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- PDB-7qlg: CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT L... -

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Basic information

Entry
Database: PDB / ID: 7qlg
TitleCRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT L259V COMPLEXED WITH FE, NADH, AND GLYCEROL
ComponentsLactaldehyde reductase
KeywordsOXIDOREDUCTASE / 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
Lactaldehyde reductase / Iron-type alcohol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase
Similarity search - Domain/homology
: / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Lactaldehyde reductase
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSridhar, S. / Kiema, T.R. / Widertsen, M. / Wierenga, R.K.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Other private194-0638 Olle Engkvist Byggmastare Foundation Sweden
CitationJournal: 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
DepositionDec 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
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 / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 19, 2023Group: 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 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Lactaldehyde reductase
BBB: Lactaldehyde reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7619
Polymers83,0432
Non-polymers1,7197
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-67 kcal/mol
Surface area26420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.780, 55.360, 107.690
Angle α, β, γ (deg.)90.000, 103.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lactaldehyde reductase / / Propanediol oxidoreductase


Mass: 41521.277 Da / Num. of mol.: 2 / Mutation: 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 N 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
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / 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.: 241 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 50.64mM Sodium acetate trihydrate, pH 4.5, 15%w/v PEG 3350, 200mM Sodium Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2→51.661 Å / Num. obs: 53704 / % possible obs: 98.9 % / Redundancy: 3.14 % / Biso Wilson estimate: 18.366 Å2 / CC1/2: 0.971 / Rpim(I) all: 0.153 / Net I/σ(I): 7.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.25 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 53704 / CC1/2: 0.414 / Rpim(I) all: 0.752 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RRM

1rrm


Resolution: 2→51.661 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.181 / SU ML: 0.135 / Cross valid method: FREE R-VALUE / ESU R: 0.18 / ESU R Free: 0.16
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2271 2602 4.846 %
Rwork0.1862 51088 -
all0.188 --
obs-53690 98.78 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.391 Å2
Baniso -1Baniso -2Baniso -3
1--2.601 Å2-0 Å2-1.058 Å2
2--1.538 Å2-0 Å2
3---1.411 Å2
Refinement stepCycle: LAST / Resolution: 2→51.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5692 0 108 241 6041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0135916
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175640
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.648066
X-RAY DIFFRACTIONr_angle_other_deg1.2651.57912969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3665766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9322.593270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68815915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3341534
X-RAY DIFFRACTIONr_chiral_restr0.0660.2807
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026757
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021253
X-RAY DIFFRACTIONr_nbd_refined0.1940.21189
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.25077
X-RAY DIFFRACTIONr_nbtor_refined0.1480.22894
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.22473
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2259
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2950.26
X-RAY DIFFRACTIONr_nbd_other0.1960.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2270.24
X-RAY DIFFRACTIONr_mcbond_it1.0462.033064
X-RAY DIFFRACTIONr_mcbond_other1.0462.0293063
X-RAY DIFFRACTIONr_mcangle_it1.6643.043827
X-RAY DIFFRACTIONr_mcangle_other1.6643.0413828
X-RAY DIFFRACTIONr_scbond_it1.6562.3032852
X-RAY DIFFRACTIONr_scbond_other1.6562.3042853
X-RAY DIFFRACTIONr_scangle_it2.7063.354238
X-RAY DIFFRACTIONr_scangle_other2.7053.3514239
X-RAY DIFFRACTIONr_lrange_it3.63824.8026457
X-RAY DIFFRACTIONr_lrange_other3.63724.8066458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.3032020.2883785X-RAY DIFFRACTION99.1791
2.052-2.1080.2861800.2693668X-RAY DIFFRACTION99.4058
2.108-2.1690.3311940.2583551X-RAY DIFFRACTION99.1265
2.169-2.2360.2771860.2433467X-RAY DIFFRACTION99.4555
2.236-2.3090.2491770.233369X-RAY DIFFRACTION99.3834
2.309-2.390.2451410.2113280X-RAY DIFFRACTION98.9586
2.39-2.480.2441590.2033148X-RAY DIFFRACTION99.6084
2.48-2.5820.2311700.1853024X-RAY DIFFRACTION99.5016
2.582-2.6960.2251690.1872882X-RAY DIFFRACTION99.1873
2.696-2.8280.2271240.1812793X-RAY DIFFRACTION99.0829
2.828-2.9810.2331280.1722654X-RAY DIFFRACTION99.1094
2.981-3.1610.2111120.1752533X-RAY DIFFRACTION99.0266
3.161-3.3790.1931310.1652327X-RAY DIFFRACTION99.3533
3.379-3.650.2191210.1522211X-RAY DIFFRACTION98.9393
3.65-3.9980.191910.1432001X-RAY DIFFRACTION97.8027
3.998-4.4690.181920.1461799X-RAY DIFFRACTION96.875
4.469-5.1590.204800.1411603X-RAY DIFFRACTION96.5577
5.159-6.3140.225690.1771352X-RAY DIFFRACTION96.4043
6.314-8.9130.174500.1521048X-RAY DIFFRACTION95.3125
8.913-51.60.162260.183594X-RAY DIFFRACTION92.8144

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