PDB-5o9d: Crystal structure of R. ruber ADH-A, mutant Y294F, W295A, Y54F, F...

ID or keywords:

Entry

Database: PDB / ID: 5o9d

Title

Crystal structure of R. ruber ADH-A, mutant Y294F, W295A, Y54F, F43H, H39Y

Components

Alcohol dehydrogenase

Keywords

OXIDOREDUCTASE / alcohol dehydrogenase mutant variant / NADH-dependent / Zn2+-dependent / Rossmann fold

Function / homology

Function and homology information

oxidoreductase activity / zinc ion binding
Similarity search - Function

Biological species

Rhodococcus sp. M8 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.79 Å

Authors

Dobritzsch, D. / Maurer, D. / Hamnevik, E. / Enugala, T.R. / Widersten, M.

Funding support

Sweden, 1items

Citation

Journal: FEBS J. / Year: 2017
Title: Relaxation of nonproductive binding and increased rate of coenzyme release in an alcohol dehydrogenase increases turnover with a nonpreferred alcohol enantiomer.
Authors: Hamnevik, E. / Enugala, T.R. / Maurer, D. / Ntuku, S. / Oliveira, A. / Dobritzsch, D. / Widersten, M.

History

Deposition	Jun 19, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 11, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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	5o9d.cif.gz	525.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5o9d.ent.gz	434.2 KB	Display	PDB format
PDBx/mmJSON format	5o9d.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5o9d_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	5o9d_full_validation.pdf.gz	1.5 MB	Display
Data in XML	5o9d_validation.xml.gz	61.5 KB	Display
Data in CIF	5o9d_validation.cif.gz	91.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o9/5o9d ftp://data.pdbj.org/pub/pdb/validation_reports/o9/5o9d	HTTPS FTP

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Related structure data

Related structure data	5o8hC 5o8qC 5o9fC 3jv7S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6fg0-d 3jv7-d 2xaa-d 5o9f-d 5o8h-d 2ejv-1 6ffx-d 6ffz-d 5od3-d 5o8q-2 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
Related items in Molecule of the Month	#13 - Jan 2001 Alcohol Dehydrogenase similarity (9) #32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: Alcohol dehydrogenase

B: Alcohol dehydrogenase

C: Alcohol dehydrogenase

D: Alcohol dehydrogenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: homology

Unit cell

Length a, b, c (Å)	65.492, 104.828, 109.009
Angle α, β, γ (deg.)	90.00, 91.13, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	THR	THR	A	A	1 - 346	1 - 346
2	1	THR	THR	B	B	1 - 346	1 - 346
1	2	THR	THR	A	A	1 - 346	1 - 346
2	2	THR	THR	C	C	1 - 346	1 - 346
1	3	VAL	VAL	A	A	1 - 344	1 - 344
2	3	VAL	VAL	D	D	1 - 344	1 - 344
1	4	THR	THR	B	B	1 - 346	1 - 346
2	4	THR	THR	C	C	1 - 346	1 - 346
1	5	VAL	VAL	B	B	1 - 344	1 - 344
2	5	VAL	VAL	D	D	1 - 344	1 - 344
1	6	VAL	VAL	C	C	1 - 344	1 - 344
2	6	VAL	VAL	D	D	1 - 344	1 - 344

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Alcohol dehydrogenase Mass: 35968.887 Da / Num. of mol.: 4 / Mutation: Y294F, W295A, Y54F, F43H, H39Y Source method: isolated from a genetically manipulated source Details: C-terminal His-tag, 5 mutations as compared to wildtype ADH-A sequence Source: (gene. exp.) Rhodococcus sp. M8 (bacteria) / Gene: BKE56_025765 / Plasmid: pGT7ADHA-5H / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: A0A1Q8I6M1
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#4: Chemical	ChemComp-9ON / (2~{S})-2-methylpentanedioic acid Mass: 146.141 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₀O₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1208 / 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: 2.36 Å³/Da / Density % sol: 47.4 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 17% PAA5100, 0.1 M Tris pH 8, 4 mM NAD+, 10 mM MgCl2, 7.5 mg/ml ADH-A

