PDB-2yq5: Crystal Structure of D-isomer specific 2-hydroxyacid dehydrogenas...

ID or keywords:

Entry

Database: PDB / ID: 2yq5

Title

Crystal Structure of D-isomer specific 2-hydroxyacid dehydrogenase from Lactobacillus delbrueckii ssp. bulgaricus: NAD complexed form

Components

D-ISOMER SPECIFIC 2-HYDROXYACID DEHYDROGENASE

Keywords

OXIDOREDUCTASE

Function / homology

Function and homology information

D-lactate dehydrogenase (NAD+) activity / NAD binding
Similarity search - Function

Biological species

LACTOBACILLUS DELBRUECKII SUBSP. BULGARICUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Holton, S.J. / Anandhakrishnan, M. / Geerlof, A. / Wilmanns, M.

Citation

Journal: J.Struct.Biol. / Year: 2013
Title: Structural Characterization of D-Isomer Specific 2-Hydroxyacid Dehydrogenase from Lactobacillus Delbrueckii Ssp. Bulgaricus
Authors: Holton, S.J. / Anandhakrishnan, M. / Geerlof, A. / Wilmanns, M.

History

Deposition	Nov 5, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 21, 2012	Provider: repository / Type: Initial release
Revision 1.1	Feb 20, 2013	Group: Database references
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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	2yq5.cif.gz	509.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2yq5.ent.gz	425.7 KB	Display	PDB format
PDBx/mmJSON format	2yq5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2yq5_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	2yq5_full_validation.pdf.gz	1.5 MB	Display
Data in XML	2yq5_validation.xml.gz	49.8 KB	Display
Data in CIF	2yq5_validation.cif.gz	66 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yq/2yq5 ftp://data.pdbj.org/pub/pdb/validation_reports/yq/2yq5	HTTPS FTP

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Related structure data

Related structure data	2yq4C 1dxyS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4prk-1 4prl-1 2yq4-d 6eit-d 4zgs-1 4hy3-d 3ts8-d 5ubt-d 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: D-ISOMER SPECIFIC 2-HYDROXYACID DEHYDROGENASE

B: D-ISOMER SPECIFIC 2-HYDROXYACID DEHYDROGENASE

C: D-ISOMER SPECIFIC 2-HYDROXYACID DEHYDROGENASE

D: D-ISOMER SPECIFIC 2-HYDROXYACID DEHYDROGENASE

A: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

B: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

C: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

D: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

hetero molecules

155 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	92.718, 110.012, 147.736
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
1	2	A
2	2	B
3	2	C
4	2	D
1	3	A
2	3	B
3	3	C
4	3	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	5	A	1 - 90
2	1	1	5	B	1 - 90
3	1	1	5	C	1 - 90
4	1	1	5	D	1 - 90
1	1	2	5	A	94 - 207
2	1	2	5	B	94 - 207
3	1	2	5	C	94 - 207
4	1	2	5	D	94 - 207
1	1	3	5	A	208 - 330
2	1	3	5	B	208 - 330
3	1	3	5	C	208 - 330
4	1	3	5	D	208 - 330

NCS ensembles :

ID
1
2
3

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(-0.943732, 0.054592, -0.326174), (0.040789, -0.959536, -0.278616), (-0.328186, -0.276244, 0.903318)	15.72401, 40.12016, 8.10421
3	given	(-0.997632, 0.001115, 0.068771), (0.012185, 0.986918, 0.160762), (-0.067693, 0.161219, -0.984594)	3.4619, -7.0085, 69.20895
4	given	(0.922547, -0.018788, 0.385428), (-0.039172, -0.998214, 0.045102), (0.383892, -0.056707, -0.921635)	-12.95768, 29.963, 71.83703

