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- PDB-2d8a: Crystal Structure of PH0655 from Pyrococcus horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 2d8a
TitleCrystal Structure of PH0655 from Pyrococcus horikoshii OT3
ComponentsProbable L-threonine 3-dehydrogenase
KeywordsOXIDOREDUCTASE / Pyrococcus horikoshii OT3 / Structural genomics / PH0655 / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


L-threonine 3-dehydrogenase / L-threonine 3-dehydrogenase activity / L-threonine catabolic process to glycine / threonine metabolic process / NADP+ binding / amino acid binding / NAD+ binding / protein homotetramerization / zinc ion binding / cytoplasm
Similarity search - Function
L-threonine 3-dehydrogenase / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain ...L-threonine 3-dehydrogenase / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-threonine 3-dehydrogenase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsAsada, Y. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of PH0655 from Pyrococcus horikoshii OT3
Authors: Asada, Y. / Kunishima, N.
History
DepositionDec 2, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2006Provider: 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: Probable L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1447
Polymers38,1541
Non-polymers9906
Water4,738263
1
A: Probable L-threonine 3-dehydrogenase
hetero molecules

A: Probable L-threonine 3-dehydrogenase
hetero molecules

A: Probable L-threonine 3-dehydrogenase
hetero molecules

A: Probable L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,57728
Polymers152,6154
Non-polymers3,96224
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)85.084, 89.436, 122.413
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-649-

HOH

21A-650-

HOH

31A-687-

HOH

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Components

#1: Protein Probable L-threonine 3-dehydrogenase / PH0655


Mass: 38153.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O58389, L-threonine 3-dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 3.05 Å3/Da / Density % sol: 59.67 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 5.9
Details: 25% (v/v) 1,2-propanediol, 10% (v/v) glycerol, Imidazole pH 8.0, 0.2M Zn(OAc)2, pH 5.9, MICROBATCH, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97924 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 3, 2005
RadiationMonochromator: Bending Magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. all: 29497 / Num. obs: 29497 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 31.492 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.051 / Net I/σ(I): 16.3
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 7 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 5.08 / Num. unique all: 2926 / Rsym value: 0.244 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.05→28.41 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1481 -RANDOM
Rwork0.204 ---
all0.206 29497 --
obs0.206 29497 99.3 %-
Displacement parametersBiso mean: 37.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.46 Å20 Å20 Å2
2---5.6 Å20 Å2
3---1.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.05→28.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 49 263 2852
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 2.05→2.14 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.261 171 -
Rwork0.235 --
obs-3374 96.9 %

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