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 3, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9686 Å / Relative weight: 1
Reflection	Resolution: 1.79→28.31 Å / Num. obs: 137475 / % possible obs: 99 % / Redundancy: 3.4 % / B_iso Wilson estimate: 13.2 Å² / CC_1/2: 0.991 / R_merge(I) obs: 0.114 / R_pim(I) all: 0.072 / Net I/σ(I): 6.7
Reflection shell	Resolution: 1.79→1.82 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.672 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 6245 / CC_1/2: 0.573 / R_pim(I) all: 0.441 / % possible all: 90

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3jv7

3jv7

Resolution: 1.79→28.3 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.951 / SU B: 4.688 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.103 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19131	6892	5 %	RANDOM
R_work	0.1703	-	-	-
obs	0.17134	130487	99.23 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 23.03 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.64 Å²	0 Å²	0.7 Å²
2-	-	0.2 Å²	0 Å²
3-	-	-	-0.87 Å²

Refinement step

Cycle: 1 / Resolution: 1.79→28.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9873	0	224	1208	11305

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	10313
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	9710
X-RAY DIFFRACTION	r_angle_refined_deg	1.46	1.993	14106
X-RAY DIFFRACTION	r_angle_other_deg	0.927	3	22359
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.729	5	1385
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.759	22.829	357
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.281	15	1430
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.943	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	1663
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	11722
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2054
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	0.45	1.061	5534
X-RAY DIFFRACTION	r_mcbond_other	0.45	1.061	5533
X-RAY DIFFRACTION	r_mcangle_it	0.787	1.59	6912
X-RAY DIFFRACTION	r_mcangle_other	0.787	1.59	6913
X-RAY DIFFRACTION	r_scbond_it	0.7	1.183	4779
X-RAY DIFFRACTION	r_scbond_other	0.692	1.182	4777
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.141	1.738	7191
X-RAY DIFFRACTION	r_long_range_B_refined	5.143	15.091	11728
X-RAY DIFFRACTION	r_long_range_B_other	5.144	15.096	11729
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	20888	0.04
1	2	B	20888	0.04
2	1	A	20884	0.05
2	2	C	20884	0.05
3	1	A	20694	0.04
3	2	D	20694	0.04
4	1	B	20978	0.04
4	2	C	20978	0.04
5	1	B	20902	0.03
5	2	D	20902	0.03
6	1	C	20686	0.05
6	2	D	20686	0.05

LS refinement shell

Resolution: 1.79→1.836 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.284	448	-
R_work	0.278	9449	-
obs	-	-	97.09 %

