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- PDB-2yut: Crystal Structure of Putative Short-Chain Oxidoreductase TTHB094 ... -

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Basic information

Entry
Database: PDB / ID: 2yut
TitleCrystal Structure of Putative Short-Chain Oxidoreductase TTHB094 from Thermus thermophilus HB8
ComponentsPutative short-chain oxidoreductase
KeywordsOXIDOREDUCTASE / Alpha and beta proteins (a/b) / NAD(P)-binding Rossmann-fold domains / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Putative short-chain oxidoreductase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsAgari, Y. / Shinkai, A. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of Putative Short-Chain Oxidoreductase TTHB094 from Thermus thermophilus HB8
Authors: Agari, Y. / Shinkai, A. / Kuramitsu, S.
History
DepositionApr 6, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative short-chain oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5292
Polymers21,7861
Non-polymers7431
Water2,144119
1
A: Putative short-chain oxidoreductase
hetero molecules

A: Putative short-chain oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0594
Polymers43,5722
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area5590 Å2
ΔGint-27 kcal/mol
Surface area18420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)149.091, 149.091, 47.721
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

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Components

#1: Protein Putative short-chain oxidoreductase


Mass: 21786.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q53W68
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.5164.98
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop6.210% 1,4-Dioxane, 1.6M Ammonium Sulfate, 0.1M MES, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, hanging drop6.210% 1,4-Dioxane, 1.8M Ammonium Sulfate, 0.1M MES, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B210.97888
SYNCHROTRONSPring-8 BL26B221
Detector
TypeIDDetectorDateDetails
RIGAKU JUPITER 2101CCDJun 27, 2006A fixed exit Si double crystal monochromator followed by a two dimensional focusing mirror which is coated in rhodium.
RIGAKU JUPITER 2102CCDOct 7, 2006A fixed exit Si double crystal monochromator followed by a two dimensional focusing mirror which is coated in rhodium.
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Fixed exit Si double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2Fixed exit Si double crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.978881
211
ReflectionResolution: 1.93→44.18 Å / Num. all: 23182 / Num. obs: 23182 / % possible obs: 99.7 % / Redundancy: 20.51 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.5
Reflection shellResolution: 1.93→2 Å / Redundancy: 21.09 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 9.1 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
CrystalCleardata reduction
CrystalCleardata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→23.86 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2348231.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1633 10 %RANDOM
Rwork0.19 ---
all0.194 16364 --
obs0.19 16364 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 75.5628 Å2 / ksol: 0.442622 e/Å3
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.31 Å2-0.23 Å20 Å2
2---4.31 Å20 Å2
3---8.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.2→23.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1489 0 48 119 1656
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.261.5
X-RAY DIFFRACTIONc_mcangle_it4.862
X-RAY DIFFRACTIONc_scbond_it6.642
X-RAY DIFFRACTIONc_scangle_it8.372.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 279 10.5 %
Rwork0.209 2370 -
obs-2649 99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3nap_prodrug.paramnap_prodrug.top

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