PDB-5x20: The ternary structure of D-mandelate dehydrogenase with NADH and ...

ID or keywords:

Entry

Database: PDB / ID: 5x20

Title

The ternary structure of D-mandelate dehydrogenase with NADH and anilino(oxo)acetate

Components

2-dehydropantoate 2-reductase

Keywords

OXIDOREDUCTASE / Rossmann Fold / Dehydrogenase / NADH binding

Function / homology

Function and homology information

2-dehydropantoate 2-reductase / 2-dehydropantoate 2-reductase activity / pantothenate biosynthetic process / NADP binding / cytoplasm
Similarity search - Function

Biological species

Enterococcus faecium DO (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Furukawa, N. / Miyanaga, A. / Nakajima, M. / Taguchi, H.

Citation

Journal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: The ternary complex structure of d-mandelate dehydrogenase with NADH and anilino(oxo)acetate.
Authors: Furukawa, N. / Miyanaga, A. / Nakajima, M. / Taguchi, H.

History

Deposition	Jan 29, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 5, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 6, 2017	Group: Data collection / Database references / Category: citation / diffrn_source Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site
Revision 1.2	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5x20.cif.gz	662.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5x20_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	5x20_full_validation.pdf.gz	2 MB	Display
Data in XML	5x20_validation.xml.gz	66.4 KB	Display
Data in CIF	5x20_validation.cif.gz	88.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x2/5x20 ftp://data.pdbj.org/pub/pdb/validation_reports/x2/5x20	HTTPS FTP

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Related structure data

Related structure data	3wfiS 3wfj S: Starting model for refinement
Similar structure data	5ayv-d 4yca-d 3wfj-2 6dq5-2 6dq6-2 3wfj-1 1vbu-d 6do1-2 3hwr-d 5l9a-d 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

Related structure data

3wfiS

3wfj

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#127 - Jul 2010 Crystallins similarity (2) #111 - Mar 2009 Hydrogenase similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: 2-dehydropantoate 2-reductase

B: 2-dehydropantoate 2-reductase

C: 2-dehydropantoate 2-reductase

D: 2-dehydropantoate 2-reductase

E: 2-dehydropantoate 2-reductase

F: 2-dehydropantoate 2-reductase

hetero molecules

214 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 2-dehydropantoate 2-reductase

B: 2-dehydropantoate 2-reductase

hetero molecules

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

2

C: 2-dehydropantoate 2-reductase

D: 2-dehydropantoate 2-reductase

hetero molecules

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

3

E: 2-dehydropantoate 2-reductase

F: 2-dehydropantoate 2-reductase

hetero molecules

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

Unit cell

Length a, b, c (Å)	96.300, 111.950, 108.940
Angle α, β, γ (deg.)	90.00, 96.65, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	1 - 312
2	1	B	1 - 312
1	2	A	1 - 311
2	2	C	1 - 311
1	3	A	1 - 312
2	3	D	1 - 312
1	4	A	50 - 310
2	4	E	7 - 310
1	5	A	102 - 311
2	5	F	102 - 311
1	6	B	1 - 311
2	6	C	1 - 311
1	7	B	1 - 312
2	7	D	1 - 312
1	8	B	50 - 310
2	8	E	7 - 310
1	9	B	102 - 311
2	9	F	102 - 311
1	10	C	1 - 310
2	10	D	1 - 310
1	11	C	50 - 310
2	11	E	7 - 310
1	12	C	102 - 310
2	12	F	102 - 310
1	13	D	50 - 310
2	13	E	7 - 310
1	14	D	102 - 311
2	14	F	102 - 311
1	15	E	102 - 310
2	15	F	102 - 310

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein	2-dehydropantoate 2-reductase / Ketopantoate reductase Mass: 34372.484 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecium DO (bacteria) / Gene: panE, HMPREF0351_10295 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q3Y316, 2-dehydropantoate 2-reductase

#1: Protein

2-dehydropantoate 2-reductase / Ketopantoate reductase

Mass: 34372.484 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Enterococcus faecium DO (bacteria) / Gene: panE, HMPREF0351_10295 / Plasmid: pET3a / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q3Y316, 2-dehydropantoate 2-reductase

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Non-polymers , 5 types, 388 molecules

#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-AOT / 2-oxidanylidene-2-phenylazanyl-ethanoic acid Mass: 165.146 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₈H₇NO₃
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.83 Å³/Da / Density % sol: 56.51 %
Crystal grow	Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1 M cacodylate-Na (pH 5.0), 0.17 M ammonium sulfate, 22.5% PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 26, 2014
Radiation	Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.4→43.98 Å / Num. obs: 89403 / % possible obs: 99.6 % / Redundancy: 3.6 % / Net I/σ(I): 8.7
Reflection shell	Resolution: 2.4→2.53 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 12887 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0032	refinement
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3WFI

3wfi

Resolution: 2.4→29.82 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.92 / SU B: 12.048 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.304 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21831	4479	5 %	RANDOM
R_work	0.18413	-	-	-
obs	0.18588	84874	99.54 %	-

