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- PDB-2d0i: Crystal Structure PH0520 protein from Pyrococcus horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 2d0i
TitleCrystal Structure PH0520 protein from Pyrococcus horikoshii OT3
Componentsdehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / 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, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 333aa long hypothetical dehydrogenase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsLokanath, N.K. / Terao, Y. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure PH0520 protein from Pyrococcus horikoshii OT3
Authors: Lokanath, N.K. / Terao, Y. / Kunishima, N.
History
DepositionAug 2, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 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
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dehydrogenase
B: dehydrogenase
C: dehydrogenase
D: dehydrogenase


Theoretical massNumber of molelcules
Total (without water)152,4464
Polymers152,4464
Non-polymers00
Water18,5551030
1
A: dehydrogenase
B: dehydrogenase


Theoretical massNumber of molelcules
Total (without water)76,2232
Polymers76,2232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-23 kcal/mol
Surface area26990 Å2
MethodPISA
2
C: dehydrogenase
D: dehydrogenase


Theoretical massNumber of molelcules
Total (without water)76,2232
Polymers76,2232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-27 kcal/mol
Surface area27090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.756, 63.739, 131.978
Angle α, β, γ (deg.)90.00, 103.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
dehydrogenase /


Mass: 38111.473 Da / Num. of mol.: 4
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: GenBank: 14590422, UniProt: O58256*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1030 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 5.8
Details: Sodium Cacodylate, PEG 4000, pH 5.8, microbatch, temperature 295.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B111
SYNCHROTRONSPring-8 BL26B120.919, 0.9203, 0.9252
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS1IMAGE PLATEMay 21, 2005Graphite
RIGAKU RAXIS V2IMAGE PLATEOct 30, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9191
30.92031
40.92521
ReflectionResolution: 1.95→50 Å / Num. all: 105186 / Num. obs: 101628 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 6.8
Reflection shellResolution: 1.95→2.02 Å / % possible all: 98.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→34.69 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2361923.3 / 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
Rfree0.265 5136 5.1 %RANDOM
Rwork0.235 ---
obs0.235 101628 97 %-
all-105186 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.7255 Å2 / ksol: 0.318178 e/Å3
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.54 Å20 Å22.42 Å2
2--5.29 Å20 Å2
3----9.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.95→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10732 0 0 1030 11762
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.012
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 798 5 %
Rwork0.292 15214 -
obs--94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramprotein.top

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