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- PDB-7r3d: CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT N... -

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Basic information

Entry
Database: PDB / ID: 7r3d
TitleCRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT N151G, L259V COMPLEXED WITH FE, NADH, AND GLYCEROL (Absence of Nicotinamide ring)
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. / 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
ADENOSINE-5-DIPHOSPHORIBOSE / : / Lactaldehyde reductase
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSridhar, S. / Kiema, T.R. / Wierenga, R. / 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
DepositionFeb 7, 2022Deposition 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)84,1596
Polymers82,9282
Non-polymers1,2304
Water10,719595
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-73 kcal/mol
Surface area26520 Å2
Unit cell
Length a, b, c (Å)62.960, 95.110, 69.360
Angle α, β, γ (deg.)90.000, 116.480, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: fucO, Z4116, ECs3659
Production host: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Strain (production host): XL1-Blue / References: UniProt: P0A9S2, lactaldehyde reductase
#2: 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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / 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: 45.09 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bistris pH 5.5; 25% Polyethylene glycol 8000; 0.2M ammonium formate 9.25 mg/ml dissolved in 20mM Tris-HCl, pH7.5 that was supplemented with 0.5mM Fe and 10mM NADH and incubated for 10 ...Details: 0.1M Bistris pH 5.5; 25% Polyethylene glycol 8000; 0.2M ammonium formate 9.25 mg/ml dissolved in 20mM Tris-HCl, pH7.5 that was supplemented with 0.5mM Fe and 10mM NADH and incubated for 10 min at room temperature.

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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 PILATUS 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: 1.4→48.53 Å / Num. obs: 141933 / % possible obs: 99 % / Redundancy: 3.12 % / Biso Wilson estimate: 16.97 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.038 / Net I/σ(I): 10.9
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2.86 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6998 / CC1/2: 0.807 / Rpim(I) all: 0.405 / % possible all: 99

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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: 1.4→48.53 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.088 / SU ML: 0.042 / Cross valid method: FREE R-VALUE / ESU R: 0.054 / ESU R Free: 0.056
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1794 6883 4.851 %
Rwork0.1564 135015 -
all0.158 --
obs-141898 98.934 %
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: 18.664 Å2
Baniso -1Baniso -2Baniso -3
1-0.914 Å20 Å20.095 Å2
2--0.886 Å20 Å2
3----1.266 Å2
Refinement stepCycle: LAST / Resolution: 1.4→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5700 0 74 595 6369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135958
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175701
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.648136
X-RAY DIFFRACTIONr_angle_other_deg1.4591.57913117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.335786
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.45422.401279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74915939
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1631537
X-RAY DIFFRACTIONr_chiral_restr0.0720.2817
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021277
X-RAY DIFFRACTIONr_nbd_refined0.2160.21297
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.25414
X-RAY DIFFRACTIONr_nbtor_refined0.1620.22981
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22644
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2478
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.170.27
X-RAY DIFFRACTIONr_nbd_other0.1520.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1160.215
X-RAY DIFFRACTIONr_mcbond_it1.0291.8053090
X-RAY DIFFRACTIONr_mcbond_other1.0281.8043089
X-RAY DIFFRACTIONr_mcangle_it1.5532.7073864
X-RAY DIFFRACTIONr_mcangle_other1.5522.7083865
X-RAY DIFFRACTIONr_scbond_it1.6972.0332868
X-RAY DIFFRACTIONr_scbond_other1.6962.0332869
X-RAY DIFFRACTIONr_scangle_it2.622.9624262
X-RAY DIFFRACTIONr_scangle_other2.6192.9624263
X-RAY DIFFRACTIONr_lrange_it3.68722.9696932
X-RAY DIFFRACTIONr_lrange_other3.54222.4696781
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4360.2645240.2569947X-RAY DIFFRACTION98.895
1.436-1.4760.254560.2399763X-RAY DIFFRACTION99.127
1.476-1.5180.2294660.2199462X-RAY DIFFRACTION99.1214
1.518-1.5650.2124620.1989171X-RAY DIFFRACTION99.0947
1.565-1.6170.2134730.198917X-RAY DIFFRACTION99.0297
1.617-1.6730.1864350.1778622X-RAY DIFFRACTION99.6589
1.673-1.7360.1984190.1668392X-RAY DIFFRACTION99.5706
1.736-1.8070.1894400.1687992X-RAY DIFFRACTION99.5396
1.807-1.8880.1884110.1597688X-RAY DIFFRACTION99.4597
1.888-1.980.1953760.1597370X-RAY DIFFRACTION99.2695
1.98-2.0870.1813500.1556985X-RAY DIFFRACTION99.1484
2.087-2.2130.1633630.1496563X-RAY DIFFRACTION98.8722
2.213-2.3660.1932950.1486197X-RAY DIFFRACTION98.5578
2.366-2.5550.1722980.1435768X-RAY DIFFRACTION98.3942
2.555-2.7990.1612870.1445275X-RAY DIFFRACTION98.1818
2.799-3.1290.1832650.1474734X-RAY DIFFRACTION97.6558
3.129-3.6130.1471830.1464210X-RAY DIFFRACTION97.449
3.613-4.4230.1481820.1333586X-RAY DIFFRACTION97.8701
4.423-6.2480.1861300.1422811X-RAY DIFFRACTION98.197
6.248-48.530.17680.151562X-RAY DIFFRACTION97.8979

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