PDB-8wl4: The structure of D-mandelate dehydrogenase with L103G and T143G m...

ID or keywords:

Entry

Database: PDB / ID: 8wl4

Title

The structure of D-mandelate dehydrogenase with L103G and T143G mutations

Components

2-dehydropantoate 2-reductase

Keywords

OXIDOREDUCTASE / D-mandelate dehydrogenase

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

Levilactobacillus brevis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

Liu, F. / Rao, Z.M.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: The structure of D-mandelate dehydrogenase with L103G and T143G mutations
Authors: Liu, F. / Rao, Z.M.

History

Deposition	Sep 29, 2023	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Oct 2, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8wl4.cif.gz	240.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8wl4.ent.gz	195.4 KB	Display	PDB format
PDBx/mmJSON format	8wl4.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8wl4_validation.pdf.gz	434.8 KB	Display	wwPDB validaton report
Full document	8wl4_full_validation.pdf.gz	439.2 KB	Display
Data in XML	8wl4_validation.xml.gz	24.6 KB	Display
Data in CIF	8wl4_validation.cif.gz	32.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wl/8wl4 ftp://data.pdbj.org/pub/pdb/validation_reports/wl/8wl4	HTTPS FTP

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Related structure data

Similar structure data	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	#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

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

1

A: 2-dehydropantoate 2-reductase

B: 2-dehydropantoate 2-reductase

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

Unit cell

Length a, b, c (Å)	82.620, 131.990, 58.640
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-414- HOH
2	1	B-413- HOH

#1: Protein	2-dehydropantoate 2-reductase / D-mandelate dehydrogenase / Ketopantoate reductase Mass: 33284.559 Da / Num. of mol.: 2 / Mutation: A103G,T143G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Levilactobacillus brevis (bacteria) / Gene: CNR30_12720, UCCLB556_2064, LbMDH / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A7Z6MKR0, 2-dehydropantoate 2-reductase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

2-dehydropantoate 2-reductase / D-mandelate dehydrogenase / Ketopantoate reductase

Mass: 33284.559 Da / Num. of mol.: 2 / Mutation: A103G,T143G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Levilactobacillus brevis (bacteria) / Gene: CNR30_12720, UCCLB556_2064, LbMDH / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A7Z6MKR0, 2-dehydropantoate 2-reductase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.4 Å³/Da / Density % sol: 48.78 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, hanging drop Details: 0.4 M NaCl, 0.05M Tris pH 8.5, 25% Polyethylene glycol 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.9786 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 14, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.55→44.96 Å / Num. obs: 19800 / % possible obs: 96.8 % / Redundancy: 2.5 % / CC_1/2: 0.996 / Net I/σ(I): 9.7
Reflection shell	Resolution: 2.55→2.66 Å / Num. unique obs: 19800 / CC_1/2: 0.996

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.55→44.96 Å / Cor.coef. F_o:F_c: 0.903 / Cor.coef. F_o:F_c free: 0.837 / SU B: 24.624 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29449	863	4.4 %	RANDOM
R_work	0.24622	-	-	-
obs	0.24834	18936	96.6 %	-

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: 42.329 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-10.25 Å²	0 Å²	-1.58 Å²
2-	-	-1.05 Å²	0 Å²
3-	-	-	11.3 Å²

Refinement step

Cycle: 1 / Resolution: 2.55→44.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4678	0	0	40	4718

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	4790
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4562
X-RAY DIFFRACTION	r_angle_refined_deg	1.132	1.935	6554
X-RAY DIFFRACTION	r_angle_other_deg	0.745	3	10464
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.539	5	630
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.622	26.602	206
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.698	15	754
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.167	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.059	0.2	792
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	5602
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1036
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	0.694	2.427	2500
X-RAY DIFFRACTION	r_mcbond_other	0.694	2.427	2499
X-RAY DIFFRACTION	r_mcangle_it	1.284	3.642	3126
X-RAY DIFFRACTION	r_mcangle_other	1.284	3.642	3127
X-RAY DIFFRACTION	r_scbond_it	0.334	2.415	2288
X-RAY DIFFRACTION	r_scbond_other	0.334	2.415	2289
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	0.699	3.624	3425
X-RAY DIFFRACTION	r_long_range_B_refined	2.763	28.591	5385
X-RAY DIFFRACTION	r_long_range_B_other	2.753	28.583	5380
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 9959 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.03 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 2.55→2.616 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.309	52	-
R_work	0.308	1250	-
obs	-	-	86.74 %

