PDB-4xcv: Probable 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 i...

ID or keywords:

Entry

Database: PDB / ID: 4xcv

Title

Probable 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADPH

Components

NADP-dependent 2-hydroxyacid dehydrogenase

Keywords

OXIDOREDUCTASE / PSI-Biology / New York Structural Genomics Research Consortium / 2-hydroxyacid dehydrogenase /

NADP / 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: 1.4 Å

Authors

Langner, K.M. / Shabalin, I.G. / Handing, K.B. / Gasiorowska, O.A. / Stead, M. / Hillerich, B.S. / Chowdhury, S. / Hammonds, J. / Zimmerman, M.D. / Al Obadi, N. ...

Funding support

United States, 1items

Citation

Journal: to be published
Title: Crystal structure of 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADPH
Authors: Langner, K.M. / Shabalin, I.G. / Handing, K.B. / Gasiorowska, O.A. / Zimmerman, M.D. / Minor, W.

History

Deposition	Dec 18, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 31, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jan 28, 2015	Group: Structure summary
Revision 1.2	Nov 22, 2017	Group: Derived calculations / Refinement description ...Derived calculations / Refinement description / Source and taxonomy / Structure summary Category: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_keywords Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	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 1.5	Sep 27, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4xcv.cif.gz	158.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4xcv.ent.gz	121.8 KB	Display	PDB format
PDBx/mmJSON format	4xcv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xc/4xcv ftp://data.pdbj.org/pub/pdb/validation_reports/xc/4xcv	HTTPS FTP

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Related structure data

Related structure data	3kboS S: Starting model for refinement
Similar structure data	6cdf-2 3ga0-2 2dbr-2 3jtm-2 2w2l-1 2w2k-d 5f8c-1 5xvs-d 4ebf-2 2d0i-1 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	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: NADP-dependent 2-hydroxyacid dehydrogenase

hetero molecules

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

1

A: NADP-dependent 2-hydroxyacid dehydrogenase

hetero molecules

A: NADP-dependent 2-hydroxyacid dehydrogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	65.663, 65.663, 151.458
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-648- HOH

Details

biological unit is the same as asym.

#1: Protein	NADP-dependent 2-hydroxyacid dehydrogenase Mass: 35519.516 Da / Num. of mol.: 1 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 / Nicotinamide adenine dinucleotide phosphate Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₃₀N₇O₁₇P₃
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.3 Å³/Da / Density % sol: 46.61 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP 10 mM NADP and 10 mM glycolic acid were mixed with 0.2 ul of the MCSG-I condition ...Details: 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP 10 mM NADP and 10 mM glycolic acid were mixed with 0.2 ul of the MCSG-I condition #45 (0.2 M Sodium Chloride, 0.1 M Tris:HCl pH 8.5, 25% (w/v) PEG 3350) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization the protein was incubated with 1/50 v/v of 2 mg/ml TEV solution at 289 K.

Crystal

Density Matthews: 2.3 Å³/Da / Density % sol: 46.61 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP 10 mM NADP and 10 mM glycolic acid were mixed with 0.2 ul of the MCSG-I condition ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97912 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2014

Radiation

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

Radiation wavelength

Wavelength: 0.97912 Å / Relative weight: 1

Reflection

Resolution: 1.4→50 Å / Num. obs: 62557 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / B_iso Wilson estimate: 13.8 Å² / R_merge(I) obs: 0.067 / R_pim(I) all: 0.025 / R_rim(I) all: 0.072 / R_sym value: 0.067 / Χ²: 1.346 / Net I/av σ(I): 30.92 / Net I/σ(I): 10.3 / Num. measured all: 426874

