	4711	479
6.9-27.101	0.91	0.92	0.86	1469	1246	223

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
MOLREP		phasing
RESOLVE	2.08	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 1w3n

1w3n

Resolution: 1.8→29.35 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.966 / SU B: 4.249 / SU ML: 0.064 / 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: 0.071 / ESU R Free: 0.073 / 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	0.179	5421	5 %	RANDOM
R_work	0.157	-	-	-
obs	0.158	107995	99.96 %	-
all	-	108033	-	-

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: 13.196 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.18 Å²	1.09 Å²	0 Å²
2-	-	2.18 Å²	0 Å²
3-	-	-	-3.27 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→29.35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4598	0	1	410	5009

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	4736
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3238
X-RAY DIFFRACTION	r_angle_refined_deg	1.472	1.995	6429
X-RAY DIFFRACTION	r_angle_other_deg	0.891	3	7970
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.898	5	578
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.432	24.808	208
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.35	15	855
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.683	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.101	0.2	733
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5168
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	892
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.3	986
X-RAY DIFFRACTION	r_nbd_other	0.186	0.3	3479
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.5	2370
X-RAY DIFFRACTION	r_nbtor_other	0.09	0.5	2362
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.144	0.15	537
X-RAY DIFFRACTION	r_metal_ion_refined	0.025	0.5	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.103	0.3	10
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.174	0.3	17
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.143	0.15	29
X-RAY DIFFRACTION	r_mcbond_it	4.23	1.5	3764
X-RAY DIFFRACTION	r_mcbond_other	1.28	1.5	1152
X-RAY DIFFRACTION	r_mcangle_it	4.454	2	4721
X-RAY DIFFRACTION	r_scbond_it	8.597	3	2143
X-RAY DIFFRACTION	r_scangle_it	11.714	4.5	1708

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.317	407	-
R_work	0.27	7456	-
obs	-	7863	99.81 %

