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- PDB-1mzr: Structure of dkga from E.coli at 2.13 A resolution solved by mole... -

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Basic information

Entry
Database: PDB / ID: 1mzr
TitleStructure of dkga from E.coli at 2.13 A resolution solved by molecular replacement
Components2,5-diketo-D-gluconate reductase A
KeywordsOXIDOREDUCTASE / alpha/beta-barrel / aldo-ketoreductase / NADPH dependant / Bacterial targets at IGS-CNRS / France / BIGS / Structural Genomics
Function / homology
Function and homology information


2,5-didehydrogluconate reductase (2-dehydro-D-gluconate-forming) / 2,5-didehydrogluconate reductase activity / methylglyoxal catabolic process / alcohol dehydrogenase (NADP+) activity / L-ascorbic acid biosynthetic process / aldose reductase (NADPH) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / oxidoreductase activity / cytosol
Similarity search - Function
Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel ...Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 2,5-diketo-D-gluconic acid reductase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsAbergel, C. / Jeudy, S. / Monchois, V. / Claverie, J.M. / Bacterial targets at IGS-CNRS, France (BIGS)
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of Escherichia coli DkgA, a broad-specificity aldo-keto reductase.
Authors: Jeudy, S. / Monchois, V. / Maza, C. / Claverie, J.M. / Abergel, C.
History
DepositionOct 9, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: 2,5-diketo-D-gluconate reductase A
B: 2,5-diketo-D-gluconate reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0329
Polymers67,3732
Non-polymers6597
Water10,503583
1
A: 2,5-diketo-D-gluconate reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0615
Polymers33,6861
Non-polymers3744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2,5-diketo-D-gluconate reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9714
Polymers33,6861
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.177, 145.697, 79.511
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-730-

HOH

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Components

#1: Protein 2,5-diketo-D-gluconate reductase A


Mass: 33686.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yqhe / Plasmid: pDEST17 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q46857, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 583 / 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: 2.99 Å3/Da / Density % sol: 58.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: potassium phosphate, sodium phosphate, hepes, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110.2 mg/mlprotein1drop
220 mMMOPS1droppH8.0
31 mMbetaine1drop
42 Msodium potassium phosphate1reservoir
50.1 MHEPES1reservoirpH7.0
62.5 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2001
RadiationMonochromator: monochromator 0.98 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.13→37.1 Å / Num. all: 43958 / Num. obs: 43958 / % possible obs: 96.7 % / Observed criterion σ(F): 9 / Observed criterion σ(I): 3 / Redundancy: 4.9 % / Biso Wilson estimate: 26.751 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 8.6
Reflection shellResolution: 2.13→2.2 Å / Redundancy: 4.8 % / Num. unique all: 4340 / Rsym value: 0.282 / % possible all: 98.3
Reflection
*PLUS
Highest resolution: 2.16 Å / Lowest resolution: 20 Å / Num. obs: 39423
Reflection shell
*PLUS
% possible obs: 96.7 % / Num. unique obs: 3932 / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A80

1a80


Resolution: 2.13→19.91 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 4271 -RANDOM
Rwork0.175 ---
all-43958 --
obs-43824 96.1 %-
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1--6.75 Å20 Å20 Å2
2--9.71 Å20 Å2
3----2.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.13→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4388 0 37 583 5008
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_deg0.89
LS refinement shellResolution: 2.13→2.2 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.259 726 -
Rwork0.212 --
obs-6313 98.3 %
Refinement
*PLUS
Rfactor obs: 0.172 / Rfactor Rfree: 0.221 / Rfactor Rwork: 0.172 / Highest resolution: 2.16 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.7

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