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- PDB-4oec: Crystal structure of glycerophosphodiester phosphodiesterase from... -

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Basic information

Entry
Database: PDB / ID: 4oec
TitleCrystal structure of glycerophosphodiester phosphodiesterase from Thermococcus kodakarensis KOD1
ComponentsGlycerophosphoryl diester phosphodiesterase
KeywordsHYDROLASE / TIM Barrel
Function / homology
Function and homology information


phosphoric diester hydrolase activity / lipid metabolic process / metal ion binding
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 speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsAtsuta, Y. / You, D.J. / Takano, K. / Koga, Y. / Kanaya, S.
CitationJournal: To be Published
Title: Crystal structure of glycerophosphodiester phosphodiesterase from Thermococcus kodakarensis KOD1
Authors: Atsuta, Y. / You, D.J. / Takano, K. / Koga, Y. / Kanaya, S.
History
DepositionJan 13, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycerophosphoryl diester phosphodiesterase
B: Glycerophosphoryl diester phosphodiesterase
C: Glycerophosphoryl diester phosphodiesterase
D: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3218
Polymers114,2244
Non-polymers974
Water12,484693
1
A: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5802
Polymers28,5561
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5802
Polymers28,5561
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5802
Polymers28,5561
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5802
Polymers28,5561
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.724, 132.034, 171.639
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glycerophosphoryl diester phosphodiesterase


Mass: 28555.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: TK1397 / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus
References: UniProt: Q5JGZ3, glycerophosphodiester phosphodiesterase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 693 / 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: 2.17 Å3/Da / Density % sol: 43.28 % / Mosaicity: 0.507 ° / Mosaicity esd: 0.002 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30%(w/v) PEG4000, 0.2M Magnesium chloride hexahydrate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Jul 4, 2012
RadiationMonochromator: horizontal focusing mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 79998 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.6 % / Rmerge(I) obs: 0.142 / Rsym value: 0.142 / Net I/σ(I): 23.493
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
1.9-1.9314.40.55839431100
1.93-1.9714.40.49439561100
1.97-2.0114.30.41639601100
2.01-2.0514.40.37639351100
2.05-2.0914.30.34539861100
2.09-2.1414.50.30438991100
2.14-2.1914.20.26640201100
2.19-2.2514.20.23939051100
2.25-2.3213.90.21940021100
2.32-2.3914.10.20439511100
2.39-2.4813.80.18439591100
2.48-2.5813.70.16940331100
2.58-2.713.70.1639651100
2.7-2.8413.70.15339881100
2.84-3.0213.50.1424029199.9
3.02-3.2513.30.1374018199.9
3.25-3.5813.20.1314059199.9
3.58-4.0911.50.1154026198.9
4.09-5.1610.20.1014041198.2
5.16-50130.0954323199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2otd

2otd


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.2426 / WRfactor Rwork: 0.1901 / FOM work R set: 0.8283 / SU B: 3.673 / SU ML: 0.111 / SU R Cruickshank DPI: 0.1734 / SU Rfree: 0.1639 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2499 3998 5 %RANDOM
Rwork0.1942 ---
all0.197 ---
obs0.197 79606 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.6 Å2 / Biso mean: 30.063 Å2 / Biso min: 13.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å2-0 Å2-0 Å2
2--1.91 Å20 Å2
3----2.99 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8016 0 4 693 8713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0228140
X-RAY DIFFRACTIONr_angle_refined_deg0.9781.98211008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2325988
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.31224.388392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.998151560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1111572
X-RAY DIFFRACTIONr_chiral_restr0.0890.21264
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0216036
X-RAY DIFFRACTIONr_mcbond_it1.5071.54940
X-RAY DIFFRACTIONr_mcangle_it2.33528008
X-RAY DIFFRACTIONr_scbond_it3.90633200
X-RAY DIFFRACTIONr_scangle_it5.9734.53000
LS refinement shellResolution: 1.9→1.943 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 277 -
Rwork0.213 5316 -
all-5593 -
obs--96.7 %

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