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.4-1.42	6.4	0.914	2.1	2891	0.777	0.361	0.986	0.792	89
1.42-1.45	6.8	0.81		2923	0.794	0.311	0.871	0.833	90.3
1.45-1.48	6.7	0.652		2950	0.879	0.248	0.7	0.885	91.8
1.48-1.51	6.6	0.548		2974	0.901	0.211	0.589	0.855	92.2
1.51-1.54	6.5	0.455		3025	0.925	0.18	0.492	0.997	92.7
1.54-1.58	6.4	0.384		3049	0.936	0.15	0.415	0.877	93.8
1.58-1.62	6.3	0.318		3071	0.953	0.125	0.343	0.912	94.5
1.62-1.66	6.3	0.272		3108	0.965	0.108	0.294	0.931	95.5
1.66-1.71	6.2	0.226		3107	0.975	0.09	0.244	0.942	96.1
1.71-1.76	6.2	0.19		3162	0.984	0.076	0.205	1.009	96.2
1.76-1.83	6.3	0.154		3178	0.987	0.062	0.167	1.031	97
1.83-1.9	6.3	0.121		3195	0.992	0.049	0.131	1.146	97.6
1.9-1.99	6.4	0.109		3226	0.995	0.044	0.118	1.433	97.7
1.99-2.09	6.6	0.084		3209	0.996	0.034	0.091	1.458	97.9
2.09-2.22	6.8	0.067		3227	0.997	0.027	0.072	1.444	97.6
2.22-2.39	7.1	0.068		3221	0.997	0.027	0.073	1.784	97.3
2.39-2.63	7.5	0.061		3244	0.997	0.023	0.066	1.943	96.9
2.63-3.02	7.9	0.05		3234	0.998	0.018	0.053	1.988	96
3.02-3.8	8.3	0.042		3225	0.998	0.015	0.045	2.218	94.7
3.8-50	8.6	0.038		3338	0.998	0.014	0.04	2.127	91.4

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		phasing
MOLREP		phasing
HKL-3000		data scaling
Coot		model building
REFMAC	5.8.0073	refinement
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3KBO

3kbo

Resolution: 1.4→50 Å / Cor.coef. F_o:F_c: 0.975 / Cor.coef. F_o:F_c free: 0.965 / WR_factor R_free: 0.1728 / WR_factor R_work: 0.1448 / FOM work R set: 0.8842 / SU B: 1.756 / SU ML: 0.037 / SU R Cruickshank DPI: 0.0559 / SU R_free: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1775	3104	5 %	RANDOM
R_work	0.1493	59503	-	-
obs	0.1507	59503	94.87 %	-

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 max: 58.9 Å² / B_iso mean: 20.534 Å² / B_iso min: 7.97 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.4 Å²	-0 Å²	-0 Å²
2-	-	0.4 Å²	-0 Å²
3-	-	-	-0.81 Å²

Refinement step

Cycle: final / Resolution: 1.4→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2473	0	55	499	3027
B_iso mean	-	-	11.71	33.9	-
Num. residues	-	-	-	-	317

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.019	2699
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2610
X-RAY DIFFRACTION	r_angle_refined_deg	1.748	1.99	3679
X-RAY DIFFRACTION	r_angle_other_deg	1.07	3	6012
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.414	5	338
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.159	23.178	129
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.633	15	464
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.329	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	410
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	3027
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	626
X-RAY DIFFRACTION	r_mcbond_it	0.699	0.772	1295
X-RAY DIFFRACTION	r_mcbond_other	0.699	0.772	1294
X-RAY DIFFRACTION	r_mcangle_it	1.106	1.159	1623

LS refinement shell

Resolution: 1.401→1.437 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.246	220	-
R_work	0.238	3989	-
all	-	4209	-
obs	-	-	87.89 %

