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- PDB-3qvq: The structure of an Oleispira antarctica phosphodiesterase OLEI02... -

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Basic information

Entry
Database: PDB / ID: 3qvq
TitleThe structure of an Oleispira antarctica phosphodiesterase OLEI02445 in complex with the product sn-glycerol-3-phosphate
ComponentsPhosphodiesterase Olei02445
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta hydrolase
Function / homologyPhosphatidylinositol (PI) phosphodiesterase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / SN-GLYCEROL-3-PHOSPHATE / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesOleispira antarctica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.602 Å
AuthorsSinger, A.U. / Kagan, O. / Evdokimova, E. / Cuff, M.E. / Edwards, A.M. / Joachimiak, A. / Yakunin, A.F. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The structure of an Oleispira antarctica phosphodiesterase OLEI02445 in complex with the product sn-glycerol-3-phosphate
Authors: Singer, A.U. / Kagan, O. / Evdokimova, E. / Cuff, M.E. / Edwards, A.M. / Joachimiak, A. / Yakunin, A.F. / Savchenko, A.
History
DepositionFeb 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphodiesterase Olei02445
B: Phosphodiesterase Olei02445
C: Phosphodiesterase Olei02445
D: Phosphodiesterase Olei02445
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,37151
Polymers112,1724
Non-polymers2,19847
Water16,592921
1
A: Phosphodiesterase Olei02445
D: Phosphodiesterase Olei02445
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,19026
Polymers56,0862
Non-polymers1,10424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-173 kcal/mol
Surface area19380 Å2
MethodPISA
2
B: Phosphodiesterase Olei02445
hetero molecules

C: Phosphodiesterase Olei02445
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,18025
Polymers56,0862
Non-polymers1,09423
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y+1/2,-z+1/21
Buried area5160 Å2
ΔGint-170 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.861, 92.717, 125.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Phosphodiesterase Olei02445


Mass: 28043.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: TEV cleaved / Source: (gene. exp.) Oleispira antarctica (bacteria) / Gene: OLEI02445 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: glycerophosphocholine phosphodiesterase

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Non-polymers , 8 types, 968 molecules

#2: Chemical
ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H9O6P
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 921 / 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: 2.09 Å3/Da / Density % sol: 41.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Magnesium Chloride, 0.1M Bis-Tris pH6.5, 25% PEG3350, cocrystallized with 2.5mM Glycero-3Phosphocholine, and cryoprotected with Paratone-N oil, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 28, 2009 / Details: Mirrors
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 1.6→37.259 Å / Num. all: 123770 / Num. obs: 122939 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 31.893
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 5.2 / Num. unique all: 5694 / Rsym value: 0.374 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6_289)refinement
SHELXCDphasing
SHELXEmodel building
REFMAC5.2.0019refinement
HKL-3000data collection
HKL-3000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD
Starting model: none

Resolution: 1.602→37.259 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 19.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2011 11860 5.04 %random
Rwork0.1724 ---
obs0.1738 235396 98.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.945 Å2 / ksol: 0.391 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.4442 Å2-0 Å2-0 Å2
2---1.9223 Å20 Å2
3----2.5219 Å2
Refinement stepCycle: LAST / Resolution: 1.602→37.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7803 0 101 921 8825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138435
X-RAY DIFFRACTIONf_angle_d0.99311553
X-RAY DIFFRACTIONf_dihedral_angle_d17.1582997
X-RAY DIFFRACTIONf_chiral_restr0.0721243
X-RAY DIFFRACTIONf_plane_restr0.0041498
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.6025-1.65970.243110850.2054210792216493
1.6597-1.72620.241511990.1948224532365299
1.7262-1.80480.21711590.1818225212368099
1.8048-1.89990.211412200.1701224872370799
1.8999-2.01890.193912530.16072261723870100
2.0189-2.17480.188211480.15332261623764100
2.1748-2.39360.190111470.162264023787100
2.3936-2.73990.204512240.1741226052382999
2.7399-3.45160.196711480.174224962364499
3.4516-37.26940.183312770.1629220222329998

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