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- PDB-5br4: E. coli lactaldehyde reductase (FucO) M185C mutant -

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Basic information

Entry
Database: PDB / ID: 5br4
TitleE. coli lactaldehyde reductase (FucO) M185C mutant
ComponentsLactaldehyde reductase
KeywordsOXIDOREDUCTASE / NADH / FucO / Mutant
Function / homology
Function and homology information


lactaldehyde reductase activity / glycol catabolic process / propanediol metabolic process / lactaldehyde reductase / R-lactaldehyde reductase activity / S-lactaldehyde reductase activity / fucose catabolic process / L-fucose catabolic process / rhamnose catabolic process / alcohol dehydrogenase (NAD+) activity ...lactaldehyde reductase activity / glycol catabolic process / propanediol metabolic process / lactaldehyde reductase / R-lactaldehyde reductase activity / S-lactaldehyde reductase activity / fucose catabolic process / L-fucose catabolic process / rhamnose catabolic process / alcohol dehydrogenase (NAD+) activity / ferrous iron binding / nucleotide binding / protein homodimerization activity / metal ion binding / cytosol
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 / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Rossmann fold - #1970 ...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 / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Lactaldehyde reductase / Lactaldehyde reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.91 Å
AuthorsCahn, J.K.B. / Brinkmann-Chen, S. / Arnold, F.H.
CitationJournal: Protein Eng.Des.Sel. / Year: 2016
Title: Mutations in adenine-binding pockets enhance catalytic properties of NAD(P)H-dependent enzymes.
Authors: Cahn, J.K. / Baumschlager, A. / Brinkmann-Chen, S. / Arnold, F.H.
History
DepositionMay 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lactaldehyde reductase
B: Lactaldehyde reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,33513
Polymers83,4592
Non-polymers1,87611
Water21,0241167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-97 kcal/mol
Surface area27320 Å2
Unit cell
Length a, b, c (Å)69.697, 63.769, 91.674
Angle α, β, γ (deg.)90.00, 111.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lactaldehyde reductase / / Propanediol oxidoreductase


Mass: 41729.516 Da / Num. of mol.: 2 / Mutation: M185C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fucO, Z4116, ECs3659 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A9S2, UniProt: P0A9S1*PLUS, lactaldehyde reductase

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Non-polymers , 5 types, 1178 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: 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
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1167 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 12% PEG3350, 200 mM ammonium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2014 / Details: K-B focusing mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 0.909→85.5 Å / Num. all: 491073 / Num. obs: 491073 / % possible obs: 91.8 % / Redundancy: 2.7 % / Rpim(I) all: 0.044 / Rrim(I) all: 0.077 / Rsym value: 0.062 / Net I/av σ(I): 10.1 / Net I/σ(I): 8.8 / Num. measured all: 1333897
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
0.91-0.962.52.250.3145409580381.6692.250.474.6
0.96-1.022.71.370.6181887671590.9771.370.891.1
1.02-1.092.70.6911.1174497642930.4920.6911.692.8
1.09-1.172.70.3692.1167689613920.2620.3692.995.2
1.17-1.292.70.2373.3155446566100.1680.2374.495.2
1.29-1.442.80.1525.1145023522560.1080.1526.697.2
1.44-1.662.80.07610.2126768457910.0540.07611.996.4
1.66-2.032.80.04117.6108750391240.0290.04120.997.4
2.03-2.872.80.0223083236299940.0160.02237.496.2
2.87-36.5342.80.01538.645192164160.0110.0155494.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.87
Highest resolutionLowest resolution
Rotation36.53 Å1.3 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
SCALA3.3.21data scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RRM

1rrm


Resolution: 0.91→85.5 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.984 / SU B: 0.835 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.016 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14747 24378 5 %RANDOM
Rwork0.12908 ---
obs0.12999 466646 91.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.369 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20.4 Å2
2---0.33 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 0.91→85.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5711 0 112 1167 6990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0196057
X-RAY DIFFRACTIONr_bond_other_d0.0020.025845
X-RAY DIFFRACTIONr_angle_refined_deg2.0371.9828286
X-RAY DIFFRACTIONr_angle_other_deg1.344313448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1380.2964
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0216929
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021305
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6851.0823114
X-RAY DIFFRACTIONr_mcbond_other1.6681.0813113
X-RAY DIFFRACTIONr_mcangle_it2.0171.6273899
X-RAY DIFFRACTIONr_mcangle_other2.0211.6283900
X-RAY DIFFRACTIONr_scbond_it6.2811.3772943
X-RAY DIFFRACTIONr_scbond_other6.2811.3772943
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5811.9384368
X-RAY DIFFRACTIONr_long_range_B_refined8.88314.7456539
X-RAY DIFFRACTIONr_long_range_B_other8.88214.7466539
X-RAY DIFFRACTIONr_rigid_bond_restr6.66311902
X-RAY DIFFRACTIONr_sphericity_free41.855225
X-RAY DIFFRACTIONr_sphericity_bonded17.426512717
LS refinement shellResolution: 0.909→0.932 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 1197 -
Rwork0.359 22931 -
obs--61.11 %

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