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	1.3786	-0.5216	-0.5125	2.1608	0.6644	3.5293	-0.0357	-0.1077	-0.2293	0.197	0.043	-0.0228	0.305	0.1994	-0.0073	0.1284	-0.0025	0.0292	0.0663	0.0523	0.1058	-62.3323	-37.1417	151.6607
2	0.7139	0.1997	0.3166	0.9249	-0.2128	1.8977	-0.0307	-0.0133	-0.1297	0.0712	-0.0121	0.0458	0.0862	-0.0518	0.0428	0.0396	0.0023	0.0265	0.0037	-0.0012	0.0419	-62.9032	-21.7149	139.9796
3	1.4643	0.4442	-0.5974	1.0655	-0.144	1.7744	-0.0549	0.1131	-0.1576	-0.0494	0.0069	0.0798	0.1538	-0.15	0.0479	0.0283	-0.0038	-0.0085	0.0216	-0.0195	0.0404	-63.0961	-24.0396	132.587
4	1.357	0.2779	0.2118	2.7392	0.9518	3.4627	0.0549	0.0888	0.2054	-0.2383	0.0126	-0.0915	-0.3563	0.1372	-0.0675	0.1304	0.0355	-0.0049	0.0751	0.0329	0.0847	-65.491	25.9459	120.8025
5	0.8396	-0.3062	-0.2969	1.0616	-0.3998	1.8454	0.0047	0.0244	0.0785	-0.0447	-0.0162	0.0534	-0.0932	-0.0693	0.0115	0.0311	0.0161	-0.0224	0.0092	-0.0087	0.027	-64.9673	10.708	132.9118
6	1.576	-0.4399	0.6295	0.9866	-0.1415	1.9475	-0.0431	-0.1035	0.1082	0.0528	0.0103	0.096	-0.1276	-0.1815	0.0328	0.0144	0.0119	0.0036	0.0188	-0.0086	0.026	-66.2483	12.9306	140.0362
7	1.6518	-0.2666	-0.2613	3.7967	-0.1808	1.6202	0.0688	-0.3942	-0.0834	0.415	-0.1057	0.1033	0.0091	-0.0198	0.0369	0.1567	-0.0096	-0.0478	0.251	0.0367	0.061	-37.6926	-7.1114	172.6367
8	1.1154	0.5658	0.0025	1.6201	-0.6093	1.0363	0.0146	-0.2287	-0.0675	0.1606	-0.0283	-0.0693	0.0512	0.0528	0.0138	0.0636	0.0326	-0.0212	0.0742	-0.0011	0.0208	-40.0134	-5.4453	155.8766
9	4.4759	-0.4611	0.1286	1.564	-0.3628	1.2754	0.0065	-0.0218	0.4037	-0.0294	-0.0023	-0.1561	-0.2264	0.1824	-0.0042	0.0683	-0.0172	-0.0141	0.0432	-0.0289	0.0751	-36.72	14.8709	147.6265
10	1.1613	-0.105	0.4786	0.9285	-0.2611	1.1988	-0.0056	-0.2026	0.0229	0.1974	0.0056	-0.2457	-0.0204	0.1695	-0	0.0812	-0.0035	-0.0501	0.1294	-0.0141	0.0713	-32.9446	0.1515	158.5294
11	1.1564	0.1371	-0.008	3.5732	0.2431	2.1624	0.0608	0.4703	0.0682	-0.4263	-0.0282	0.0672	-0.1584	0.0404	-0.0326	0.2261	-0.0113	0.0637	0.3997	0.0378	0.1746	-34.6904	0.3314	102.8571
12	1.6889	-0.514	0.7981	1.4245	-0.2737	1.9043	-0.0226	0.3795	0.1301	-0.2739	0.0244	-0.1273	-0.1648	0.172	-0.0019	0.1076	-0.0233	0.0204	0.1158	0.0023	0.0447	-40.4335	0.2795	117.0219
13	1.8156	0.2357	-0.1332	2.1171	-0.0427	1.1503	-0.0105	0.04	-0.2103	0.0656	0.0192	-0.2395	0.1229	0.1695	-0.0087	0.0239	0.0297	-0.0068	0.0719	-0.0153	0.0486	-34.1412	-16.3446	127.5903
14	2.4087	-0.5597	-0.5248	2.6314	0.3621	3.5672	0.025	0.305	0.0321	-0.2262	0.0376	-0.2376	0.157	0.3239	-0.0626	0.1416	-0.0201	0.089	0.3417	-0.0093	0.2113	-22.7686	-6.2332	111.3202

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 79
2	X-RAY DIFFRACTION	2	A	80 - 231
3	X-RAY DIFFRACTION	3	A	232 - 346
4	X-RAY DIFFRACTION	4	B	1 - 80
5	X-RAY DIFFRACTION	5	B	81 - 231
6	X-RAY DIFFRACTION	6	B	232 - 346
7	X-RAY DIFFRACTION	7	C	1 - 80
8	X-RAY DIFFRACTION	8	C	81 - 197
9	X-RAY DIFFRACTION	9	C	198 - 282
10	X-RAY DIFFRACTION	10	C	283 - 346
11	X-RAY DIFFRACTION	11	D	1 - 80
12	X-RAY DIFFRACTION	12	D	81 - 174
13	X-RAY DIFFRACTION	13	D	175 - 311
14	X-RAY DIFFRACTION	14	D	312 - 345

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