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	6.953	5.2213	2.5686	16.1644	8.5001	11.0005	-0.0943	0.2132	-0.1167	-0.1232	0.1843	-0.1577	0.1018	-0.1383	-0.09	0.0387	-0.0112	0.0328	0.1182	0.0188	0.0603	18.38	0.481	18.959
2	2.7491	0.0534	0.6303	5.5278	-0.9791	1.6496	0.1499	-0.1059	-0.2629	-0.1871	-0.103	0.1706	0.3867	0.0036	-0.047	0.1215	-0.0259	0.0008	0.0939	-0.0111	0.0831	21.541	-6.559	24.227
3	4.5515	-0.7714	-1.6994	6.7007	0.2363	3.5178	-0.1092	0.1914	-0.1446	-0.0547	0.0786	0.3526	0.1587	-0.3647	0.0306	0.0502	-0.0285	0.0133	0.1428	-0.0074	0.0811	9.063	-0.205	22.915
4	2.7338	-1.5335	-2.2325	1.8732	0.4511	3.5505	0.1054	0.5068	-0.0455	-0.1632	-0.1364	0.2347	-0.0327	-0.511	0.031	0.0502	-0.0144	-0.0122	0.1875	0.0047	0.0763	16.17	3.772	12.531
5	2.9629	-1.4973	-1.6464	2.701	0.6809	5.2808	0.2992	0.7413	-0.0925	-0.254	-0.398	0.22	0.1621	-1.0866	0.0989	0.1334	0.0174	-0.021	0.3765	-0.0212	0.0787	19.541	2.408	4.731
6	0.9906	-0.1648	-0.0162	3.0477	1.0456	1.8849	-0.0251	-0.0809	0.0399	0.1311	-0.0299	0.0373	0.0067	-0.051	0.0551	0.0339	-0.0076	0.0035	0.0365	-0.0107	0.0495	35.443	-21.16	0.563
7	3.3126	0.0551	-0.7881	4.0034	-0.6173	1.9661	0.0122	0.0572	-0.0061	-0.0723	0.0232	0.2393	0.1293	-0.1343	-0.0353	0.0944	-0.0369	0.0037	0.0372	-0.0173	0.071	33.948	-42.869	-4.858
8	0.6276	-0.327	0.037	1.3657	-0.4563	0.9355	-0.0096	0.0765	0.0791	-0.1382	-0.0193	-0.125	0.0117	-0.0453	0.0288	0.0603	-0.0066	0.0131	0.0482	0.0073	0.0759	38.838	-12.972	-11.853
9	1.0127	-0.1092	-0.4789	1.6629	0.7139	1.5276	-0.0255	0.133	0.0589	-0.223	-0.0201	0.1336	-0.0804	-0.2641	0.0457	0.0757	-0.0109	-0.0239	0.0808	0.0025	0.068	24.215	-12.908	-11.672
10	5.6735	-2.5013	0.9528	5.8053	-1.1388	3.3263	0.0955	0.4312	-0.1108	-0.3418	-0.125	-0.0511	0.3036	0.0696	0.0296	0.1625	-0.0295	0.0141	0.0999	-0.0398	0.0324	32.686	-23.654	-20.53
11	0.6709	-0.1585	-0.2314	1.5941	0.6829	1.4493	-0.0687	0.0937	0.0087	-0.0925	-0.0407	0.1853	0.0538	-0.2347	0.1093	0.0539	-0.0285	-0.0098	0.0824	-0.0164	0.0783	21.386	-19.082	-8.834
12	1.5312	0.5944	-0.4064	1.1337	-0.1921	1.1516	-0.0536	0.0729	-0.0171	-0.1282	0.0067	0.107	0.0607	-0.2403	0.0469	0.0565	-0.024	-0.0112	0.0981	-0.0196	0.0788	19.46	-25.46	-6.439
13	2.3222	0.493	-0.5876	4.6199	2.33	5.1793	-0.0067	-0.1121	0.0529	0.0775	-0.0675	0.1691	0.0582	-0.1183	0.0743	0.0198	0.0039	0.004	0.0567	-0.0064	0.0682	25.246	-24.644	1.151
14	0.307	-0.0724	-0.6949	0.6819	0.3845	3.2522	0.0837	-0.0204	0.0471	-0.0722	-0.0954	-0.0255	0.0271	0.018	0.0117	0.0728	-0.01	0.0108	0.0719	0.0084	0.0761	29.545	2.613	10.594

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 13
2	X-RAY DIFFRACTION	2	A	14 - 31
3	X-RAY DIFFRACTION	3	A	32 - 43
4	X-RAY DIFFRACTION	4	A	44 - 77
5	X-RAY DIFFRACTION	5	A	78 - 93
6	X-RAY DIFFRACTION	6	A	94 - 117
7	X-RAY DIFFRACTION	7	A	118 - 132
8	X-RAY DIFFRACTION	8	A	133 - 194
9	X-RAY DIFFRACTION	9	A	195 - 215
10	X-RAY DIFFRACTION	10	A	216 - 227
11	X-RAY DIFFRACTION	11	A	228 - 246
12	X-RAY DIFFRACTION	12	A	247 - 272
13	X-RAY DIFFRACTION	13	A	273 - 289
14	X-RAY DIFFRACTION	14	A	290 - 319

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