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: 37.36 Å²

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refinement step

Cycle: 1 / Resolution: 2.4→29.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12866	0	478	342	13686

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.019	13535
X-RAY DIFFRACTION	r_bond_other_d	0.009	0.02	13005
X-RAY DIFFRACTION	r_angle_refined_deg	1.759	2	18262
X-RAY DIFFRACTION	r_angle_other_deg	1.521	3.001	30030
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.847	5	1657
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.537	26.161	560
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.198	15	2422
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.834	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	2102
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	14920
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	2839
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	2.321	2.605	6670
X-RAY DIFFRACTION	r_mcbond_other	2.321	2.605	6669
X-RAY DIFFRACTION	r_mcangle_it	3.575	3.885	8310
X-RAY DIFFRACTION	r_mcangle_other	3.575	3.886	8311
X-RAY DIFFRACTION	r_scbond_it	3.136	2.971	6865
X-RAY DIFFRACTION	r_scbond_other	3.136	2.971	6865
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.88	4.295	9952
X-RAY DIFFRACTION	r_long_range_B_refined	6.498	20.444	15260
X-RAY DIFFRACTION	r_long_range_B_other	6.487	20.412	15159
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	19749	0.08
1	2	B	19749	0.08
2	1	A	19322	0.09
2	2	C	19322	0.09
3	1	A	19236	0.1
3	2	D	19236	0.1
4	1	A	13458	0.11
4	2	E	13458	0.11
5	1	A	10177	0.12
5	2	F	10177	0.12
6	1	B	19424	0.09
6	2	C	19424	0.09
7	1	B	19220	0.1
7	2	D	19220	0.1
8	1	B	13416	0.11
8	2	E	13416	0.11
9	1	B	10117	0.12
9	2	F	10117	0.12
10	1	C	19036	0.1
10	2	D	19036	0.1
11	1	C	13420	0.11
11	2	E	13420	0.11
12	1	C	10047	0.13
12	2	F	10047	0.13
13	1	D	13366	0.11
13	2	E	13366	0.11
14	1	D	10072	0.12
14	2	F	10072	0.12
15	1	E	10104	0.12
15	2	F	10104	0.12

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.3	337	-
R_work	0.239	6122	-
obs	-	-	98.73 %

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	0.7407	0.0363	0.3769	0.342	0.0527	0.2331	-0.0584	-0.0018	0.0355	0.0154	0.0096	0.0161	0.0081	0.0065	0.0488	0.0442	-0.0013	0.019	0.0519	-0.0066	0.0506	29.353	-26.019	24.817
2	0.418	-0.0958	-0.0369	0.1468	0.0183	0.4155	-0.0141	0.0968	-0.059	-0.005	-0.0525	0.0088	0.0195	-0.0653	0.0666	0.0617	-0.0094	0.0007	0.0651	-0.029	0.0479	72.86	-23.844	40.983
3	0.806	0.4279	-0.5333	0.677	-0.6316	0.6352	-0.0301	-0.1211	-0.1752	0.0187	-0.2052	-0.2322	-0.0192	0.1761	0.2353	0.026	0.0237	0.0094	0.1037	0.1007	0.1573	25.319	-0.059	46.302
4	0.2559	-0.286	0.0223	0.7804	0.1448	0.3772	0.0017	-0.0141	0.0109	0.0993	0.0579	-0.066	-0.0502	-0.0111	-0.0596	0.08	0.0083	0.0099	0.0292	0.0248	0.0577	6.698	16.44	10.446
5	0.8384	0.393	1.0844	0.3926	0.3702	1.4981	-0.3645	0.1794	0.294	-0.1807	-0.0111	0.1396	-0.4483	0.2964	0.3756	0.1606	-0.0915	-0.1325	0.1482	0.0991	0.1234	69.254	13.372	30.365
6	0.1317	-0.1306	0.306	0.1347	-0.354	1.2008	0.1672	-0.0015	-0.0379	-0.1465	0.0207	0.0493	0.2229	-0.1451	-0.1879	0.2616	0.0309	-0.0286	0.0607	0.0534	0.0596	55.2347	4.5164	-7.4754

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 312
2	X-RAY DIFFRACTION	1	A	401 - 410
3	X-RAY DIFFRACTION	2	B	1 - 311
4	X-RAY DIFFRACTION	2	B	401 - 409
5	X-RAY DIFFRACTION	3	C	1 - 312
6	X-RAY DIFFRACTION	3	A	411
7	X-RAY DIFFRACTION	3	C	401 - 413
8	X-RAY DIFFRACTION	4	D	7 - 311
9	X-RAY DIFFRACTION	4	D	401 - 405
10	X-RAY DIFFRACTION	5	E	1 - 312
11	X-RAY DIFFRACTION	5	E	401 - 407
12	X-RAY DIFFRACTION	6	F	102 - 312
13	X-RAY DIFFRACTION	6	F	401

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