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- PDB-7qni: CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT L259V -

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Basic information

Entry
Database: PDB / ID: 7qni
TitleCRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT L259V
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 / alcohol dehydrogenase (NAD+) activity / metal ion binding
Similarity search - Function
Lactaldehyde reductase / Iron-type alcohol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 2. / : / Fe-containing alcohol dehydrogenase family, C-terminal / 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
CITRIC ACID / Lactaldehyde reductase
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsSridhar, S. / Kiema, T.R. / Wierenga, R.K. / Widersten, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Other privateOlle Engkvist Byggmastare Foundation - 194-0638 Sweden
CitationJournal: Febs J. / Year: 2023
Title: Structures of lactaldehyde reductase, FucO, link enzyme activity to hydrogen bond networks and conformational dynamics.
Authors: Zavarise, A. / Sridhar, S. / Kiema, T.R. / Wierenga, R.K. / Widersten, M.
History
DepositionDec 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Lactaldehyde reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7132
Polymers41,5211
Non-polymers1921
Water2,756153
1
AAA: Lactaldehyde reductase
hetero molecules

AAA: Lactaldehyde reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4274
Polymers83,0432
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area4190 Å2
ΔGint-17 kcal/mol
Surface area29410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.412, 108.360, 123.902
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11AAA-501-

HOH

21AAA-562-

HOH

31AAA-636-

HOH

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Components

#1: Protein Lactaldehyde reductase / Propanediol oxidoreductase


Mass: 41521.277 Da / Num. of mol.: 1 / Mutation: L259V, S315G
Source method: isolated from a genetically manipulated source
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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.24 Å3/Da / Density % sol: 45.04 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.1M Sodium citrate, pH 5.6; 20% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 28, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.73→54.24 Å / Num. obs: 39368 / % possible obs: 100 % / Redundancy: 13.23 % / Biso Wilson estimate: 28.434 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.021 / Net I/σ(I): 18
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2151 / CC1/2: 0.759 / Rpim(I) all: 0.494 / % possible all: 100

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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: 1.73→54.239 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.269 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / ESU R: 0.112 / ESU R Free: 0.107
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2133 1927 4.899 %
Rwork0.1831 37407 -
all0.185 --
obs-39334 99.952 %
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: 34.522 Å2
Baniso -1Baniso -2Baniso -3
1-3.871 Å20 Å2-0 Å2
2---2.881 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.73→54.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2884 0 13 153 3050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132966
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172828
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.6364043
X-RAY DIFFRACTIONr_angle_other_deg1.2941.5776506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5865392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79622.536138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84215466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8941517
X-RAY DIFFRACTIONr_chiral_restr0.060.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023414
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02632
X-RAY DIFFRACTIONr_nbd_refined0.2060.2615
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1660.22624
X-RAY DIFFRACTIONr_nbtor_refined0.1510.21468
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21343
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2131
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0530.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1810.225
X-RAY DIFFRACTIONr_nbd_other0.1860.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1450.29
X-RAY DIFFRACTIONr_mcbond_it1.8353.51553
X-RAY DIFFRACTIONr_mcbond_other1.8323.4991552
X-RAY DIFFRACTIONr_mcangle_it2.795.2451941
X-RAY DIFFRACTIONr_mcangle_other2.795.2461942
X-RAY DIFFRACTIONr_scbond_it2.3613.8441412
X-RAY DIFFRACTIONr_scbond_other2.3363.8411409
X-RAY DIFFRACTIONr_scangle_it3.8015.6382098
X-RAY DIFFRACTIONr_scangle_other3.85.642099
X-RAY DIFFRACTIONr_lrange_it5.07342.7213281
X-RAY DIFFRACTIONr_lrange_other5.05942.6623265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.7750.3461330.3372745X-RAY DIFFRACTION99.9653
1.775-1.8240.31320.2992669X-RAY DIFFRACTION100
1.824-1.8760.3031370.2812579X-RAY DIFFRACTION99.8897
1.876-1.9340.2791350.2552528X-RAY DIFFRACTION100
1.934-1.9980.2591230.2252435X-RAY DIFFRACTION99.8829
1.998-2.0680.2241440.212352X-RAY DIFFRACTION99.96
2.068-2.1460.2441120.2062287X-RAY DIFFRACTION100
2.146-2.2330.2381180.1972183X-RAY DIFFRACTION100
2.233-2.3330.2081060.1712145X-RAY DIFFRACTION100
2.333-2.4460.2011180.1711999X-RAY DIFFRACTION100
2.446-2.5790.2141120.1681915X-RAY DIFFRACTION99.9507
2.579-2.7350.248930.1751824X-RAY DIFFRACTION99.8958
2.735-2.9240.249870.1791743X-RAY DIFFRACTION100
2.924-3.1580.214820.1891606X-RAY DIFFRACTION100
3.158-3.4590.205770.1811493X-RAY DIFFRACTION100
3.459-3.8670.161660.1581359X-RAY DIFFRACTION100
3.867-4.4640.168480.1481205X-RAY DIFFRACTION100
4.464-5.4660.188540.1541039X-RAY DIFFRACTION100
5.466-7.7230.185300.185822X-RAY DIFFRACTION99.8828
7.723-54.230.224200.17479X-RAY DIFFRACTION98.6166

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