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- PDB-3rl5: Rat metallophosphodiesterase MPPED2 H67R Mutant -

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Basic information

Entry
Database: PDB / ID: 3rl5
TitleRat metallophosphodiesterase MPPED2 H67R Mutant
ComponentsMetallophosphoesterase MPPED2
KeywordsHYDROLASE / alpha-beta fold / metallophosphodiesterase / active site mutant / single nucleotide polymorphism
Function / homology
Function and homology information


GMP binding / phosphoric diester hydrolase activity / AMP binding / manganese ion binding / Hydrolases; Acting on ester bonds
Similarity search - Function
Calcineurin-like phosphoesterase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Metallophosphoesterase MPPED2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.26 Å
AuthorsPodobnik, M. / Dermol, U.
Citation
Journal: J.Mol.Biol. / Year: 2011
Title: Unique utilization of a phosphoprotein phosphatase fold by a mammalian phosphodiesterase associated with WAGR syndrome.
Authors: Dermol, U. / Janardan, V. / Tyagi, R. / Visweswariah, S.S. / Podobnik, M.
#1: Journal: J.Biol.Chem. / Year: 2009
Title: Characterization of an evolutionatily conserved metallophosphoesterase that is expressed in the fetal brain and associated with the WAGR syndrome
Authors: Tyagi, R. / Shenoy, A.R. / Visweswariah, S.S.
#2: Journal: J.Biol.Chem. / Year: 2009
Title: A mycobacterial cyclic AMP phosphodiesterase that moonlights as a modifier of cell wall permeability
Authors: Podobnik, M. / Tyagi, R. / Matange, N. / Dermol, U. / Gupta, A.K. / Mattoo, R. / Seshardi, K. / Visweswariah, S.S.
#3: Journal: J.Mol.Biol. / Year: 2007
Title: Structural and biochemical analysis of the Rv0805 cyclic nucleotide phosphodiesterase from Mycobacterium tuberculosis
Authors: Shenoy, A.R. / Capuder, M. / Draskovic, P. / Lamba, D. / Visweswariah, S.S. / Podobnik, M.
#4: Journal: Biochemistry / Year: 2005
Title: The Rv0805 Gene from Mycobacterium tuberculosis Encodes a 3',5'-Cyclic Nucleotide Phosphodiesterase: Biochemical and Mutational Analysis
Authors: Shenoy, A.R. / Sreenath, N. / Podobnik, M. / Kovacevic, M. / Visweswariah, S.S.
History
DepositionApr 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallophosphoesterase MPPED2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7225
Polymers33,5181
Non-polymers2044
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.622, 69.848, 47.182
Angle α, β, γ (deg.)90.000, 103.520, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Metallophosphoesterase MPPED2 / 239FB / Fetal brain protein 239 homolog / Metallophosphoesterase domain-containing protein 2


Mass: 33517.723 Da / Num. of mol.: 1 / Mutation: H67R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Mpped2 / Plasmid: pProExHTc / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B1WBP0, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Ammonium nitrate, PEG 3350, CaCl2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.99996 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 22, 2009 / Details: monochromators, mirrors
RadiationMonochromator: Double crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 1.26→50 Å / Num. all: 84002 / Num. obs: 83943 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 11.242 Å2 / Rmerge(I) obs: 0.059 / Χ2: 1 / Net I/σ(I): 16.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.26-1.293.90.25155120.998199.2
1.29-1.3240.19755591.0021100
1.32-1.364.10.16555851.0011100
1.36-1.44.10.14255561.0011100
1.4-1.444.10.116562411100
1.44-1.494.10.103555911100
1.49-1.554.10.089561011100
1.55-1.624.20.07656050.9991100
1.62-1.714.20.06655730.9991100
1.71-1.824.20.05956131.0021100
1.82-1.964.20.051560811100
1.96-2.154.20.04656181.0011100
2.15-2.474.30.04156091.0021100
2.47-3.114.30.04256310.9991100
3.11-504.20.06556811199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å20.75 Å
Translation3 Å20.75 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER1.3.1phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.26→20.75 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.1778 / WRfactor Rwork: 0.1526 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.9159 / SU B: 1.016 / SU ML: 0.021 / SU R Cruickshank DPI: 0.0436 / SU Rfree: 0.0418 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1744 8430 10 %RANDOM
Rwork0.1519 ---
obs0.1542 83935 99.92 %-
all-84002 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 56.65 Å2 / Biso mean: 16.8614 Å2 / Biso min: 7.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å2-0.39 Å2
2---0.1 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.26→20.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 10 285 2545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222328
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.9523177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2795277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42323.964111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.55615359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2531512
X-RAY DIFFRACTIONr_chiral_restr0.0940.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021819
X-RAY DIFFRACTIONr_nbd_refined0.1990.21094
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21616
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2253
X-RAY DIFFRACTIONr_metal_ion_refined0.0920.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3010.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0610.216
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1260.21
X-RAY DIFFRACTIONr_mcbond_it1.3891.51425
X-RAY DIFFRACTIONr_mcangle_it2.04522291
X-RAY DIFFRACTIONr_scbond_it3.12431025
X-RAY DIFFRACTIONr_scangle_it3.4754.5886
X-RAY DIFFRACTIONr_rigid_bond_restr2.93932450
X-RAY DIFFRACTIONr_sphericity_free5.163287
X-RAY DIFFRACTIONr_sphericity_bonded4.0932258
LS refinement shellResolution: 1.26→1.292 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.176 622 -
Rwork0.144 5471 -
all-6093 -
obs--99.33 %

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