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	4.2825	-2.6398	-1.8552	4.6687	1.4412	0.8335	-0.1862	-0.2173	0.2682	-0.0181	0.301	-0.2148	0.0643	0.1167	-0.1148	0.2089	0.0256	-0.087	0.087	0.0111	0.2019	25.9425	29.3747	15.2804
2	0.8551	-1.3247	0.2773	3.6623	-0.0268	0.4106	-0.1149	-0.0776	0.0859	0.2712	0.0139	-0.2598	0.0388	0.0933	0.1011	0.222	0.0325	-0.0168	0.1378	0.0173	0.1737	36.1734	26.4043	15.6871
3	2.9178	1.6674	-0.7071	1.9727	-0.1144	0.258	-0.263	-0.0635	-0.1996	0.3709	0.1608	0.2111	0.218	0.0884	0.1021	0.4189	0.1365	0.0786	0.0846	0.0036	0.2636	22.8631	15.4386	17.0381
4	1.1084	-2.5271	-0.2526	5.7808	0.594	0.0845	-0.1073	-0.0609	-0.0063	0.1943	0.074	0.0499	0.0172	-0.0818	0.0333	0.2374	0.0279	0.0224	0.3527	-0.1009	0.1538	14.5178	16.4078	12.0491
5	1.2557	-0.4212	1.2807	0.9154	0.3453	2.0869	-0.1778	-0.0185	0.0961	-0.0292	-0.076	0.0957	-0.2477	-0.1027	0.2539	0.2815	0.0032	-0.0121	0.0112	0.0012	0.2512	18.1779	28.3301	8.459
6	0.6832	0.3297	-0.4977	0.7566	-0.0737	0.8525	0.0684	0.0169	0.1657	0.0055	0.072	-0.1384	-0.1164	-0.0398	-0.1404	0.2626	0.02	0.0292	0.0945	-0.0006	0.1939	21.8946	13.6785	-10.8782
7	3.2679	-2.3728	-0.3863	1.8064	0.2276	0.1004	0.091	-0.0192	0.2179	-0.0179	0.0098	-0.107	0.0176	-0.007	-0.1007	0.2576	0.0109	-0.037	0.1455	-0.0076	0.1977	18.0218	1.6559	-5.6035
8	3.0998	1.6963	0.3441	1.2139	0.1114	0.0803	-0.1202	-0.0032	-0.2664	-0.1243	0.0954	-0.1159	-0.0275	-0.0052	0.0248	0.2804	-0.0673	-0.0021	0.0967	0.0267	0.2319	32.2481	-27.2249	13.7988
9	2.0821	-1.5543	0.5727	2.8988	0.6996	0.9349	-0.1459	0.0773	-0.0084	-0.1887	0.1805	0.1288	-0.1555	0.2048	-0.0346	0.3474	-0.0794	-0.1158	0.0732	-0.0522	0.2477	22.864	-15.1095	12.2656
10	1.0811	2.095	-0.4228	4.677	-0.5212	0.3133	-0.0837	0.2341	-0.0743	-0.0867	0.0061	-0.0189	0.0199	-0.3056	0.0776	0.2729	-0.0057	-0.0803	0.3607	-0.1129	0.1403	14.5142	-16.1068	17.2873
11	0.6844	0.0211	-1.2161	0.6902	-0.0489	2.1721	-0.2359	0.0778	-0.1598	0.0627	-0.0919	0.0878	0.3833	-0.1439	0.3278	0.2759	-0.0192	-0.0303	0.0267	-0.0639	0.2674	18.1703	-28.0207	20.8658
12	0.5824	0.1303	0.5825	0.8283	-0.2022	0.8088	0.0525	-0.0041	-0.1659	-0.0256	0.059	-0.1443	0.114	-0.0629	-0.1115	0.2732	0.0042	-0.0256	0.0958	-0.0111	0.2034	21.8828	-13.3716	40.2016
13	3.0228	0.3291	1.2322	1.2095	0.2423	0.5162	0.1246	0.0816	0.0179	-0.1466	-0.1135	-0.0185	0.0203	0.0091	-0.0111	0.2755	0.0023	0.0033	0.1624	0.0068	0.152	18.0094	-1.3203	34.939

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-2 - 21
2	X-RAY DIFFRACTION	2	A	22 - 61
3	X-RAY DIFFRACTION	3	A	62 - 93
4	X-RAY DIFFRACTION	4	A	94 - 117
5	X-RAY DIFFRACTION	5	A	118 - 178
6	X-RAY DIFFRACTION	6	A	179 - 275
7	X-RAY DIFFRACTION	7	A	276 - 309
8	X-RAY DIFFRACTION	8	B	-2 - 61
9	X-RAY DIFFRACTION	9	B	62 - 93
10	X-RAY DIFFRACTION	10	B	94 - 117
11	X-RAY DIFFRACTION	11	B	118 - 178
12	X-RAY DIFFRACTION	12	B	179 - 275
13	X-RAY DIFFRACTION	13	B	276 - 309

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