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- PDB-2oog: Crystal structure of glycerophosphoryl diester phosphodiesterase ... -

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Basic information

Entry
Database: PDB / ID: 2oog
TitleCrystal structure of glycerophosphoryl diester phosphodiesterase from Staphylococcus aureus
ComponentsGlycerophosphoryl diester phosphodiesterase
KeywordsHYDROLASE / PHOSPHATASE / GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / New York SGX Research Center for Structural Genomics / NYSGRC / NYSGXRC
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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPatskovsky, Y. / Fedorov, E. / Toro, R. / Sauder, J.M. / Smith, D. / Freeman, J. / Maletic, M. / Powell, A. / Gheyi, T. / Wasserman, S.R. ...Patskovsky, Y. / Fedorov, E. / Toro, R. / Sauder, J.M. / Smith, D. / Freeman, J. / Maletic, M. / Powell, A. / Gheyi, T. / Wasserman, S.R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase from Staphylococcus Aureus
Authors: Patskovsky, Y. / Sauder, J.M. / Smith, D. / Freeman, J. / Maletic, M. / Powell, A. / Gheyi, T. / Wasserman, S.R. / Burley, S.K. / Almo, S.C.
History
DepositionJan 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2007Group: 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_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.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 1.5Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,41057
Polymers199,8506
Non-polymers4,56051
Water16,051891
1
A: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,21411
Polymers33,3081
Non-polymers90610
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,39113
Polymers33,3081
Non-polymers1,08212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6545
Polymers33,3081
Non-polymers3464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,29912
Polymers33,3081
Non-polymers99011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8347
Polymers33,3081
Non-polymers5266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0189
Polymers33,3081
Non-polymers7108
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.312, 183.546, 176.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B
32C
42D
52E
62F

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNLEULEUAA44 - 22814 - 198
21GLNGLNLEULEUBB44 - 22814 - 198
31GLNGLNLEULEUCC44 - 22814 - 198
41GLNGLNLEULEUDD44 - 22814 - 198
51GLNGLNLEULEUEE44 - 22814 - 198
61GLNGLNLEULEUFF44 - 22814 - 198
12ILEILEILEILEAA245 - 308215 - 278
22ILEILEILEILEBB245 - 308215 - 278
32ILEILEILEILECC245 - 308215 - 278
42ILEILEILEILEDD245 - 308215 - 278
52ILEILEILEILEEE245 - 308215 - 278
62ILEILEILEILEFF245 - 308215 - 278

NCS ensembles :
ID
1
2

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Components

#1: Protein
Glycerophosphoryl diester phosphodiesterase


Mass: 33308.273 Da / Num. of mol.: 6
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: A0A0H3K7S1*PLUS, glycerophosphodiester phosphodiesterase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 891 / 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: 3.19 Å3/Da / Density % sol: 61.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: O.1M HEPES PH 7.5, 25% PEG 3350, 0.2M AMMONIUM SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9794 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 16, 2006 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 124065 / Num. obs: 124065 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 47.63 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.054 / Net I/σ(I): 8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.8 / Num. unique all: 12275 / Rsym value: 0.36 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHASERphasing
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YDY

1ydy


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.714 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.254 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28044 3742 3 %RANDOM
Rwork0.23484 ---
obs0.2362 120201 97.16 %-
all-120201 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.26 Å2
Baniso -1Baniso -2Baniso -3
1--1.89 Å20 Å20 Å2
2--1.05 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13120 0 270 891 14281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02113875
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.95718724
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.81451669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.27224.89730
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.704152495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1051563
X-RAY DIFFRACTIONr_chiral_restr0.1620.21957
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210513
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1370.35960
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.59016
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.51534
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0140.51
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.348
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.521
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.13938270
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it9.072413074
X-RAY DIFFRACTIONr_scbond_it11.08156221
X-RAY DIFFRACTIONr_scangle_it14.21875614
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1421tight positional0.130.2
12B1421tight positional0.140.2
13C1421tight positional0.120.2
14D1421tight positional0.120.2
15E1421tight positional0.160.2
16F1421tight positional0.140.2
21A515tight positional0.110.2
22B515tight positional0.10.2
23C515tight positional0.140.2
24D515tight positional0.090.2
25E515tight positional0.120.2
26F515tight positional0.110.2
11A1421tight thermal9.2220
12B1421tight thermal13.5920
13C1421tight thermal14.1920
14D1421tight thermal8.0420
15E1421tight thermal13.2920
16F1421tight thermal8.2220
21A515tight thermal9.7720
22B515tight thermal19.2720
23C515tight thermal17.9120
24D515tight thermal11.5220
25E515tight thermal17.5520
26F515tight thermal9.1420
LS refinement shellResolution: 2.2→2.26 Å / Rfactor Rfree error: 0.003 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 265 -
Rwork0.267 8619 -
obs-8619 96.32 %

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