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- PDB-3rl3: Rat metallophosphodiesterase MPPED2 -

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Basic information

Entry
Database: PDB / ID: 3rl3
TitleRat metallophosphodiesterase MPPED2
ComponentsMetallophosphoesterase MPPED2
KeywordsHYDROLASE / alpha-beta fold / metallophosphodiesterase / wild type / GMP
Function / homology
Function and homology information


phosphoric diester hydrolase activity / GMP binding / 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
GUANOSINE-5'-MONOPHOSPHATE / : / Metallophosphoesterase MPPED2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.42 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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)34,45413
Polymers33,4991
Non-polymers95512
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.887, 69.752, 46.984
Angle α, β, γ (deg.)90.000, 103.140, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 33498.676 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 316 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: MnCl2, PEG 3350, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.97626 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 15, 2009 / Details: monochromators, mirrors
RadiationMonochromator: Double crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.42→50 Å / Num. all: 58321 / Num. obs: 57595 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 16.093 Å2 / Rmerge(I) obs: 0.08 / Χ2: 1 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.42-1.453.80.49137701197.3
1.45-1.493.90.41937510.998198
1.49-1.533.90.33338200.998198.3
1.53-1.5740.26838090.998198.2
1.57-1.6340.2338141.002198.3
1.63-1.6840.18437851.002198.9
1.68-1.7540.16238461.002198.7
1.75-1.8340.13438091.002199.1
1.83-1.9340.1138590.999199.4
1.93-2.0540.09438561199.4
2.05-2.2140.08338351199.6
2.21-2.434.10.07838770.999199.8
2.43-2.7840.07239010.999199.9
2.78-3.54.10.066390211100
3.5-5040.06639610.999199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.66 Å
Translation2.5 Å47.66 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: 1.42→47.67 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.2004 / WRfactor Rwork: 0.1719 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8986 / SU B: 1.881 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0711 / SU Rfree: 0.0616 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1871 5810 10.1 %RANDOM
Rwork0.16 ---
obs0.1627 57591 98.72 %-
all-58321 --
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: 55.39 Å2 / Biso mean: 18.2092 Å2 / Biso min: 8.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å2-0.34 Å2
2--0.29 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.42→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2218 0 38 304 2560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222349
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.963218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2775278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40323.964111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.45215352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.951511
X-RAY DIFFRACTIONr_chiral_restr0.0960.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021840
X-RAY DIFFRACTIONr_nbd_refined0.1980.21099
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21645
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2239
X-RAY DIFFRACTIONr_metal_ion_refined0.0180.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.214
X-RAY DIFFRACTIONr_mcbond_it1.1591.51417
X-RAY DIFFRACTIONr_mcangle_it1.75122290
X-RAY DIFFRACTIONr_scbond_it2.53831072
X-RAY DIFFRACTIONr_scangle_it3.1754.5928
X-RAY DIFFRACTIONr_rigid_bond_restr1.95232489
X-RAY DIFFRACTIONr_sphericity_free4.5593314
X-RAY DIFFRACTIONr_sphericity_bonded2.80932271
LS refinement shellResolution: 1.42→1.454 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 420 -
Rwork0.233 3633 -
all-4053 -
obs--93.97 %

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