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- PDB-2bi4: Lactaldehyde:1,2-propanediol oxidoreductase of Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 2bi4
TitleLactaldehyde:1,2-propanediol oxidoreductase of Escherichia coli
ComponentsLACTALDEHYDE REDUCTASE
KeywordsOXIDOREDUCTASE / FUCO / GROUP III DEHYDROGENASE / METALO-ENZYMES / DINUCLEOTIDE COFACTOR SPECIFICITY / IRON / NAD
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 / Resolution: 2.85 Å
AuthorsMontella, C. / Bellsolell, L. / Badia, J. / Baldoma, L. / Perez, R. / Coll, M. / Aguilar, J.
CitationJournal: J.Bacteriol. / Year: 2005
Title: Crystal Structure of an Iron-Dependent Group III Dehydrogenase that Interconverts L-Lactaldehyde and L-1,2-Propanediol in Escherichia Coli
Authors: Montella, C. / Bellsolell, L. / Perez-Luque, R. / Badia, J. / Baldoma, L. / Coll, M. / Aguilar, J.
History
DepositionJan 20, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)85,0717
Polymers83,5972
Non-polymers1,4745
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)109.422, 109.422, 182.459
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein LACTALDEHYDE REDUCTASE / / PROPANEDIOL OXIDOREDUCTASE


Mass: 41798.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: ECL1 / Plasmid: PQE32 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15(PREP4)
References: UniProt: P11549, UniProt: P0A9S1*PLUS, lactaldehyde reductase
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.89 Å3/Da / Density % sol: 70 %
Crystal growpH: 6
Details: PROTEIN WAS CRYSTALLIZED FROM 0, 8M AMMONIUM SULPHATE, 0,1M MES PH6, pH 6.00

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 30, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.85→28 Å / Num. obs: 24555 / % possible obs: 81.4 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.15
Reflection shellResolution: 2.85→2.92 Å / Rmerge(I) obs: 0.15 / % possible all: 67.2

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
XDSdata scaling
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O2D

1o2d


Resolution: 2.85→28 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28724 25340 95.2 %RANDOM
Rwork0.25761 ---
obs0.25761 1286 100 %-
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.377 Å2
Baniso -1Baniso -2Baniso -3
1-3.14 Å21.57 Å20 Å2
2--3.14 Å20 Å2
3----4.71 Å2
Refinement stepCycle: LAST / Resolution: 2.85→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5690 0 91 45 5826
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014673
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.49265
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.85→2.923 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 1728 -
Rwork0.326 98 -
obs--100 %
Xplor fileSerial no: 1 / Param file: POR_FE.PAR

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