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- PDB-1lqa: TAS PROTEIN FROM ESCHERICHIA COLI IN COMPLEX WITH NADPH -

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Basic information

Entry
Database: PDB / ID: 1lqa
TitleTAS PROTEIN FROM ESCHERICHIA COLI IN COMPLEX WITH NADPH
ComponentsTas protein
KeywordsOXIDOREDUCTASE / TIM barrel / Structure 2 Function Project / S2F / Structural Genomics
Function / homology
Function and homology information


aldo-keto reductase (NADPH) activity / cellular response to amino acid starvation / 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
Chem-NDP / Protein tas
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.604 Å
AuthorsObmolova, G. / Teplyakov, A. / Khil, P.P. / Howard, A.J. / Camerini-Otero, R.D. / Gilliland, G.L. / Structure 2 Function Project (S2F)
CitationJournal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 2003
Title: Crystal structure of the Escherichia coli Tas protein, an NADP(H)-dependent aldo-keto reductase
Authors: Obmolova, G. / Teplyakov, A. / Khil, P.P. / Howard, A.J. / Camerini-Otero, R.D. / Gilliland, G.L.
History
DepositionMay 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Tas protein
B: Tas protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5804
Polymers77,0892
Non-polymers1,4912
Water15,601866
1
A: Tas protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2902
Polymers38,5441
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tas protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2902
Polymers38,5441
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-25 kcal/mol
Surface area26120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.300, 81.460, 145.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tas protein


Mass: 38544.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Tas / Plasmid: pDEST14 / Cell line (production host): B834 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9T4
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 866 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris, 15% PEG8000, 50mM Ammonium Sulfate, 0.2M Magnesium Chloride, 10mM NADPH, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 MTris1reservoirpH8.5
215 %PEG80001reservoir
350 mMammonium sulfate1reservoir
40.2 M1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.0072 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 8, 2001
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0072 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 84533 / Num. obs: 84533 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 23.8
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3455 / % possible all: 57.8
Reflection
*PLUS
Num. obs: 160862 / % possible obs: 92 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MLPHAREphasing
REFMAC5refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.604→10 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.18589 2508 3 %RANDOM
Rwork0.14515 ---
all0.14634 81579 --
obs0.14634 81579 100 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.775 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.084 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.604→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5432 0 96 866 6394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0215663
X-RAY DIFFRACTIONr_angle_refined_deg1.7961.9767713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5083690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.68915976
X-RAY DIFFRACTIONr_chiral_restr0.1260.2855
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024319
X-RAY DIFFRACTIONr_nbd_refined0.2180.32702
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.5713
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5660.384
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.260.546
X-RAY DIFFRACTIONr_mcbond_it3.11343447
X-RAY DIFFRACTIONr_mcangle_it5.28685539
X-RAY DIFFRACTIONr_scbond_it6.49782216
X-RAY DIFFRACTIONr_scangle_it9.42282174
LS refinement shellResolution: 1.604→1.644 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.191 108
Rwork0.153 3650
Refinement
*PLUS
Highest resolution: 1.6 Å / % reflection Rfree: 3 % / Rfactor Rfree: 0.186 / Rfactor Rwork: 0.146
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.8

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