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- PDB-3no3: Crystal structure of a glycerophosphodiester phosphodiesterase (B... -

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Basic information

Entry
Database: PDB / ID: 3no3
TitleCrystal structure of a glycerophosphodiester phosphodiesterase (BDI_0402) from Parabacteroides distasonis ATCC 8503 at 1.89 A resolution
Componentsglycerophosphodiester phosphodiesterase
KeywordsHYDROLASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
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
DI(HYDROXYETHYL)ETHER / Putative glycerophosphodiester phosphodiesterase
Similarity search - Component
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.89 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a glycerophosphodiester phosphodiesterase (BDI_0402) from Parabacteroides distasonis ATCC 8503 at 1.89 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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.pdbx_leaving_atom_flag / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glycerophosphodiester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0795
Polymers27,8321
Non-polymers2474
Water5,368298
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.460, 40.876, 48.328
Angle α, β, γ (deg.)90.000, 99.390, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-302-

MG

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Components

#1: Protein glycerophosphodiester phosphodiesterase


Mass: 27832.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_0402 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6L916
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (22-258) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT (22-258) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2000M magnesium chloride, 30.0000% polyethylene glycol 4000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97941,0.97915
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 14, 2010 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979411
30.979151
ReflectionResolution: 1.89→26.955 Å / Num. obs: 21375 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.126 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 8.97
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.89-1.960.3072.36524411496.1
1.96-2.040.2542.96708419698.9
2.04-2.130.1754.16278394098.6
2.13-2.240.135.16446401898.8
2.24-2.380.1016.36609409598.4
2.38-2.560.0778.36596408598.4
2.56-2.820.05710.26540404597.9
2.82-3.230.04313.56680409897.7
3.23-4.060.03417.46585401696.7
4.06-26.9550.033206538396094.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.89→26.955 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.028 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.114
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 4. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 5. MAGNESIUM IONS (MG), GLYCEROL (GOL), AND FRAGMENTS OF POLYETHYLENE GLYCOL-4000 (PEG) FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1767 1099 5.1 %RANDOM
Rwork0.15 ---
obs0.1514 21374 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.02 Å2 / Biso mean: 24.3474 Å2 / Biso min: 9.11 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20 Å20.53 Å2
2--0.59 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.89→26.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 14 298 2221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222035
X-RAY DIFFRACTIONr_bond_other_d0.0040.021416
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.972758
X-RAY DIFFRACTIONr_angle_other_deg1.47533480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3845262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.17724.8100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62515393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2041513
X-RAY DIFFRACTIONr_chiral_restr0.1040.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022262
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02392
X-RAY DIFFRACTIONr_mcbond_it0.711.51224
X-RAY DIFFRACTIONr_mcbond_other0.2321.5493
X-RAY DIFFRACTIONr_mcangle_it1.2221993
X-RAY DIFFRACTIONr_scbond_it2.4983811
X-RAY DIFFRACTIONr_scangle_it3.6234.5752
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 73 -
Rwork0.211 1477 -
all-1550 -
obs--97.92 %
Refinement TLS params.Method: refined / Origin x: -24.503 Å / Origin y: 23.306 Å / Origin z: 11.998 Å
111213212223313233
T0.076 Å2-0.0067 Å20.0114 Å2-0.1042 Å20.0004 Å2--0.01 Å2
L1.2309 °20.1625 °20.007 °2-0.6547 °2-0.0329 °2--1.0679 °2
S-0.0424 Å °0.1765 Å °-0.0114 Å °-0.0671 Å °0.0315 Å °-0.0784 Å °0.0177 Å °0.2084 Å °0.0109 Å °

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