PDB-5tsd: Crystal structure of NADPH-dependent 2-hydroxyacid dehydrogenase ...

ID or keywords:

Entry

Database: PDB / ID: 5tsd

Title

Crystal structure of NADPH-dependent 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADPH and oxalate

Components

Probable hydroxyacid dehydrogenase protein

Keywords

OXIDOREDUCTASE / Rhizobium etli / NADPH / 2-hydroxyacid dehydrogenase / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC

Function / homology

Function and homology information

NAD binding / oxidoreductase activity
Similarity search - Function

Biological species

Rhizobium etli (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Matelska, D. / Shabalin, I.G. / Kutner, J. / Handing, K.B. / Gasiorowska, O.A. / Cooper, D.R. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)

Funding support

United States, 1items

Citation

Journal: to be published
Title: Crystal structure of NADPH-dependent 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADPH and oxalate
Authors: Matelska, D. / Shabalin, I.G. / Kutner, J. / Handing, K.B. / Gasiorowska, O.A. / Cooper, D.R. / Minor, W.

History

Deposition	Oct 28, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 16, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Author supporting evidence / Derived calculations / Refinement description Category: pdbx_audit_support / pdbx_struct_oper_list / software Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Apr 13, 2022	Group: Database references / Structure summary / Category: audit_author / citation_author / database_2 Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Oct 4, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5tsd.cif.gz	274 KB	Display	PDBx/mmCIF format
PDB format	pdb5tsd.ent.gz	219.7 KB	Display	PDB format
PDBx/mmJSON format	5tsd.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5tsd_validation.pdf.gz	962.4 KB	Display	wwPDB validaton report
Full document	5tsd_full_validation.pdf.gz	964.6 KB	Display
Data in XML	5tsd_validation.xml.gz	30.3 KB	Display
Data in CIF	5tsd_validation.cif.gz	45.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ts/5tsd ftp://data.pdbj.org/pub/pdb/validation_reports/ts/5tsd	HTTPS FTP

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Related structure data

Related structure data	4xcvS 5bqf S: Starting model for refinement
Similar structure data	4weq-1 4nu5-d 7cxt-d 4ebf-3 2ome-1 4e5p-3 3n7u-3 3n7u-6 4u6q-1 4m0p-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
Other databases	TargetTrack: NYSGRC-014307

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#34 - Oct 2002 Dihydrofolate Reductase similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: Probable hydroxyacid dehydrogenase protein

B: Probable hydroxyacid dehydrogenase protein

hetero molecules

73.3 kDa, 2 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)	68.945, 70.124, 126.615
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
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

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 4 - 319 / Label seq-ID: 7 - 322

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

#1: Protein	Probable hydroxyacid dehydrogenase protein Mass: 35794.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium etli (strain CFN 42 / ATCC 51251) (bacteria) Strain: CFN 42 / ATCC 51251 / Gene: RHE_CH00179 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q2KDT2
#2: Chemical	ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₀N₇O₁₇P₃
#3: Chemical	ChemComp-OXD / OXALIC ACID Mass: 90.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₂O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.14 Å³/Da / Density % sol: 42.46 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 ul of 14.8 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 1 condition #93 (0.1M Bis-Tris, ...Details: 0.2 ul of 14.8 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 1 condition #93 (0.1M Bis-Tris, 25%w/v PEG 3350 pH=5.5) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/13 v/v of 1 mg/ml rTEV solution at 289 K for 3 hours

Crystal

Density Matthews: 2.14 Å³/Da / Density % sol: 42.46 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 ul of 14.8 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 1 condition #93 (0.1M Bis-Tris, ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 17, 2015 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.9→50 Å / Num. obs: 49321 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / B_iso Wilson estimate: 27.1 Å² / R_merge(I) obs: 0.077 / R_sym value: 0.077 / Net I/av σ(I): 20.6 / Net I/σ(I): 6.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	CC_1/2	Diffraction-ID	% possible all
1.9-1.93	6.5	0.863	1.71	0.748	1	99.9
1.93-1.97	6.5	0.758		0.808	1	100
1.97-2.01	6.5	0.679		0.847	1	100
2.01-2.05	6.5	0.546		0.875	1	100
2.05-2.09	6.6	0.465		0.908	1	100
2.09-2.14	6.6	0.368		0.942	1	100
2.14-2.19	6.6	0.305		0.963	1	100
2.19-2.25	6.6	0.259		0.971	1	100
2.25-2.32	6.6	0.241		0.974	1	100
2.32-2.39	6.6	0.206		0.98	1	100
2.39-2.48	6.6	0.18		0.983	1	100
2.48-2.58	6.6	0.151		0.989	1	100
2.58-2.7	6.6	0.127		0.991	1	100
2.7-2.84	6.6	0.101		0.994	1	100
2.84-3.02	6.6	0.08		0.996	1	99.8
3.02-3.25	6.6	0.062		0.997	1	99.9
3.25-3.58	6.5	0.047		0.998	1	99.9
3.58-4.09	6.5	0.04		0.999	1	99.9
4.09-5.16	6.4	0.03		0.999	1	99.9
5.16-50	6.1	0.027		0.998	1	99.7

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Processing

Software

Name	Version	Classification
MD2		data collection
HKL-3000		phasing
HKL-3000		data scaling
MOLREP		phasing
REFMAC	5.8.0151	refinement
PDB_EXTRACT	3.2	data extraction
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4xcv

