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- PDB-1v8e: Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase ... -

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Basic information

Entry
Database: PDB / ID: 1v8e
TitleCrystal Structure of Glycerophosphoryl Diester Phosphodiesterase from Thermus thermophilus HB8
Componentsputative glycerophosphoryl diester phosphodiesterase
KeywordsHYDROLASE / Glycerophosphoryl diester phosphodiesterase / Glycerophosphodiester phosphodiesterase / Thermus thermophilus / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


phosphoric diester hydrolase activity / lipid metabolic process
Similarity search - Function
Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / Phosphatidylinositol (PI) phosphodiesterase / Phosphatidylinositol-specific phospholipase X-box domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Glycerophosphoryl diester phosphodiesterase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsIshijima, J. / Ida, K. / Yutani, K. / Miyano, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of glycerophosphoryl diester phosphodiesterase from Thermus thermophilus HB8
Authors: Ishijima, J. / Ida, K. / Yutani, K. / Miyano, M.
History
DepositionJan 5, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: 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: putative glycerophosphoryl diester phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)24,4351
Polymers24,4351
Non-polymers00
Water5,242291
1
A: putative glycerophosphoryl diester phosphodiesterase

A: putative glycerophosphoryl diester phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)48,8702
Polymers48,8702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_764-x+2,-x+y+1,-z-1/31
Buried area1300 Å2
ΔGint-14 kcal/mol
Surface area18300 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.221, 74.221, 73.518
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a dimer covalently bound by disulfide bond.

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Components

#1: Protein putative glycerophosphoryl diester phosphodiesterase


Mass: 24435.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli)
References: GenBank: 55978324, UniProt: Q53W25*PLUS, glycerophosphodiester phosphodiesterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.14 Å3/Da / Density % sol: 41.96 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 8.1
Details: ammonium sulfate, dioxane, pH 8.1, Microbatch, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL45PX11.009
SYNCHROTRONSPring-8 BL26B120.9791, 0.97945, 0.96
Detector
TypeIDDetectorDate
RIGAKU RAXIS V1IMAGE PLATEApr 21, 2002
RIGAKU JUPITER 2102CCDJul 11, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1mirrorSINGLE WAVELENGTHMx-ray1
2mirrorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.0091
20.97911
30.979451
40.961
ReflectionResolution: 1.5→50 Å / Num. all: 37844 / Num. obs: 36456 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.27 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 8
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.65 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.5→48.39 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2349 3638 RANDOM
Rwork0.2047 --
all0.2075 37844 -
obs0.2075 36456 -
Displacement parametersBiso mean: 23.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.56 Å20.92 Å20 Å2
2--3.56 Å20 Å2
3----7.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.5→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 0 291 1955
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.95
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.323 552 -
Rwork0.285 --
obs-5576 89.8 %

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