PDB-7qls: CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT N...

ID or keywords:

Entry

Database: PDB / ID: 7qls

Title

CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT N151G, L259V COMPLEXED WITH FE, NADH, AND DIMETHOXYPHENYL ACETAMIDE

Components

Lactaldehyde reductase

Keywords

OXIDOREDUCTASE / FucO /

NADH /

Dehydrogenase /

aldehyde reductase

Function / homology

Function and homology information

lactaldehyde reductase / R-lactaldehyde reductase activity / S-lactaldehyde reductase activity / fucose catabolic process /

metal ion binding
Similarity search - Function

Biological species

Escherichia coli str. K-12 substr. MG1655 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Sridhar, S. / Kiema, T.R. / Wierenga, R.K. / Widersten, M.

Funding support

Sweden, 1items

Citation

Journal: Iucrj / Year: 2023
Title: Crystal structures and kinetic studies of a laboratory evolved aldehyde reductase explain the dramatic shift of its new substrate specificity.
Authors: Sridhar, S. / Zavarise, A. / Kiema, T.R. / Dalwani, S. / Eriksson, T. / Hajee, Y. / Reddy Enugala, T. / Wierenga, R.K. / Widersten, M.

History

Deposition	Dec 20, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 28, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jul 12, 2023	Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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
Revision 1.2	Jul 19, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3	Feb 7, 2024	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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PDBx/mmCIF format	7qls.cif.gz	406.6 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ql/7qls ftp://data.pdbj.org/pub/pdb/validation_reports/ql/7qls	HTTPS FTP

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Related structure data

Related structure data	7qlgC 7qlqC 7qnhC 1rrmS S: Starting model for refinement C: citing same article (ref.)
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	#213 - Sep 2017 Sirtuins similarity (1)

Deposited unit

AAA: Lactaldehyde reductase

BBB: Lactaldehyde reductase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	61.262, 86.432, 137.833
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	AAA
2	1	BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 3 - 384 / Label seq-ID: 3 - 384

Dom-ID	Component-ID	Auth asym-ID	Label asym-ID
1	1	AAA	A
2	2	BBB	B

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	Lactaldehyde reductase / / Propanediol oxidoreductase Mass: 41464.230 Da / Num. of mol.: 2 / Mutation: N151G,L259V,S315G Source method: isolated from a genetically manipulated source Details: M M A N R M I L N E T A W F G R G A V G A L T D E V K R R G Y Q K A L I V T D K T L V Q C G V V A K V T D K M D A A G L A W A I Y D G V V P N P T I T V V K E G L G V F Q N S G A D Y L I A I ...Details: M M A N R M I L N E T A W F G R G A V G A L T D E V K R R G Y Q K A L I V T D K T L V Q C G V V A K V T D K M D A A G L A W A I Y D G V V P N P T I T V V K E G L G V F Q N S G A D Y L I A I G G G T P Q D T C K A I G I I S N N P E F A D V R S L E G L S P T N K P S V P I L A I P T T A G T A A E V T I G Y V I T D E E K R R K F V C V D P H D I P Q V A F I D A D M M D G M P P A L K A A T G V D A L T H A I E G Y I T R G A W A L T D A L H I K A I E I I A G A L R G S V A G D K D A G E E M A L G Q Y V A G M G F S N V G V G L V H G M A H P L G A F Y N T P H G V A N A I L L P H V M R Y N A D F T G E K Y R D I A R V M G V K V E G M S L E E A R N A A V E A V F A L N R D V G N P P H L R D V G V R K E D I P A L A Q A A L D D V C T G G N P R E A T L E D I V E L Y H T A W T S H H H H H Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Gene: fucO, Z4116, ECs3659 / Production host: Escherichia coli (E. coli) / Variant (production host): XL1-Blue / References: UniProt: P0A9S2, lactaldehyde reductase
#2: Chemical	ChemComp-E9I / 2-(3,4-dimethoxyphenyl)ethanamide Mass: 195.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₃NO₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₃N₅O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-FE / FE (III) ION / Iron Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44.05 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1 M Sodium acetate pH 4.5; 20 % (w/v) PEG 8000; 0.2 M NaF

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 11, 2021
Radiation	Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 2.4→73.34 Å / Num. obs: 29415 / % possible obs: 100 % / Redundancy: 13.3 % / B_iso Wilson estimate: 53.437 Å² / CC_1/2: 0.999 / R_pim(I) all: 0.034 / Net I/σ(I): 14.1
Reflection shell	Resolution: 2.4→2.49 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3029 / CC_1/2: 0.776 / R_pim(I) all: 0.349 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1RRM

