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- PDB-2bl4: Lactaldehyde:1,2-propanediol oxidoreductase of Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 2bl4
TitleLactaldehyde:1,2-propanediol oxidoreductase of Escherichia coli
ComponentsLACTALDEHYDE REDUCTASE
KeywordsOXIDOREDUCTASE / FUCO / GROUP III DEHYDROGENASE / METALO-ENZYMES / DINUCLEOTIDE COFACTOR SPECIFICITY / FUCOSE METABOLISM / 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. / Perez-Luque, R. / Badia, J. / Baldoma, L. / 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
DepositionMar 1, 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
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

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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
Water84747
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 / LACTALDEHYDE-1 / 2 -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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-NAD / 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


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


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: R[OR(S)]-PROPANE-1,2-DIOL + NAD+ => R[OR(S)]-LACTALDEHYDE + NADH.

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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: 0.14 / Net I/σ(I): 8.16
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.62 / % possible all: 67.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
XDSdata scaling
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O2D

1o2d


Resolution: 2.85→28 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.85 / SU B: 40.478 / SU ML: 0.336 / Cross valid method: THROUGHOUT / ESU R: 1.313 / ESU R Free: 0.44 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.303 1366 5.1 %RANDOM
Rwork0.251 ---
obs0.254 25260 88.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.72 Å21.36 Å20 Å2
2--2.72 Å20 Å2
3----4.08 Å2
Refinement stepCycle: LAST / Resolution: 2.85→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5690 0 91 47 5828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225894
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7881.988038
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3445762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.99224.407236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.79415920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1371534
X-RAY DIFFRACTIONr_chiral_restr0.1090.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024446
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2640.23550
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.24095
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2287
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0290.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5061.53868
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.88726056
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.46832282
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4334.51982
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.92 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.528 107
Rwork0.386 1719
Refinement TLS params.Method: refined / Origin x: -0.7567 Å / Origin y: 76.2006 Å / Origin z: 103.3137 Å
111213212223313233
T-0.0844 Å2-0.0269 Å2-0.0366 Å2--0.1216 Å2-0.0011 Å2---0.0738 Å2
L0.6317 °20.2362 °2-0.2868 °2-0.7029 °2-0.3148 °2--1.5182 °2
S0.0773 Å °-0.0444 Å °0.054 Å °0.0948 Å °-0.0547 Å °-0.025 Å °-0.0631 Å °0.0541 Å °-0.0227 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 383
2X-RAY DIFFRACTION1B1002 - 1383
3X-RAY DIFFRACTION1A400
4X-RAY DIFFRACTION1B1400
5X-RAY DIFFRACTION1A401
6X-RAY DIFFRACTION1B1401
7X-RAY DIFFRACTION1S500 - 546

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