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- PDB-1u7p: X-ray Crystal Structure of the Hypothetical Phosphotyrosine Phosp... -

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Basic information

Entry
Database: PDB / ID: 1u7p
TitleX-ray Crystal Structure of the Hypothetical Phosphotyrosine Phosphatase MDP-1 of the Haloacid Dehalogenase Superfamily
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 activity, metal-dependent / histone H2AXY142 phosphatase activity / protein-tyrosine-phosphatase / non-membrane spanning 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
TUNGSTATE(VI)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 19, 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 / pdbx_struct_conn_angle / struct_conn / 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_conn.ptnr2_label_seq_id / _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
B: magnesium-dependent phosphatase-1
C: magnesium-dependent phosphatase-1
D: magnesium-dependent phosphatase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,01410
Polymers74,4214
Non-polymers5936
Water7,494416
1
A: magnesium-dependent phosphatase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8773
Polymers18,6051
Non-polymers2722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: magnesium-dependent phosphatase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6292
Polymers18,6051
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: magnesium-dependent phosphatase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8773
Polymers18,6051
Non-polymers2722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: magnesium-dependent phosphatase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6292
Polymers18,6051
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.524, 57.651, 76.621
Angle α, β, γ (deg.)90.00, 91.97, 90.00
Int Tables number4
Space group name H-MP1211
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.: 4
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: WO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 291 K / pH: 8
Details: PEG 3350, sodium acetate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 19, 2003 / Details: OSMIC MIRRORS
RadiationMonochromator: OSMIC MIRRORS, NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→76.58 Å / Num. obs: 48167 / % possible obs: 93.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 17.4 Å2 / Rsym value: 0.061 / Net I/σ(I): 19.6
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.0485 / % possible all: 88.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HIGH RESOLUTION MODEL OF MDP-1 WITHOUT MAGNESIUM BOUND

Resolution: 1.9→76.58 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 908245.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.236 4380 10.1 %RANDOM
Rwork0.19 ---
obs0.19 43298 91.5 %-
all-47331 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.5318 Å2 / ksol: 0.337413 e/Å3
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1-9.7 Å20 Å20.67 Å2
2---3.78 Å20 Å2
3----5.92 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.9→76.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5212 0 14 416 5642
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it1.992
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it3.052.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 651 10.2 %
Rwork0.259 5754 -
obs--81.7 %

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