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- PDB-1yb4: Crystal Structure of the Tartronic Semialdehyde Reductase from Sa... -

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Basic information

Entry
Database: PDB / ID: 1yb4
TitleCrystal Structure of the Tartronic Semialdehyde Reductase from Salmonella typhimurium LT2
Componentstartronic semialdehyde reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Tartronic Semialdehyde Reductase / Salmonella typhimurium LT2 / PSI / Protein Structure Initiative / The Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


2-hydroxy-3-oxopropionate reductase / 2-hydroxy-3-oxopropionate reductase activity / glyoxylate metabolic process / NAD binding / NADP binding
Similarity search - Function
2-hydroxy-3-oxopropionate reductase / 3-hydroxyisobutyrate dehydrogenase-related, conserved site / 3-hydroxyisobutyrate dehydrogenase signature. / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 ...2-hydroxy-3-oxopropionate reductase / 3-hydroxyisobutyrate dehydrogenase-related, conserved site / 3-hydroxyisobutyrate dehydrogenase signature. / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tartronic semialdehyde reductase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsKim, Y. / Wu, R. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J Struct Funct Genomics / Year: 2009
Title: X-ray crystal structure of GarR-tartronate semialdehyde reductase from Salmonella typhimurium.
Authors: Osipiuk, J. / Zhou, M. / Moy, S. / Collart, F. / Joachimiak, A.
History
DepositionDec 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tartronic semialdehyde reductase
B: tartronic semialdehyde reductase


Theoretical massNumber of molelcules
Total (without water)63,5942
Polymers63,5942
Non-polymers00
Water3,801211
1
A: tartronic semialdehyde reductase
B: tartronic semialdehyde reductase

A: tartronic semialdehyde reductase
B: tartronic semialdehyde reductase


Theoretical massNumber of molelcules
Total (without water)127,1874
Polymers127,1874
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)98.335, 134.255, 48.216
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein tartronic semialdehyde reductase


Mass: 31796.781 Da / Num. of mol.: 2 / Fragment: Tartronic Semialdehyde Reductase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: Q8ZR83, 2-hydroxy-3-oxopropionate reductase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG8000, TrisHCl, magnesium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.9794
SYNCHROTRONAPS 19-ID20.9794
Detector
TypeIDDetectorDateDetails
SBC-21CCDFeb 12, 2004mirrors
ADSC Q3152CCDDec 4, 2004mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal monochromator, SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
2Double crystal monochromator, SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.38→33.35 Å / Num. all: 25548 / Num. obs: 24924 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 8.7
Reflection shellResolution: 2.38→2.53 Å / % possible all: 98.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→33.35 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 381716.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.304 2305 10 %RANDOM
Rwork0.229 ---
all0.236 23070 --
obs0.236 23070 89.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.0818 Å2 / ksol: 0.311781 e/Å3
Displacement parametersBiso mean: 40.3 Å2
Baniso -1Baniso -2Baniso -3
1--4.94 Å20 Å20 Å2
2---5.83 Å20 Å2
3---10.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.4→33.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4322 0 0 211 4533
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.831.5
X-RAY DIFFRACTIONc_mcangle_it2.912
X-RAY DIFFRACTIONc_scbond_it3.312
X-RAY DIFFRACTIONc_scangle_it4.542.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.419 324 9.4 %
Rwork0.316 3111 -
obs-3111 81.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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