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- PDB-7r0p: CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT F... -

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Basic information

Entry
Database: PDB / ID: 7r0p
TitleCRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT F254I 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 / : / 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. / : / Fe-containing alcohol dehydrogenase family, C-terminal / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Lactaldehyde reductase
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsShruthi, S. / Tiila, R.K. / Rikkert, W. / Mikael, W.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Other governmentOlle 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 2, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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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)85,55623
Polymers83,0632
Non-polymers2,49421
Water9,998555
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.980, 86.161, 147.652
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 3 - 386 / Label seq-ID: 3 - 386

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Lactaldehyde reductase / Propanediol oxidoreductase


Mass: 41531.320 Da / Num. of mol.: 2 / Mutation: F254I
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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M Sodium acetate pH 4.5, 15% w/v PEG 3350, 0.25M Sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→42.77 Å / Num. obs: 98360 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 12.12 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.036 / Net I/σ(I): 11.6
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 10.77 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4837 / CC1/2: 0.854 / Rpim(I) all: 0.309 / % possible all: 100

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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: 1.6→42.77 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.534 / SU ML: 0.052 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.076
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1771 4792 4.876 %
Rwork0.1561 93476 -
all0.157 --
obs-98268 99.988 %
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: 17.241 Å2
Baniso -1Baniso -2Baniso -3
1--0.691 Å2-0 Å2-0 Å2
2---0.968 Å20 Å2
3---1.659 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5712 0 158 555 6425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0136057
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175820
X-RAY DIFFRACTIONr_angle_refined_deg1.431.6458243
X-RAY DIFFRACTIONr_angle_other_deg1.471.57813382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3685790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85222.286280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74915945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.731538
X-RAY DIFFRACTIONr_chiral_restr0.0780.2825
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026912
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021290
X-RAY DIFFRACTIONr_nbd_refined0.2290.21359
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.25647
X-RAY DIFFRACTIONr_nbtor_refined0.1630.23011
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22636
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2457
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1260.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.170.217
X-RAY DIFFRACTIONr_nbd_other0.1620.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1750.217
X-RAY DIFFRACTIONr_mcbond_it1.091.6393106
X-RAY DIFFRACTIONr_mcbond_other1.0871.6383105
X-RAY DIFFRACTIONr_mcangle_it1.6292.4583890
X-RAY DIFFRACTIONr_mcangle_other1.6292.4593891
X-RAY DIFFRACTIONr_scbond_it1.871.8952951
X-RAY DIFFRACTIONr_scbond_other1.871.8962952
X-RAY DIFFRACTIONr_scangle_it2.8762.734345
X-RAY DIFFRACTIONr_scangle_other2.8762.7314346
X-RAY DIFFRACTIONr_lrange_it4.29121.0636999
X-RAY DIFFRACTIONr_lrange_other4.15420.6536867
X-RAY DIFFRACTIONr_ncsr_local_group_10.0670.0512675
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.067290.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.067290.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6420.2113300.2116856X-RAY DIFFRACTION100
1.642-1.6870.2383610.2066631X-RAY DIFFRACTION100
1.687-1.7350.2313170.1956500X-RAY DIFFRACTION100
1.735-1.7890.2293370.1876282X-RAY DIFFRACTION100
1.789-1.8480.1892970.1726127X-RAY DIFFRACTION100
1.848-1.9120.1882990.1655922X-RAY DIFFRACTION99.9839
1.912-1.9850.1853080.1585721X-RAY DIFFRACTION100
1.985-2.0660.1812740.1555525X-RAY DIFFRACTION100
2.066-2.1570.1742440.1515314X-RAY DIFFRACTION99.982
2.157-2.2630.1572640.1425033X-RAY DIFFRACTION100
2.263-2.3850.1572430.1344828X-RAY DIFFRACTION100
2.385-2.530.1612390.1374600X-RAY DIFFRACTION100
2.53-2.7040.1592090.1414285X-RAY DIFFRACTION100
2.704-2.9210.1752100.1494034X-RAY DIFFRACTION100
2.921-3.1990.1652050.1553701X-RAY DIFFRACTION100
3.199-3.5770.1731810.1553377X-RAY DIFFRACTION100
3.577-4.130.1631390.1463027X-RAY DIFFRACTION100
4.13-5.0570.1641560.1412527X-RAY DIFFRACTION100
5.057-7.1480.211130.1812018X-RAY DIFFRACTION100
7.148-42.770.16660.1511168X-RAY DIFFRACTION99.1961

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