#1: Protein	D-ISOMER SPECIFIC 2-HYDROXYACID DEHYDROGENASE / 2-HYDROXYACID DEHYDROGENASE Mass: 38029.238 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LACTOBACILLUS DELBRUECKII SUBSP. BULGARICUS (bacteria) Plasmid: PETM-13 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q1GAA2
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.14 Å³/Da / Density % sol: 61 % / Description: NONE
Crystal grow	Details: 25% PEG 3350, 200MM MGCL2, 100MM HEPES PH7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8726 Å / Relative weight: 1
Reflection	Resolution: 2.75→49.24 Å / Num. obs: 39722 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / R_merge(I) obs: 0.1 / Net I/σ(I): 12.7
Reflection shell	Resolution: 2.75→2.9 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.56 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0029	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DXY

1dxy

Resolution: 2.75→44.99 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.891 / SU B: 28.999 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R Free: 0.381 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25895	1953	4.9 %	RANDOM
R_work	0.18763	-	-	-
obs	0.19122	37669	99.1 %	-

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: 47.897 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.7 Å²	0 Å²	0 Å²
2-	-	3.65 Å²	0 Å²
3-	-	-	-0.95 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→44.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10154	0	176	39	10369

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.02	10549
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.678	1.992	14369
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.999	5	1299
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.898	25.07	426
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.826	15	1774
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.654	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.113	0.2	1688
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	7756
X-RAY DIFFRACTION	r_gen_planes_other
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
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

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	344	medium positional	0.25	0.5
1	2	B	344	medium positional	0.3	0.5
1	3	C	344	medium positional	0.29	0.5
1	4	D	344	medium positional	0.31	0.5
2	1	A	456	medium positional	0.17	0.5
2	2	B	456	medium positional	0.18	0.5
2	3	C	456	medium positional	0.18	0.5
2	4	D	456	medium positional	0.23	0.5
3	1	A	484	medium positional	0.24	0.5
3	2	B	484	medium positional	0.27	0.5
3	3	C	484	medium positional	0.37	0.5
3	4	D	484	medium positional	0.31	0.5
1	1	A	328	loose positional	0.66	5
1	2	B	328	loose positional	0.72	5
1	3	C	328	loose positional	0.78	5
1	4	D	328	loose positional	0.72	5
2	1	A	449	loose positional	0.34	5
2	2	B	449	loose positional	0.37	5
2	3	C	449	loose positional	0.39	5
2	4	D	449	loose positional	0.39	5
3	1	A	431	loose positional	0.44	5
3	2	B	431	loose positional	0.58	5
3	3	C	431	loose positional	0.55	5
3	4	D	431	loose positional	0.51	5
1	1	A	344	medium thermal	3.07	2
1	2	B	344	medium thermal	2.13	2
1	3	C	344	medium thermal	2.27	2
1	4	D	344	medium thermal	3.32	2
2	1	A	456	medium thermal	1.66	2
2	2	B	456	medium thermal	1.86	2
2	3	C	456	medium thermal	1.45	2
2	4	D	456	medium thermal	1.23	2
3	1	A	484	medium thermal	2.27	2
3	2	B	484	medium thermal	2.34	2
3	3	C	484	medium thermal	2.41	2
3	4	D	484	medium thermal	2.52	2
1	1	A	328	loose thermal	3.3	10
1	2	B	328	loose thermal	2.48	10
1	3	C	328	loose thermal	3.13	10
1	4	D	328	loose thermal	3.9	10
2	1	A	449	loose thermal	2.35	10
2	2	B	449	loose thermal	2.49	10
2	3	C	449	loose thermal	2	10
2	4	D	449	loose thermal	2.02	10
3	1	A	431	loose thermal	2.81	10
3	2	B	431	loose thermal	3.29	10
3	3	C	431	loose thermal	3.13	10
3	4	D	431	loose thermal	3.16	10

LS refinement shell

Resolution: 2.75→2.821 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.437	126	-
R_work	0.285	2767	-
obs	-	-	99.83 %

