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

ID or keywords:

Entry

Database: PDB / ID: 7qlq

Title

CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT N151G, L259V COMPLEXED WITH FE, NAD, 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 / alcohol dehydrogenase (NAD+) activity / metal ion binding
Similarity search - Function

Biological species

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

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

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

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	7qlq.cif.gz	405.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7qlq_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	7qlq_full_validation.pdf.gz	1.9 MB	Display
Data in XML	7qlq_validation.xml.gz	28 KB	Display
Data in CIF	7qlq_validation.cif.gz	38 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ql/7qlq ftp://data.pdbj.org/pub/pdb/validation_reports/ql/7qlq	HTTPS FTP

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Related structure data

Related structure data	7qlgC 7qlsC 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

84.8 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)	61.291, 85.455, 137.226
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: SER / End label comp-ID: SER / Auth seq-ID: 3 - 385 / Label seq-ID: 3 - 385

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)

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Protein , 1 types, 2 molecules AAABBB

#1: Protein	Lactaldehyde reductase / Propanediol oxidoreductase Mass: 41494.258 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) / References: UniProt: P0A9S2, lactaldehyde reductase

#1: Protein

Lactaldehyde reductase / Propanediol oxidoreductase

Mass: 41494.258 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 ...
Source: (gene. exp.)

Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: fucO, Z4116, ECs3659 / Production host:

Escherichia coli (E. coli) / References: UniProt: P0A9S2, lactaldehyde reductase

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Non-polymers , 6 types, 63 molecules

#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-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.17 Å³/Da / Density % sol: 43.19 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M Bis-tris pH 5.5; 20 % (w/v) PEG 6000; 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 EIGER 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: 2.6→56.02 Å / Num. obs: 22909 / % possible obs: 100 % / Redundancy: 13.8 % / B_iso Wilson estimate: 48.805 Å² / CC_1/2: 0.995 / R_pim(I) all: 0.082 / Net I/σ(I): 8.3
Reflection shell	Resolution: 2.6→2.72 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2734 / CC_1/2: 0.522 / R_pim(I) all: 0.739

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1RRM

1rrm

Resolution: 2.6→56.02 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.935 / Cross valid method: FREE R-VALUE / ESU R Free: 0.32
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2331	1104	4.832 %
R_work	0.1873	21742	-
all	0.189	-	-
obs	-	22846	99.943 %

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: 53.161 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.726 Å²	-0 Å²	-0 Å²
2-	-	0.176 Å²	-0 Å²
3-	-	-	0.55 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→56.02 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5688	0	116	54	5858

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.013	5913
X-RAY DIFFRACTION	r_bond_other_d	0.036	0.017	5634
X-RAY DIFFRACTION	r_angle_refined_deg	1.274	1.638	8057
X-RAY DIFFRACTION	r_angle_other_deg	2.32	1.584	12952
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.336	5	764
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.025	22.537	268
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.532	15	914
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.746	15	34
X-RAY DIFFRACTION	r_chiral_restr	0.05	0.2	806
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	6802
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	1248
X-RAY DIFFRACTION	r_nbd_refined	0.178	0.2	1276
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.212	0.2	4981
X-RAY DIFFRACTION	r_nbtor_refined	0.144	0.2	2888
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.061	0.2	2619
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.126	0.2	126
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.281	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.258	0.2	42
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.178	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	1.602	4.762	3064
X-RAY DIFFRACTION	r_mcbond_other	1.601	4.759	3061
X-RAY DIFFRACTION	r_mcangle_it	2.566	7.142	3824
X-RAY DIFFRACTION	r_mcangle_other	2.565	7.144	3825
X-RAY DIFFRACTION	r_scbond_it	1.636	4.984	2849
X-RAY DIFFRACTION	r_scbond_other	1.636	4.984	2850
X-RAY DIFFRACTION	r_scangle_it	2.663	7.394	4233
X-RAY DIFFRACTION	r_scangle_other	2.663	7.394	4234
X-RAY DIFFRACTION	r_lrange_it	4.176	57.636	6421
X-RAY DIFFRACTION	r_lrange_other	4.176	57.643	6422
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.066	0.05	12167

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	0.06582	0.05009
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.06582	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 (%)
2.6-2.668	0.267	91	0.267	1588	X-RAY DIFFRACTION	99.9405
2.668-2.741	0.323	72	0.271	1536	X-RAY DIFFRACTION	100
2.741-2.82	0.288	82	0.263	1479	X-RAY DIFFRACTION	99.872
2.82-2.907	0.355	79	0.26	1454	X-RAY DIFFRACTION	99.9348
2.907-3.002	0.286	77	0.248	1404	X-RAY DIFFRACTION	100
3.002-3.107	0.286	76	0.221	1356	X-RAY DIFFRACTION	100
3.107-3.225	0.259	64	0.221	1341	X-RAY DIFFRACTION	100
3.225-3.356	0.281	65	0.216	1264	X-RAY DIFFRACTION	100
3.356-3.505	0.235	52	0.196	1249	X-RAY DIFFRACTION	100
3.505-3.676	0.231	68	0.18	1161	X-RAY DIFFRACTION	100
3.676-3.875	0.203	51	0.167	1141	X-RAY DIFFRACTION	99.9162
3.875-4.11	0.183	57	0.159	1047	X-RAY DIFFRACTION	100
4.11-4.393	0.195	49	0.145	1029	X-RAY DIFFRACTION	100
4.393-4.745	0.163	40	0.144	937	X-RAY DIFFRACTION	100
4.745-5.197	0.247	38	0.156	870	X-RAY DIFFRACTION	99.89
5.197-5.81	0.285	46	0.176	789	X-RAY DIFFRACTION	100
5.81-6.707	0.205	28	0.169	713	X-RAY DIFFRACTION	100
6.707-8.209	0.183	31	0.168	607	X-RAY DIFFRACTION	100
8-10	0.142	25	0.138	490	X-RAY DIFFRACTION	100
11.589-56.02	0.306	13	0.246	287	X-RAY DIFFRACTION	97.7199

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	2.4277	-0.5966	0.0032	1.6353	0.3137	2.1318	-0.0391	-0.52	-0.035	0.3184	0.0328	-0.2964	0.0921	0.3801	0.0064	0.0755	-0.0325	-0.05	0.2616	0.0111	0.0786	-3.64	-9.065	26.197
2	3.7604	-0.9387	-0.3582	2.4198	0.19	2.0582	0.0647	0.1366	-0.3713	-0.3219	-0.1286	0.1457	0.102	-0.0086	0.0638	0.0534	0.0051	-0.0114	0.0665	-0.0202	0.0387	-15.094	-16.078	4.749
3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.1769	0	0	0.1769	0	0.1769	0	0	0
4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.1769	0	0	0.1769	0	0.1769	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 - 385
3	X-RAY DIFFRACTION	3	ALL	AAA	3 - 185
4	X-RAY DIFFRACTION	4	ALL	AAA	186 - 384

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