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- PDB-1og6: ydhF, an aldo-keto reductase from E.coli complexed with NADPH -

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Basic information

Entry
Database: PDB / ID: 1og6
TitleydhF, an aldo-keto reductase from E.coli complexed with NADPH
ComponentsHYPOTHETICAL OXIDOREDUCTASE YDHF
KeywordsOXIDOREDUCTASE / ALDO-KETO REDUCTASE / ALPHA/BETA BARREL / NADPH-DEPENDANT / BACTERIAL TARGETS AT IGS-CNRS / FRANCE / BIGS / STRUCTURAL GENOMICS
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity / cytosol
Similarity search - Function
: / NADP-dependent oxidoreductase domain / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Oxidoreductase YdhF
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsJeudy, S. / Abergel, C. / Claverie, J.M.
CitationJournal: To be Published
Title: Crystal Structure of Ydhf, an Aldo-Keto Reductase from Escherichia Coli
Authors: Jeudy, S. / Abergel, C. / Claverie, J.M.
History
DepositionApr 24, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYPOTHETICAL OXIDOREDUCTASE YDHF
B: HYPOTHETICAL OXIDOREDUCTASE YDHF
C: HYPOTHETICAL OXIDOREDUCTASE YDHF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,1766
Polymers100,9453
Non-polymers2,2303
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)174.529, 174.529, 97.923
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.118185, -0.986255, -0.115467), (0.018144, 0.114118, -0.993302), (0.992826, -0.119488, 0.004408)-23.299, 35.734, 58.741
2given(-0.08051, 0.02073, 0.99654), (-0.99324, 0.08224, -0.08195), (-0.08365, -0.9964, 0.01397)38.488, 55.968, 25.241

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Components

#1: Protein HYPOTHETICAL OXIDOREDUCTASE YDHF / YDHF


Mass: 33648.496 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: THERE IS A RATIO ONE TO ONE PROTEIN MOLECULE AND NADP
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76187
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.93 Å3/Da / Density % sol: 58 %
Crystal growpH: 7
Details: IMIDAZOLE/MALATE 0.2M AMMONIUM SULFATE 0.1M PH7.0, POLY ETHYLENE GLYCOL 16%, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 15, 2002 / Details: MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.8→29.88 Å / Num. obs: 27329 / % possible obs: 99 % / Redundancy: 4.8 % / Biso Wilson estimate: 66.8 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 6.1
Reflection shellResolution: 2.8→2.98 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 1.8 / % possible all: 96

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.91 Å / Rfactor Rfree error: 0.023 / Data cutoff high absF: 3042373.64 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: FOUR DISORDERED RESIDUES MISSED IN THE CHAIN B
RfactorNum. reflection% reflectionSelection details
Rfree0.238 110 0.4 %RANDOM
Rwork0.207 ---
obs0.207 27305 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.409 Å2 / ksol: 0.282 e/Å3
Displacement parametersBiso mean: 35.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.93 Å23.73 Å20 Å2
2---3.93 Å20 Å2
3---7.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7080 0 144 199 7423
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.31
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it1.572
X-RAY DIFFRACTIONc_scangle_it2.552.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.063 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.089 2 0 %
Rwork0.34 4497 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3NADP.PARAMNADP.TOP

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