PDB-3oet: D-Erythronate-4-Phosphate Dehydrogenase complexed with NAD

ID or keywords:

Entry

Database: PDB / ID: 3oet

Title

D-Erythronate-4-Phosphate Dehydrogenase complexed with NAD

Components

Erythronate-4-phosphate dehydrogenase

Keywords

OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Erythronate-4-phosphate dehydrogenase / NAD / Salmonella typhimurium LT2

Function / homology

Function and homology information

4-phosphoerythronate dehydrogenase / 4-phosphoerythronate dehydrogenase activity / 'de novo' pyridoxal 5'-phosphate biosynthetic process / pyridoxine biosynthetic process / NAD binding / protein dimerization activity / cytosol
Similarity search - Function

Biological species

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.36 Å

Authors

Filippova, E.V. / Wawrzak, Z. / Onopriyenko, O. / Savchenko, A. / Edwards, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: D-Erythronate-4-Phosphate Dehydrogenase complexed with NAD
Authors: Filippova, E.V. / Wawrzak, Z. / Onopriyenko, O. / Savchenko, A. / Edwards, A. / Anderson, W.F.

History

Deposition	Aug 13, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 25, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Sep 6, 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 / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Dec 6, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3oet.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb3oet.ent.gz	971.9 KB	Display	PDB format
PDBx/mmJSON format	3oet.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oe/3oet ftp://data.pdbj.org/pub/pdb/validation_reports/oe/3oet	HTTPS FTP

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Related structure data

Related structure data	2o4cS S: Starting model for refinement
Similar structure data	5dt9-1 3wxm-1 3od1-d 2o4c-d 3mk7-2 3rc8-d 3mk7-1 3zrl-d 5djq-2 4h1l-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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
Other databases	TargetDB: idp90820

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Erythronate-4-phosphate dehydrogenase

B: Erythronate-4-phosphate dehydrogenase

C: Erythronate-4-phosphate dehydrogenase

D: Erythronate-4-phosphate dehydrogenase

E: Erythronate-4-phosphate dehydrogenase

F: Erythronate-4-phosphate dehydrogenase

G: Erythronate-4-phosphate dehydrogenase

H: Erythronate-4-phosphate dehydrogenase

hetero molecules

340 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Erythronate-4-phosphate dehydrogenase

H: Erythronate-4-phosphate dehydrogenase

hetero molecules

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

2

B: Erythronate-4-phosphate dehydrogenase

E: Erythronate-4-phosphate dehydrogenase

hetero molecules

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

3

C: Erythronate-4-phosphate dehydrogenase

F: Erythronate-4-phosphate dehydrogenase

hetero molecules

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

4

D: Erythronate-4-phosphate dehydrogenase

G: Erythronate-4-phosphate dehydrogenase

hetero molecules

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

5

A: Erythronate-4-phosphate dehydrogenase

hetero molecules

defined by software
42.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

B: Erythronate-4-phosphate dehydrogenase

hetero molecules

defined by software
42.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

C: Erythronate-4-phosphate dehydrogenase

hetero molecules

defined by software
42.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

D: Erythronate-4-phosphate dehydrogenase

hetero molecules

defined by software
42.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

9

E: Erythronate-4-phosphate dehydrogenase

hetero molecules

defined by software
42.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

10

F: Erythronate-4-phosphate dehydrogenase

hetero molecules

defined by software
42.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

11

G: Erythronate-4-phosphate dehydrogenase

hetero molecules

defined by software
42.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

12

H: Erythronate-4-phosphate dehydrogenase

hetero molecules

defined by software
42.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	93.279, 167.765, 103.949
Angle α, β, γ (deg.)	90.00, 93.88, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Erythronate-4-phosphate dehydrogenase Mass: 41856.012 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / Gene: pdxB, STM2370 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL References: UniProt: P60802, 4-phosphoerythronate dehydrogenase
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.42 Å³/Da / Density % sol: 49.25 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% PEG 3350,0.2M NH4 Acetate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9795 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 12, 2010 / Details: MIRRORS
Radiation	Monochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.36→103.7 Å / Num. all: 128763 / Num. obs: 128763 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / B_iso Wilson estimate: 51.9 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 20.3
Reflection shell	Resolution: 2.36→2.39 Å / Redundancy: 6.3 % / R_merge(I) obs: 0.64 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
CCP4		model building
MrBUMP		phasing
PHENIX		model building
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-3000		data scaling
CCP4		phasing
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDBID 2O4C