4xcv

Resolution: 1.9→50 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.955 / SU B: 6.45 / SU ML: 0.101 / SU R Cruickshank DPI: 0.1429 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.132
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1976	2311	4.7 %	RANDOM
R_work	0.1546	-	-	-
obs	0.1566	46819	99.95 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 127.05 Å² / B_iso mean: 36.901 Å² / B_iso min: 17.51 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.89 Å²	0 Å²	-0 Å²
2-	-	-0.69 Å²	0 Å²
3-	-	-	-0.21 Å²

Refinement step

Cycle: final / Resolution: 1.9→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4882	0	108	592	5582
B_iso mean	-	-	25.19	44.37	-
Num. residues	-	-	-	-	632

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	5118
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	4855
X-RAY DIFFRACTION	r_angle_refined_deg	1.328	1.966	6966
X-RAY DIFFRACTION	r_angle_other_deg	0.918	3	11136
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.475	5	636
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.432	23.26	227
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.253	15	823
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.591	15	45
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	780
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	5935
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1170
X-RAY DIFFRACTION	r_mcbond_it	2.247	1.902	2532
X-RAY DIFFRACTION	r_mcbond_other	2.246	1.902	2531
X-RAY DIFFRACTION	r_mcangle_it	2.886	2.845	3163

Refine LS restraints NCS

Ens-ID: 1 / Number: 19498 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.248	166	-
R_work	0.244	3422	-
all	-	3588	-
obs	-	-	99.92 %

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	3.1789	-0.8894	-0.0788	3.7862	2.9706	3.6515	0.1079	0.3374	-0.0316	-0.2829	-0.081	0.1719	-0.4073	-0.1292	-0.0269	0.1511	0.0108	0.014	0.1429	-0.0522	0.1049	-24.851	-0.755	51.604
2	3.3612	-0.942	-0.1921	2.227	0.0091	1.7634	-0.1084	-0.2429	-0.0531	0.2846	0.0755	0.2217	-0.081	-0.208	0.0328	0.1554	-0.0076	0.0432	0.0838	-0.0202	0.0928	-19.075	-3.483	62.994
3	1.4662	1.1426	-1.2306	2.8299	-1.421	1.8123	0.0039	-0.0065	0.2086	-0.0014	0.0301	0.1538	-0.0752	-0.0028	-0.0341	0.0551	0.0023	-0.0482	0.0296	-0.0054	0.0915	8.129	13.78	44.652
4	2.0323	0.2412	-0.6918	0.9038	0.0538	1.7923	-0.0787	-0.232	-0.029	0.1367	0.017	-0.1137	0.3007	0.2292	0.0618	0.1184	0.0436	-0.0556	0.0667	0.0243	0.0901	13.348	1.142	57.869
5	2.04	0.0757	0.2121	2.0676	0.0281	2.3322	-0.0385	-0.1398	0.1123	0.1226	0.0196	0.0106	-0.0624	0.11	0.0189	0.0747	-0.0142	-0.0483	0.0345	-0.0233	0.0893	4.879	15.063	59.955
6	4.4829	0.4085	2.3741	1.8575	0.0105	4.2212	0.0464	0.0443	-0.2909	0.1097	-0.0838	-0.0049	0.1209	0.0567	0.0373	0.1029	0.0002	0.0441	0.0545	-0.0323	0.1127	-12.231	-11.522	56.266
7	8.6528	-0.7227	-1.4212	2.9794	0.1511	7.23	0.0607	-0.4795	0.8727	0.0217	-0.0488	0.2066	-1.1315	0.0654	-0.0119	0.3783	-0.0341	-0.1398	0.1485	0.0175	0.6561	39.84	19.027	35.135
8	5.5233	0.4621	2.6727	1.9625	2.2607	3.5203	-0.6526	0.8256	1.7631	-0.5654	0.12	-0.2182	-0.9527	0.5691	0.5326	0.5586	-0.14	-0.1665	0.4134	0.3396	0.8059	43.937	18.655	27.571
9	2.8819	-0.9742	-0.9837	0.7272	0.029	1.6474	0.0635	0.16	0.3105	-0.0668	-0.0674	-0.1844	0.008	0.1748	0.004	0.086	-0.0131	-0.0468	0.0579	0.0404	0.1267	17.95	12.647	34.6
10	1.5481	0.3065	0.2227	1.1778	0.2476	1.5318	-0.0259	0.1103	-0.0972	-0.1355	-0.0237	0.0418	0.2363	-0.016	0.0495	0.1283	-0.0162	-0.0353	0.0212	-0.0083	0.0776	8.524	0.205	28.285
11	1.5317	0.1117	0.1026	1.2341	0.0048	2.046	0.0191	0.1278	0.1289	-0.1226	-0.0299	0.0801	-0.0275	-0.1427	0.0108	0.0583	0.0103	-0.0249	0.04	0.0434	0.1015	9.245	16.925	25.99
12	6.4936	-0.5011	1.3712	0.7355	0.1323	0.4073	-0.0684	0.0397	0.027	0.0457	0.0324	0.0067	-0.0269	0.0894	0.0359	0.1587	0.0311	0.0016	0.1803	0.0451	0.1919	37.169	4.841	30.55

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 41
2	X-RAY DIFFRACTION	2	A	42 - 94
3	X-RAY DIFFRACTION	3	A	95 - 130
4	X-RAY DIFFRACTION	4	A	131 - 204
5	X-RAY DIFFRACTION	5	A	205 - 288
6	X-RAY DIFFRACTION	6	A	289 - 319
7	X-RAY DIFFRACTION	7	B	4 - 22
8	X-RAY DIFFRACTION	8	B	23 - 66
9	X-RAY DIFFRACTION	9	B	67 - 130
10	X-RAY DIFFRACTION	10	B	131 - 195
11	X-RAY DIFFRACTION	11	B	196 - 285
12	X-RAY DIFFRACTION	12	B	286 - 319

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