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	8.2366	-0.297	0.6764	2.9304	-0.3087	5.485	-0.1672	-0.4046	-0.4168	0.304	0.203	-0.795	0.1665	1.0692	-0.0358	0.424	0.1178	-0.1151	0.6088	0.0506	0.5097	32.5692	-3.8696	58.6139
2	1.8728	-0.0584	-0.0911	1.1896	-0.3548	1.1805	-0.0116	-0.038	0.0664	0.1924	-0.0502	-0.0626	-0.2777	0.257	0.0618	0.2902	-0.0598	0.004	0.1647	-0.0066	0.0273	5.5386	20.3556	53.1847
3	1.9818	-0.6179	-0.1801	2.502	0.0778	1.4901	-0.02	-0.3047	0.0209	0.2054	-0.0564	-0.3028	-0.2601	0.4176	0.0764	0.2826	-0.0926	-0.0902	0.3293	0.0311	0.0857	14.8222	15.3304	62.6854
4	10.6437	0.6333	2.0266	3.9782	0.7428	2.5134	-0.3887	-0.4264	0.5831	0.17	0.3556	0.9472	-0.4131	-1.1417	0.0332	0.5519	0.1708	0.1312	0.7185	0.0748	0.5724	-34.2951	29.1507	52.3628
5	1.9373	-0.2741	0.8021	1.414	-0.3376	2.1201	0.0308	-0.039	-0.1126	0.0487	-0.0475	0.0751	0.1456	0.0558	0.0167	0.204	-0.0097	0.0037	0.0872	0.0108	0.013	-5.8201	6.048	48.8965
6	1.371	-0.0554	-0.0607	1.92	-0.6574	1.3723	0.0065	-0.1211	-0.0574	-0.0702	0.0976	0.4075	-0.0605	-0.2021	-0.1041	0.2174	0.0082	0.0183	0.1361	-0.0048	0.1123	-18.0698	8.4258	55.7387
7	8.9777	-1.668	1.3797	4.263	0.4942	5.2858	0.1388	0.1982	-0.3322	-0.0927	-0.1459	0.2782	0.222	-0.6478	0.0071	0.3329	-0.0554	-0.0412	0.1229	-0.0145	0.0581	-28.3006	1.4236	12.9698
8	2.6509	1.0941	0.0196	1.3595	-0.1819	0.6545	0.0487	0.0918	0.0773	-0.1026	-0.1125	-0.0442	-0.1367	0.0982	0.0638	0.2359	0.0104	-0.0055	0.0691	0.0197	0.0124	-1.5181	24.6879	24.0527
9	2.4491	2.0628	-0.0582	2.6948	-0.5845	0.7292	-0.0832	0.1867	0.1672	-0.2099	0.0243	0.196	-0.0311	-0.0405	0.0588	0.2769	0.0321	-0.0308	0.105	0.0031	0.0468	-10.7277	22.4514	13.6564
10	10.2959	2.4286	1.2471	2.8681	-1.1849	2.0354	-0.2085	-0.2005	0.1295	-0.0153	-0.0541	-0.6184	-0.444	0.674	0.2627	0.5633	-0.0862	0.0585	0.7857	0.1478	0.7045	38.4046	34.1176	28.2264
11	1.8888	0.0741	0.5651	1.8904	-0.6592	1.2666	0.0512	0.1274	-0.1085	-0.1896	-0.1857	-0.192	0.3473	0.4535	0.1346	0.271	0.0783	0.0419	0.1996	0.0344	0.0607	10.3931	10.1399	23.8721
12	1.94	0.682	0.7131	2.9538	0.5835	1.6801	0.0328	0.156	-0.076	-0.153	-0.1354	-0.4941	0.22	0.6544	0.1027	0.3015	0.0837	0.1175	0.3735	0.0848	0.161	22.1036	14.7883	17.5176

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 90
2	X-RAY DIFFRACTION	2	A	94 - 207
3	X-RAY DIFFRACTION	3	A	208 - 330
4	X-RAY DIFFRACTION	4	B	2 - 90
5	X-RAY DIFFRACTION	5	B	94 - 207
6	X-RAY DIFFRACTION	6	B	208 - 330
7	X-RAY DIFFRACTION	7	C	2 - 90
8	X-RAY DIFFRACTION	8	C	94 - 207
9	X-RAY DIFFRACTION	9	C	208 - 330
10	X-RAY DIFFRACTION	10	D	2 - 90
11	X-RAY DIFFRACTION	11	D	94 - 207
12	X-RAY DIFFRACTION	12	D	208 - 330

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