2o4c

Resolution: 2.36→30.19 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.917 / SU B: 17.941 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25331	6470	5 %	RANDOM
R_work	0.1903	-	-	-
obs	0.19346	122293	98.58 %	-
all	-	122293	-	-

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: 46.667 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.05 Å²	0 Å²	1.24 Å²
2-	-	0.13 Å²	0 Å²
3-	-	-	1.09 Å²

Refine analyze

Luzzati coordinate error obs: 0.3 Å

Refinement step

Cycle: LAST / Resolution: 2.36→30.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22878	0	352	556	23786

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	23744
X-RAY DIFFRACTION	r_angle_refined_deg	1.46	1.998	32325
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.802	5	2975
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.606	23.245	1020
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.496	15	3843
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.222	15	214
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	3749
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	17839
X-RAY DIFFRACTION	r_mcbond_it	0.602	1.5	14860
X-RAY DIFFRACTION	r_mcangle_it	1.183	2	23836
X-RAY DIFFRACTION	r_scbond_it	2.401	3	8884
X-RAY DIFFRACTION	r_scangle_it	3.747	4.5	8489

LS refinement shell

Resolution: 2.36→2.422 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.313	438	-
R_work	0.226	8177	-
obs	-	-	89.56 %

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	9.0341	-2.0828	-2.6028	8.3745	5.326	6.2361	-0.0992	-0.098	-1.2744	1.0708	0.3256	-0.1273	0.7813	0.5876	-0.2264	0.2685	0.1069	-0.0876	0.3298	-0.1555	0.4166	31.9452	25.1013	2.0831
2	2.0796	0.1825	0.5018	0.7437	0.2295	1.5233	-0.0044	0.0457	-0.0452	0.0943	0.0208	-0.0002	-0.0132	0.0095	-0.0164	0.1308	0.0315	-0.0074	0.0647	-0.0262	0.0113	11.4367	44.1605	13.1925
3	7.8297	1.4357	-0.7335	3.7062	-0.8211	3.2481	0.0204	0.4718	-0.5599	-0.537	0.5677	0.9033	0.4797	-0.4243	-0.5881	0.1817	-0.1105	-0.1377	0.3052	0.2282	0.667	-33.6898	22.712	-25.4264
4	0.8551	-0.2402	0.0715	1.3919	-0.4174	0.874	-0.0054	-0.0407	-0.0072	-0.0154	0.0847	0.2117	0.0471	-0.1466	-0.0793	0.0378	-0.0246	-0.0053	0.0497	0.0271	0.0424	-14.8728	42.6559	-35.2971
5	6.9281	1.3738	-0.7685	3.8251	-1.2649	3.1661	-0.0396	-0.5242	0.3621	0.2784	0.3451	0.5709	-0.2136	-0.2942	-0.3055	0.2444	0.1744	0.0391	0.4855	0.2411	0.5349	-32.3588	95.5515	24.9304
6	1.3544	0.4542	-0.258	1.0486	-0.3616	1.1774	0.0589	0.103	0.0894	-0.0063	0.0355	0.1456	-0.0549	-0.1354	-0.0944	0.0727	0.0369	0.005	0.0334	0.0208	0.055	-12.7167	76.3897	35.9848
