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

ID or keywords:

Entry

Database: PDB / ID: 7qnh

Title

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

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 /

MOLECULAR REPLACEMENT / Resolution: 2.2 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	7qnh.cif.gz	388.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7qnh_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	7qnh_full_validation.pdf.gz	1.4 MB	Display
Data in XML	7qnh_validation.xml.gz	29.1 KB	Display
Data in CIF	7qnh_validation.cif.gz	41.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qn/7qnh ftp://data.pdbj.org/pub/pdb/validation_reports/qn/7qnh	HTTPS FTP

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Related structure data

Related structure data	7qlgC 7qlqC 7qlsC 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	#102 - Jun 2008 Lactate Dehydrogenase similarity (1) #93 - Sep 2007 Citrate Synthase 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)	69.539, 54.647, 106.562
Angle α, β, γ (deg.)	90.000, 103.405, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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)

#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-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₉N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: 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
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.37 Å³/Da / Density % sol: 48.17 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 50.64 mM Sodium acetate trihydrate, pH 4.5; 15 % (w/v) PEG 3350; 200 mM sodium formate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54178 Å
Detector	Type: Bruker PHOTON II / Detector: PIXEL / Date: Apr 21, 2021
Radiation	Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54178 Å / Relative weight: 1
Reflection	Resolution: 2.2→51.883 Å / Num. obs: 39813 / % possible obs: 99.8 % / Redundancy: 1.92 % / B_iso Wilson estimate: 14.11 Å² / CC_1/2: 0.988 / R_pim(I) all: 0.082 / Net I/σ(I): 5.3
Reflection shell	Resolution: 2.2→2.27 Å / Redundancy: 1.94 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3466 / CC_1/2: 0.85 / R_pim(I) all: 0.292 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
PROTEUM PLUS		data reduction
Aimless		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1RRM

1rrm

Resolution: 2.2→51.883 Å / Cor.coef. F_o:F_c: 0.918 / Cor.coef. F_o:F_c free: 0.902 / Cross valid method: FREE R-VALUE / ESU R: 0.306 / ESU R Free: 0.206
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2324	1962	4.929 %
R_work	0.2095	37842	-
all	0.211	-	-
obs	-	39804	99.719 %

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: 21.805 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.998 Å²	0 Å²	0.736 Å²
2-	-	-1.101 Å²	-0 Å²
3-	-	-	2.468 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→51.883 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5684	0	96	176	5956

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	5893
X-RAY DIFFRACTION	r_bond_other_d	0.036	0.017	5614
X-RAY DIFFRACTION	r_angle_refined_deg	1.499	1.64	8035
X-RAY DIFFRACTION	r_angle_other_deg	2.331	1.579	12910
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.104	5	764
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.978	22.537	268
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.95	15	912
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.69	15	34
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	804
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	6738
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	1248
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	1345
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.217	0.2	5245
X-RAY DIFFRACTION	r_nbtor_refined	0.154	0.2	2875
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.062	0.2	2529
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	249
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.077	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.179	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.289	0.2	78
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.041	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	0.846	1.704	3062
X-RAY DIFFRACTION	r_mcbond_other	0.845	1.703	3061
X-RAY DIFFRACTION	r_mcangle_it	1.344	2.553	3824
X-RAY DIFFRACTION	r_mcangle_other	1.344	2.555	3825
X-RAY DIFFRACTION	r_scbond_it	1.044	1.854	2831
X-RAY DIFFRACTION	r_scbond_other	1.044	1.855	2832
X-RAY DIFFRACTION	r_scangle_it	1.709	2.726	4211
X-RAY DIFFRACTION	r_scangle_other	1.709	2.727	4212
X-RAY DIFFRACTION	r_lrange_it	2.99	20.892	6580
X-RAY DIFFRACTION	r_lrange_other	2.978	20.88	6567
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.076	0.05	12118

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	0.07556	0.05008
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.07556	0.05008

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 (%)
2.2-2.257	0.304	151	0.29	2765	X-RAY DIFFRACTION	99.6923
2.257-2.319	0.265	159	0.252	2716	X-RAY DIFFRACTION	99.7225
2.319-2.386	0.256	133	0.25	2613	X-RAY DIFFRACTION	99.5288
2.386-2.46	0.254	122	0.227	2565	X-RAY DIFFRACTION	99.7032
2.46-2.54	0.26	124	0.237	2478	X-RAY DIFFRACTION	99.7699
2.54-2.629	0.262	126	0.222	2379	X-RAY DIFFRACTION	99.8406
2.629-2.728	0.245	121	0.222	2357	X-RAY DIFFRACTION	99.8388
2.728-2.84	0.26	136	0.204	2191	X-RAY DIFFRACTION	99.7856
2.84-2.966	0.264	125	0.214	2135	X-RAY DIFFRACTION	99.9558
2.966-3.111	0.292	103	0.22	2050	X-RAY DIFFRACTION	99.8146
3.111-3.279	0.209	99	0.207	1971	X-RAY DIFFRACTION	99.9035
3.279-3.477	0.206	82	0.206	1876	X-RAY DIFFRACTION	99.898
3.477-3.717	0.226	91	0.219	1731	X-RAY DIFFRACTION	99.4541
3.717-4.015	0.231	63	0.199	1635	X-RAY DIFFRACTION	99.7064
4.015-4.397	0.202	69	0.175	1518	X-RAY DIFFRACTION	99.6234
4.397-4.915	0.222	65	0.172	1370	X-RAY DIFFRACTION	99.722
4.915-5.673	0.213	68	0.178	1199	X-RAY DIFFRACTION	99.7638
5.673-6.943	0.18	48	0.166	1038	X-RAY DIFFRACTION	99.908
6.943-9.797	0.107	56	0.115	796	X-RAY DIFFRACTION	99.6491
9.797-51.88	0.203	21	0.2	459	X-RAY DIFFRACTION	97.3631

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	0.7303	-0.1757	0.1049	1.1736	0.0056	1.0083	0.0042	0.0178	0.0075	-0.026	-0.0217	0.0918	0.0491	-0.0611	0.0174	0.0452	-0.0051	-0.0019	0.1256	0.003	0.0082	1.547	5.941	12.387
2	1.7611	-0.2433	-0.0459	0.6033	-0.0163	0.3397	-0.0062	-0.3032	-0.1989	0.2062	0.0097	0.1005	0.0619	0.0228	-0.0036	0.1405	-0.0032	0.0177	0.2252	0.0458	0.0348	-1.235	-0.081	36.68
3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.1339	0	0	0.1339	0	0.1339	0	0	0
4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.1339	0	0	0.1339	0	0.1339	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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