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

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Basic information

Entry
Database: PDB / ID: 7qnf
TitleCRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT N151G, L259V COMPLEXED WITH FE, NAD+, AND ETHYLENE GLYCOL
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
ADENOSINE-5-DIPHOSPHORIBOSE / : / FORMIC ACID / Lactaldehyde reductase
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)84,68515
Polymers82,9282
Non-polymers1,75713
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-56 kcal/mol
Surface area25850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.838, 85.765, 136.681
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AAABBB

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

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Non-polymers , 5 types, 279 molecules

#2: 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
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Bis-tris pH 8.5, 20 % (w/v) PEG 6000, 0.2 M NaF

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 6, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.14→36.71 Å / Num. obs: 40916 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 32.565 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.07 / Net I/σ(I): 8.4
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3299 / CC1/2: 0.522 / Rpim(I) all: 0.976

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Processing

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

1rrm


Resolution: 2.14→36.707 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: FREE R-VALUE / ESU R: 0.252 / ESU R Free: 0.194
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2257 2050 5.02 %
Rwork0.1786 38784 -
all0.181 --
obs-40834 99.929 %
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: 41.637 Å2
Baniso -1Baniso -2Baniso -3
1--1.843 Å2-0 Å2-0 Å2
2--0.588 Å2-0 Å2
3---1.254 Å2
Refinement stepCycle: LAST / Resolution: 2.14→36.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5684 0 108 266 6058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0135914
X-RAY DIFFRACTIONr_bond_other_d0.0360.0175653
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.6428048
X-RAY DIFFRACTIONr_angle_other_deg2.3241.57912998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4595768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7622.472271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55615917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7371535
X-RAY DIFFRACTIONr_chiral_restr0.0620.2806
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026732
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021252
X-RAY DIFFRACTIONr_nbd_refined0.20.21348
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.25229
X-RAY DIFFRACTIONr_nbtor_refined0.1510.22866
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0610.22483
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0990.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1630.221
X-RAY DIFFRACTIONr_nbd_other0.2050.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1930.24
X-RAY DIFFRACTIONr_mcbond_it0.7922.753069
X-RAY DIFFRACTIONr_mcbond_other0.7922.7513070
X-RAY DIFFRACTIONr_mcangle_it1.2714.1223835
X-RAY DIFFRACTIONr_mcangle_other1.2714.1233836
X-RAY DIFFRACTIONr_scbond_it0.942.9192845
X-RAY DIFFRACTIONr_scbond_other0.942.9192846
X-RAY DIFFRACTIONr_scangle_it1.5054.314212
X-RAY DIFFRACTIONr_scangle_other1.5044.314213
X-RAY DIFFRACTIONr_lrange_it3.59833.9796629
X-RAY DIFFRACTIONr_lrange_other3.55433.8276589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.1960.3311610.2932803X-RAY DIFFRACTION99.9663
2.196-2.2560.3141430.2812764X-RAY DIFFRACTION99.9312
2.256-2.3210.3151380.2582651X-RAY DIFFRACTION99.9642
2.321-2.3930.2961420.2342634X-RAY DIFFRACTION99.8921
2.393-2.4710.261400.2182521X-RAY DIFFRACTION99.8499
2.471-2.5580.2831030.2082444X-RAY DIFFRACTION99.9608
2.558-2.6540.2971400.2042363X-RAY DIFFRACTION100
2.654-2.7630.2221280.1942285X-RAY DIFFRACTION100
2.763-2.8850.2561180.2032204X-RAY DIFFRACTION100
2.885-3.0260.212940.1872096X-RAY DIFFRACTION100
3.026-3.190.2121130.1922021X-RAY DIFFRACTION100
3.19-3.3830.261090.1951872X-RAY DIFFRACTION100
3.383-3.6160.2511030.191791X-RAY DIFFRACTION99.9472
3.616-3.9060.184870.1621685X-RAY DIFFRACTION99.9436
3.906-4.2780.153800.1251545X-RAY DIFFRACTION99.9385
4.278-4.7830.187630.1231420X-RAY DIFFRACTION100
4.783-5.5220.207710.141247X-RAY DIFFRACTION100
5.522-6.760.183580.1531071X-RAY DIFFRACTION99.9115
6.76-9.5480.139390.12863X-RAY DIFFRACTION99.8893
8-100.218200.178504X-RAY DIFFRACTION97.7612
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.5532-0.2071-0.12582.4496-0.20261.19550.0657-0.4612-0.0580.1851-0.0725-0.34560.01040.1590.00670.0497-0.0408-0.01270.23510.02070.0669-3.944-8.86826.194
22.8127-0.87820.28521.96680.15751.09910.02740.0247-0.32-0.43340.0110.09510.04080.0045-0.03840.1475-0.0260.00730.0191-0.00280.0516-15.191-15.9264.754
31.3910.50410.01922.89030.24331.87470.0355-0.12790.06640.19280.02820.0989-0.1737-0.1524-0.06370.06530.01060.02430.09360.0060.0118-24.22714.78831.703
41.5062-0.2591-0.2623.7109-0.18791.08980.08830.41010.3099-0.94840.09720.0882-0.1277-0.1755-0.18560.3573-0.02470.01060.17950.08680.0883-23.83923.1027.937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA3 - 185
2X-RAY DIFFRACTION2ALLAAA186 - 385
3X-RAY DIFFRACTION3ALLBBB3 - 185
4X-RAY DIFFRACTION4ALLBBB186 - 385

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