7	5.5787	-0.4114	1.305	7.7205	4.6615	5.8726	0.0047	0.2429	1.428	-0.9091	0.292	-0.5476	-0.756	0.5081	-0.2966	0.157	-0.0588	0.119	0.3163	-0.2279	0.7633	33.8499	93.5909	-1.4722
8	2.0062	-0.5053	-0.4162	0.8729	0.517	0.993	0.0592	-0.0735	0.2292	0.0364	0.0401	-0.0741	-0.0247	0.082	-0.0993	0.0719	-0.0116	0.017	0.016	-0.0187	0.0343	13.1934	74.8109	-12.5146
9	5.4987	-1.0779	-2.0918	2.5321	1.2512	3.9597	0.2201	0.1856	0.4407	-0.1029	-0.1255	-0.2717	-0.275	0.1041	-0.0946	0.1255	0.0208	0.0219	0.1709	0.0169	0.1682	37.4537	55.5947	-37.2762
10	1.4716	0.0923	-0.1096	1.0263	-0.043	1.0799	-0.0521	0.0261	-0.0745	-0.1246	0.0311	-0.1236	0.0959	0.1838	0.021	0.0967	0.0003	0.035	0.0398	-0.0016	0.0249	17.6868	35.5686	-41.3159
11	5.2606	0.618	2.338	2.9486	0.8662	7.2538	0.1022	-0.0521	-0.5285	-0.2654	-0.1688	0.0403	0.7777	0.5162	0.0666	0.2436	0.1022	-0.0035	0.381	-0.0229	0.6304	41.883	66.3296	32.6281
12	1.5034	-0.1688	0.1459	1.3171	-0.1253	1.0449	-0.0535	-0.0407	-0.0012	0.1206	0.0085	-0.1339	-0.0939	0.1213	0.045	0.0753	0.011	-0.0058	0.0276	0.0114	0.021	19.656	83.302	41.7907
13	7.3307	0.6677	1.1812	3.9849	1.841	1.0964	0.1932	-0.3259	-0.9001	-0.1069	-0.1552	0.4513	0.1685	-0.2627	-0.038	0.4594	-0.1292	-0.0753	0.4578	-0.0227	0.6584	-43.5761	70.5175	-10.8984
14	1.3432	-0.3049	0.3901	1.282	0.1443	1.5579	0.0702	0.2577	0.1485	-0.1016	-0.0874	0.0296	-0.0868	-0.1298	0.0172	0.0788	0.0458	0.0229	0.214	-0.0008	0.1562	-18.6934	85.6189	-18.751
15	7.7058	-0.7399	-0.4404	2.5542	-0.0905	1.3905	0.1371	0.6785	0.3327	-0.1174	-0.1791	-0.0731	-0.0934	0.1519	0.042	0.1658	0.0587	-0.0019	0.4161	-0.0277	0.166	-45.5122	48.7402	10.9064
16	3.1033	-0.1324	-0.9842	1.4075	0.1849	1.531	-0.0997	-0.054	-0.4675	0.2599	-0.001	0.1744	0.0269	-0.127	0.1007	0.1577	0.0094	0.0533	0.1394	-0.0026	0.1251	-20.6755	33.5983	18.6402

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-1 - 88
2	X-RAY DIFFRACTION	2	A	89 - 376
3	X-RAY DIFFRACTION	3	B	-2 - 88
4	X-RAY DIFFRACTION	4	B	89 - 376
5	X-RAY DIFFRACTION	5	C	-2 - 88
6	X-RAY DIFFRACTION	6	C	89 - 376
7	X-RAY DIFFRACTION	7	D	-2 - 88
8	X-RAY DIFFRACTION	8	D	89 - 377
9	X-RAY DIFFRACTION	9	E	1 - 88
10	X-RAY DIFFRACTION	10	E	89 - 375
11	X-RAY DIFFRACTION	11	F	1 - 88
12	X-RAY DIFFRACTION	12	F	89 - 376
13	X-RAY DIFFRACTION	13	G	1 - 88
14	X-RAY DIFFRACTION	14	G	89 - 375
15	X-RAY DIFFRACTION	15	H	-1 - 88
16	X-RAY DIFFRACTION	16	H	89 - 376

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