1rrm

Resolution: 2.4→73.333 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.945 / Cross valid method: FREE R-VALUE / ESU R: 0.556 / ESU R Free: 0.257
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2298	1466	4.994 %
R_work	0.197	27888	-
all	0.199	-	-
obs	-	29354	99.966 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 59.748 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.394 Å²	-0 Å²	-0 Å²
2-	-	-0.769 Å²	0 Å²
3-	-	-	3.162 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→73.333 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5692	0	102	77	5871

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.013	5906
X-RAY DIFFRACTION	r_bond_other_d	0.036	0.017	5629
X-RAY DIFFRACTION	r_angle_refined_deg	1.282	1.638	8050
X-RAY DIFFRACTION	r_angle_other_deg	2.325	1.584	12941
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.099	5	765
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.753	22.537	268
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.281	15	915
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.658	15	34
X-RAY DIFFRACTION	r_chiral_restr	0.052	0.2	805
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	6801
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	1249
X-RAY DIFFRACTION	r_nbd_refined	0.188	0.2	1250
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.219	0.2	5013
X-RAY DIFFRACTION	r_nbtor_refined	0.146	0.2	2905
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.06	0.2	2552
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.133	0.2	138
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.145	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.23	0.2	39
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.207	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	1.996	5.014	3066
X-RAY DIFFRACTION	r_mcbond_other	1.996	5.012	3065
X-RAY DIFFRACTION	r_mcangle_it	3.158	7.52	3829
X-RAY DIFFRACTION	r_mcangle_other	3.158	7.521	3830
X-RAY DIFFRACTION	r_scbond_it	1.904	5.264	2840
X-RAY DIFFRACTION	r_scbond_other	1.904	5.264	2841
X-RAY DIFFRACTION	r_scangle_it	3.119	7.804	4221
X-RAY DIFFRACTION	r_scangle_other	3.118	7.804	4222
X-RAY DIFFRACTION	r_lrange_it	4.866	60.327	6405
X-RAY DIFFRACTION	r_lrange_other	4.864	60.326	6404
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.076	0.05	11979

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.07585	0.05009
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.07585	0.05009

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.4-2.462	0.358	85	0.292	2069	X-RAY DIFFRACTION	100
2.462-2.53	0.274	93	0.27	1959	X-RAY DIFFRACTION	100
2.53-2.603	0.308	92	0.26	1942	X-RAY DIFFRACTION	100
2.603-2.683	0.277	98	0.262	1879	X-RAY DIFFRACTION	100
2.683-2.771	0.318	95	0.247	1814	X-RAY DIFFRACTION	99.9476
2.771-2.868	0.316	101	0.241	1755	X-RAY DIFFRACTION	100
2.868-2.977	0.287	105	0.267	1667	X-RAY DIFFRACTION	100
2.977-3.098	0.289	88	0.245	1644	X-RAY DIFFRACTION	99.9423
3.098-3.236	0.288	81	0.228	1588	X-RAY DIFFRACTION	100
3.236-3.394	0.26	94	0.229	1483	X-RAY DIFFRACTION	100
3.394-3.577	0.244	83	0.229	1430	X-RAY DIFFRACTION	99.934
3.577-3.794	0.189	62	0.18	1373	X-RAY DIFFRACTION	100
3.794-4.056	0.233	67	0.176	1292	X-RAY DIFFRACTION	100
4.056-4.38	0.2	71	0.162	1193	X-RAY DIFFRACTION	100
4.38-4.798	0.186	52	0.148	1126	X-RAY DIFFRACTION	100
4.798-5.363	0.213	56	0.177	1005	X-RAY DIFFRACTION	100
5.363-6.192	0.192	37	0.173	930	X-RAY DIFFRACTION	100
6.192-7.579	0.153	51	0.14	763	X-RAY DIFFRACTION	100
7.579-10	0.14	34	0.116	615	X-RAY DIFFRACTION	100
8-73.3	0.246	21	0.244	361	X-RAY DIFFRACTION	98.2005

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	1.7976	0.4333	0.3865	2.9542	-0.6364	2.2257	0.0549	-0.5178	-0.0765	0.3203	0.0148	-0.0311	0.1869	-0.0706	-0.0698	0.286	-0.0667	-0.0497	0.2312	0.048	0.0169	-6.324	-14.333	32.022
2	2.6956	-0.0505	0.6925	3.7063	-0.2723	1.8419	0.1927	0.0951	-0.3796	-0.8227	0.0134	0.068	0.4914	0.0032	-0.206	0.5567	-0.0373	-0.0776	0.0696	0.0065	0.0662	-7.664	-23.196	8.354
3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.272	0	0	0.272	0	0.272	0	0	0
4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.272	0	0	0.272	0	0.272	0	0	0

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	3 - 185
2	X-RAY DIFFRACTION	2	ALL	AAA	186 - 384
3	X-RAY DIFFRACTION	3	ALL	AAA	3 - 185
4	X-RAY DIFFRACTION	4	ALL	AAA	186 - 385

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