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- PDB-2p76: Crystal structure of a Glycerophosphodiester Phosphodiesterase fr... -

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Basic information

Entry
Database: PDB / ID: 2p76
TitleCrystal structure of a Glycerophosphodiester Phosphodiesterase from Staphylococcus aureus
ComponentsGlycerophosphoryl diester phosphodiesterase
KeywordsHYDROLASE / Structural genomics / NYSGXRC / target 6255a / Phosphodiesterase / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
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 / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Glycerophosphoryl diester phosphodiesterase / Glycerophosphoryl diester phosphodiesterase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a Glycerophosphodiester Phosphodiesterase from Staphylococcus aureus
Authors: Fedorov, A.A. / Fedorov, E.V. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMar 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 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

Downloads & links

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Assembly

Deposited unit
A: Glycerophosphoryl diester phosphodiesterase
B: Glycerophosphoryl diester phosphodiesterase
C: Glycerophosphoryl diester phosphodiesterase
D: Glycerophosphoryl diester phosphodiesterase
E: Glycerophosphoryl diester phosphodiesterase
F: Glycerophosphoryl diester phosphodiesterase
G: Glycerophosphoryl diester phosphodiesterase
H: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,38724
Polymers266,4668
Non-polymers92116
Water61334
1
A: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4233
Polymers33,3081
Non-polymers1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4233
Polymers33,3081
Non-polymers1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4233
Polymers33,3081
Non-polymers1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4233
Polymers33,3081
Non-polymers1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4233
Polymers33,3081
Non-polymers1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4233
Polymers33,3081
Non-polymers1152
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4233
Polymers33,3081
Non-polymers1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4233
Polymers33,3081
Non-polymers1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.164, 115.164, 451.335
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a monomer

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Components

#1: Protein
Glycerophosphoryl diester phosphodiesterase


Mass: 33308.273 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: N315 / Gene: glpQ, SA0820 / Plasmid: BC-pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q7A6H7, UniProt: A0A0H3JTK7*PLUS, glycerophosphodiester phosphodiesterase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.24 Å3/Da / Density % sol: 62.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.3 M Sodium citrate, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2006 / Details: mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. all: 98343 / Num. obs: 98343 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 45.7 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 26.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→24.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 182745.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 4954 5 %RANDOM
Rwork0.249 ---
all0.249 98343 --
obs0.249 98343 91 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.0655 Å2 / ksol: 0.341688 e/Å3
Displacement parametersBiso mean: 60 Å2
Baniso -1Baniso -2Baniso -3
1-4.04 Å210.04 Å20 Å2
2--4.04 Å20 Å2
3----8.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 2.6→24.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17488 0 56 34 17578
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it1.822
X-RAY DIFFRACTIONc_scangle_it2.952.5
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.421 455 5.6 %
Rwork0.409 7674 -
obs--76.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4GOL_xplor_par.txtGOL_xplor_top.txt
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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