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	4.2846	4.5921	-2.4064	10.2562	-5.2474	7.1433	-0.0448	0.0874	-0.2054	-0.2913	-0.0357	0.049	0.171	-0.3494	0.0804	0.1669	0.0628	-0.024	0.1742	-0.0506	0.2092	-6.5593	70.8748	37.9188
2	1.3757	0.1409	0.2256	2.2029	0.3503	3.5837	0.0713	0.0329	-0.1477	-0.2789	-0.0987	0.1571	0.2231	-0.0292	0.0274	0.1898	0.0633	-0.0063	0.1444	-0.03	0.2103	-3.3613	68.4507	36.084
3	0.4772	0.1471	0.2921	1.4536	0.6596	3.1916	0.0684	0.027	-0.0852	-0.1252	-0.0388	-0.1488	0.2134	0.1984	-0.0296	0.1535	0.0783	0.0219	0.1635	-0.0074	0.2018	7.4561	67.4708	41.3436
4	9.8185	-3.3785	-0.6826	14.6926	6.6272	11.6587	0.0681	-0.2275	0.2961	0.1478	0.071	-0.6636	-0.481	0.5605	-0.1391	0.1326	-0.0138	-0.0517	0.2364	0.0244	0.2667	16.4144	79.2245	56.0082
5	2.8657	-1.2604	-1.098	2.6857	0.7768	4.0674	0.0937	-0.0055	0.1161	-0.1421	-0.0268	-0.4537	-0.1412	0.5412	-0.0669	0.0818	0.0226	0.0272	0.174	0.0123	0.196	14.1885	77.6191	43.9739
6	4.6112	-2.9363	-0.6846	6.0559	2.2112	4.3909	-0.039	0.0388	0.2617	-0.4689	0.037	-0.7236	-0.4179	0.6196	0.002	0.1479	0.0192	0.0404	0.0819	0.0327	0.1633	10.9233	87.8966	37.8037
7	1.5583	1.3911	0.1248	3.0144	-0.1646	1.6865	-0.0763	0.1511	-0.0243	-0.6542	-0.0235	0.0871	-0.2381	-0.0393	0.0998	0.2663	0.0975	-0.0287	0.1002	-0.0142	0.1162	-2.4581	86.41	30.4938
8	5.8918	3.2941	-5.2107	4.8122	-4.3528	14.0368	-0.2705	0.4579	0.1744	-0.4684	0.1348	0.2872	-0.6578	-0.6917	0.1358	0.3464	0.1165	-0.1426	0.1423	-0.0226	0.2426	-9.4978	92.7344	29.9249
9	2.0514	-0.0969	-0.1181	3.6185	-0.3039	4.3778	0.014	-0.0103	0.0482	-0.1388	-0.0278	0.4354	-0.0412	-0.6984	0.0139	0.0855	0.0279	-0.0475	0.2454	-0.0441	0.2545	-16.874	75.8216	41.7965
10	15.7196	4.8537	-18.0536	5.7129	-6.9609	34.9821	-0.5618	0.9103	-0.1112	-0.8265	0.2813	0.6742	0.1112	-1.6497	0.2805	0.2787	0.1705	-0.2333	0.438	0.0072	0.4626	-20.4773	87.2189	29.5686
11	1.9455	-0.6552	-0.6166	2.0397	0.8505	4.8347	0.0699	-0.0212	-0.2648	0.2314	-0.1148	-0.1953	0.4746	0.4002	0.0449	0.1387	0.003	-0.0298	0.1091	0.0385	0.2001	10.2176	63.6286	71.9535
12	1.0445	0.1668	-0.3504	2.0622	1.3828	4.9163	0.093	0.0009	-0.2127	0.1681	-0.0892	-0.0873	0.4523	0.0305	-0.0038	0.1286	-0.0147	-0.0045	0.1032	0.0266	0.1725	3.8114	65.3847	68.4908
13	0.8971	0.135	0.0118	0.987	-0.6077	3.2837	0.068	-0.0127	-0.1351	0.0878	-0.1029	0.0897	0.3296	-0.2085	0.0349	0.1518	-0.0525	0.0123	0.1264	-0.0029	0.1864	-4.4801	64.2881	65.4064
14	22.7864	3.148	-1.8681	15.6851	-3.8711	18.3903	-0.078	0.6114	0.5133	-0.3181	0.0589	0.338	-0.4546	-0.672	0.0191	0.1767	0.0586	-0.0495	0.2413	-0.0299	0.2518	-12.6036	81.1324	53.0074
15	1.7131	0.8634	-0.0964	2.6211	-0.4393	3.0971	0.0759	0.057	0.0291	0.0716	-0.0868	0.3741	-0.0172	-0.4708	0.0109	0.0756	-0.0151	0.0153	0.1662	-0.0216	0.1864	-10.3801	74.434	64.3126
16	1.43	1.3137	0.2435	4.2563	0.8385	2.5467	0.0763	-0.0411	0.223	0.3118	-0.235	0.596	-0.2631	-0.5105	0.1587	0.1255	0.0013	0.0432	0.126	-0.0364	0.1859	-9.1004	82.2914	72.2529
17	1.4455	-0.4257	-0.1987	1.8173	0.1738	2.4475	0.0014	-0.1648	-0.1016	0.4778	-0.0474	-0.0118	-0.0679	0.0506	0.046	0.1992	-0.0773	-0.0033	0.0826	0.0266	0.1114	3.7328	79.3476	80.427
18	5.0149	-3.1028	-5.8117	4.098	1.9978	16.659	-0.0711	-0.5792	-0.0969	0.6288	0.1129	-0.2923	-0.9085	0.9187	-0.0417	0.3142	-0.103	-0.1034	0.2091	0.0122	0.1985	12.5739	85.2271	83.4163
19	2.3991	0.4474	-0.1462	3.1138	0.0947	5.2702	-0.0034	-0.1291	-0.0372	0.0399	-0.0805	-0.423	0.0367	0.7934	0.084	0.0974	0.0398	-0.0339	0.2973	0.0435	0.2786	19.7984	71.883	67.0563
20	4.1801	-1.5841	-5.4346	3.292	-1.1204	10.8222	0.1619	-0.6229	0.0317	0.4932	-0.0667	-0.2402	0.0414	1.2135	-0.0953	0.4935	-0.1147	-0.0792	0.7377	-0.0014	0.5616	24.0424	79.6942	81.3554

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 - 16	1 - 16
2	2	A	A	17 - 56	17 - 56
3	3	A	A	57 - 104	57 - 104
4	4	A	A	105 - 113	105 - 113
5	5	A	A	114 - 149	114 - 149
6	6	A	A	150 - 173	150 - 173
7	7	A	A	174 - 211	174 - 211
8	8	A	A	212 - 233	212 - 233
9	9	A	A	234 - 273	234 - 273
10	10	A	A	274 - 288	274 - 288
11	11	B	B	1 - 30	1 - 30
12	12	B	B	31 - 56	31 - 56
13	13	B	B	57 - 104	57 - 104
14	14	B	B	105 - 110	105 - 110
15	15	B	B	111 - 142	111 - 142
16	16	B	B	143 - 168	143 - 168
17	17	B	B	169 - 210	169 - 210
18	18	B	B	211 - 233	211 - 233
19	19	B	B	234 - 272	234 - 272
20	20	B	B	273 - 288	273 - 288

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Validation report

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Related structure data

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Links

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Assembly

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Experimental details

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Experiment

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Sample preparation

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Data collection

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi