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- PDB-2otd: The crystal structure of the glycerophosphodiester phosphodiester... -

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Basic information

Entry
Database: PDB / ID: 2otd
TitleThe crystal structure of the glycerophosphodiester phosphodiesterase from Shigella flexneri 2a
ComponentsGlycerophosphodiester phosphodiesterase
KeywordsHYDROLASE / Glycerophosphodiester phosphodiesterase / structural genomics / MCSG / PSI-2 / Protein Structure Initiative / Midwest 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
PHOSPHATE ION / Glycerophosphodiester phosphodiesterase / Glycerophosphodiester phosphodiesterase
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsZhang, R. / Wu, R. / Clancy, S. / Jiang, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the glycerophosphodiester phosphodiesterase from Shigella flexneri 2a
Authors: Zhang, R. / Wu, R. / Clancy, S. / Jiang, S. / Joachimiak, A.
History
DepositionFeb 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Glycerophosphodiester phosphodiesterase
B: Glycerophosphodiester phosphodiesterase
C: Glycerophosphodiester phosphodiesterase
D: Glycerophosphodiester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,0878
Polymers110,7074
Non-polymers3804
Water2,378132
1
A: Glycerophosphodiester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7722
Polymers27,6771
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycerophosphodiester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7722
Polymers27,6771
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycerophosphodiester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7722
Polymers27,6771
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycerophosphodiester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7722
Polymers27,6771
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.617, 82.185, 223.202
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThis protein exists as monomer. The deposited coords represent 4 monomers in the asymmetric unit.

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Components

#1: Protein
Glycerophosphodiester phosphodiesterase


Mass: 27676.691 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: 2457T, 301 / Gene: ugpQ, SF3466, S_4296 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q83PU8, UniProt: A0A0H2V2B5*PLUS, phosphodiesterase I
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.34 Å3/Da / Density % sol: 63.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.3M KCl, 10% PEG 6000, 15% Glycerol, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2006 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 44142 / Num. obs: 44014 / % possible obs: 99.71 % / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 19.56
Reflection shellResolution: 2.6→2.668 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 1.85 / Rsym value: 0.78 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→40.06 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.903 / SU B: 22.631 / SU ML: 0.233 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.453 / ESU R Free: 0.307
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27567 2365 5.1 %RANDOM
Rwork0.22095 ---
obs0.22362 44014 99.71 %-
all-44014 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.395 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2--2.34 Å20 Å2
3----2.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.205 Å0.043 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 2.6→40.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7612 0 20 132 7764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227808
X-RAY DIFFRACTIONr_bond_other_d0.0010.025316
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.96410604
X-RAY DIFFRACTIONr_angle_other_deg0.96312952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9625976
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55223.882340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.004151320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9051556
X-RAY DIFFRACTIONr_chiral_restr0.0810.21164
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028672
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021528
X-RAY DIFFRACTIONr_nbd_refined0.230.21934
X-RAY DIFFRACTIONr_nbd_other0.2030.25656
X-RAY DIFFRACTIONr_nbtor_refined0.180.23701
X-RAY DIFFRACTIONr_nbtor_other0.0940.24275
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2250
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1320.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2820.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2710.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0041.55868
X-RAY DIFFRACTIONr_mcbond_other0.1391.51988
X-RAY DIFFRACTIONr_mcangle_it1.1427764
X-RAY DIFFRACTIONr_scbond_it1.81433374
X-RAY DIFFRACTIONr_scangle_it2.5194.52840
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 172 -
Rwork0.334 3195 -
obs--99.2 %
Refinement TLS params.Method: refined / Origin x: 95.584 Å / Origin y: 53.638 Å / Origin z: -17.387 Å
111213212223313233
T0.241 Å2-0.0384 Å2-0.0704 Å2-0.4164 Å20.0102 Å2--0.2039 Å2
L0.3351 °2-0.0374 °2-0.5785 °2-0.3394 °2-0.0827 °2--1.0632 °2
S-0.0711 Å °-0.0567 Å °0.0314 Å °-0.0778 Å °0.198 Å °0.0215 Å °0.2407 Å °0.0177 Å °-0.127 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 502 - 50
2X-RAY DIFFRACTION1AA51 - 10051 - 100
3X-RAY DIFFRACTION1AA101 - 150101 - 150
4X-RAY DIFFRACTION1AA151 - 200151 - 200
5X-RAY DIFFRACTION1AA201 - 246201 - 246
6X-RAY DIFFRACTION1BB2 - 502 - 50
7X-RAY DIFFRACTION1BB51 - 10051 - 100
8X-RAY DIFFRACTION1BB101 - 150101 - 150
9X-RAY DIFFRACTION1BB151 - 200151 - 200
10X-RAY DIFFRACTION1BB201 - 246201 - 246
11X-RAY DIFFRACTION1CC2 - 502 - 50
12X-RAY DIFFRACTION1CC51 - 10051 - 100
13X-RAY DIFFRACTION1CC101 - 150101 - 150
14X-RAY DIFFRACTION1CC151 - 200151 - 200
15X-RAY DIFFRACTION1CC201 - 246201 - 246
16X-RAY DIFFRACTION1DD2 - 502 - 50
17X-RAY DIFFRACTION1DD51 - 10051 - 100
18X-RAY DIFFRACTION1DD101 - 150101 - 150
19X-RAY DIFFRACTION1DD151 - 200151 - 200
20X-RAY DIFFRACTION1DD201 - 246201 - 246

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