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- PDB-1u7o: Magnesium Dependent Phosphatase 1 (MDP-1) -

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Basic information

Entry
Database: PDB / ID: 1u7o
TitleMagnesium Dependent Phosphatase 1 (MDP-1)
Componentsmagnesium-dependent phosphatase-1
KeywordsHYDROLASE / HAD superfamily / phosphoryl transfer / phosphotyrosine phosphatase / aspartate nucleophile / enzyme evolution / structural enzymology / class III
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / metal ion binding
Similarity search - Function
Magnesium-dependent phosphatase-1, eukaryotic/archaeal-type / Acid Phosphatase / Magnesium-dependent phosphatase-1, eukaryotic-type / HAD-superfamily phosphatase, subfamily IIIC / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Magnesium-dependent phosphatase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPeisach, E. / Selengut, J.D. / Dunaway-Mariano, D. / Allen, K.N.
Citation
Journal: Biochemistry / Year: 2004
Title: X-ray crystal structure of the hypothetical phosphotyrosine phosphatase MDP-1 of the haloacid dehalogenase superfamily
Authors: Peisach, E. / Selengut, J.D. / Dunaway-Mariano, D. / Allen, K.N.
#1: Journal: Biochemistry / Year: 2000
Title: MDP-1: A novel eukaryotic magnesium-dependent phosphatase
Authors: Selengut, J.D. / Levine, R.L.
#2: Journal: Biochemistry / Year: 2001
Title: MDP-1 is a new and distinct member of the haloacid dehalogenase family of aspartate-dependent phosphohydrolases
Authors: Selengut, J.D.
#3: Journal: Biochemistry / Year: 2000
Title: The crystal structure of bacillus cereus phosphonoacetaldehyde hydrolase: insight into catalysis of phosphorus bond cleavage and catalytic diversification within the HAD enzyme superfamily
Authors: Morais, M.C. / Zhang, W. / Baker, A.S. / Zhang, G. / Dunaway-Mariano, D. / Allen, K.N.
History
DepositionAug 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: magnesium-dependent phosphatase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7233
Polymers18,6051
Non-polymers1182
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.405, 59.405, 99.557
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological unit is a monomer

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Components

#1: Protein magnesium-dependent phosphatase-1 / MDP-1


Mass: 18605.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: AF230273 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9D967
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.4 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, sodium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 20, 2003 / Details: osmic mirrors
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→19.42 Å / Num. all: 14718 / Num. obs: 14675 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 12.5 Å2 / Limit h max: 31 / Limit h min: 0 / Limit k max: 22 / Limit k min: 0 / Limit l max: 52 / Limit l min: 0 / Observed criterion F max: 445297.83 / Observed criterion F min: 0.77 / Rsym value: 0.07 / Net I/σ(I): 20.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.4 % / Num. unique all: 1433 / Rsym value: 0.435 / % possible all: 99.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MAD phased structure at lower resolution

Resolution: 1.9→19.42 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1451 10.2 %random
Rwork0.2 ---
all0.214 14661 --
obs0.214 14263 97.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 53.5491 Å2 / ksol: 0.401103 e/Å3
Displacement parametersBiso max: 62.08 Å2 / Biso mean: 22.4 Å2 / Biso min: 9.63 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.14 Å
Luzzati d res high-1.9
Refinement stepCycle: LAST / Resolution: 1.9→19.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1301 0 8 99 1408
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg22.5
X-RAY DIFFRACTIONx_torsion_impr_deg0.84
X-RAY DIFFRACTIONx_mcbond_it1.321.5
X-RAY DIFFRACTIONx_mcangle_it2.062
X-RAY DIFFRACTIONx_scbond_it2.012
X-RAY DIFFRACTIONx_scangle_it3.022.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.9-1.990.28718010.70.23715030.0211785168394.3
1.99-2.090.25615290.21315400.0211780169295.1
2.09-2.220.2617710.20.20615600.021808173796
2.22-2.390.2519010.80.215620.0181797175297.4
2.39-2.630.25418910.50.20416060.0181834179597.8
2.63-3.010.24218710.40.21316180.0181827180598.7
3.01-3.790.1961779.70.19216570.0151852183499
3.79-19.420.19219910.10.18717660.0141984196599
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3act.paramact.top

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