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- PDB-2wm8: Crystal structure of human magnesium-dependent phosphatase 1 of t... -

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Basic information

Entry
Database: PDB / ID: 2wm8
TitleCrystal structure of human magnesium-dependent phosphatase 1 of the haloacid dehalogenase superfamily (MGC5987)
ComponentsMAGNESIUM-DEPENDENT PHOSPHATASE 1
KeywordsHYDROLASE / HALOACID DEHALOGENASE / PROTEIN PHOSPHATASE / MAGNESIUM / METAL-BINDING
Function / homology
Function and homology information


acid phosphatase activity / 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
Magnesium-dependent phosphatase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsYue, W.W. / Shafqat, N. / Pike, A.C.W. / Chaikuad, A. / Bray, J.E. / Pilka, E.W. / Burgess-Brown, N. / Hapka, E. / Filippakopoulos, P. / von Delft, F. ...Yue, W.W. / Shafqat, N. / Pike, A.C.W. / Chaikuad, A. / Bray, J.E. / Pilka, E.W. / Burgess-Brown, N. / Hapka, E. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Human Magnesium-Dependent Phosphatase 1 of the Haloacid Dehalogenase Superfamily (Mgc5987)
Authors: Yue, W.W. / Shafqat, N. / Pike, A.C.W. / Chaikuad, A. / Bray, J.E. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U.
History
DepositionJun 30, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: MAGNESIUM-DEPENDENT PHOSPHATASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5202
Polymers21,4581
Non-polymers621
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.340, 62.340, 111.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein MAGNESIUM-DEPENDENT PHOSPHATASE 1 / MDP-1


Mass: 21458.297 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-R3-PRARE2
References: UniProt: Q86V88, Hydrolases; Acting on halide bonds; In carbon-halide compounds
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.55 Å3/Da / Density % sol: 51.78 % / Description: NONE
Crystal growDetails: 0.2M NA3(CIT),20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 37274 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.3
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0089refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U1P

1u1p


Resolution: 1.75→54.45 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.445 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19816 1215 5.3 %RANDOM
Rwork0.16341 ---
obs0.16517 21741 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.697 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2--0.61 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 1.75→54.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 4 251 1636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221471
X-RAY DIFFRACTIONr_bond_other_d0.0010.021036
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.9532001
X-RAY DIFFRACTIONr_angle_other_deg0.85932510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3365185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95423.41879
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90815255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9191514
X-RAY DIFFRACTIONr_chiral_restr0.0750.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02324
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5773871
X-RAY DIFFRACTIONr_mcbond_other0.453349
X-RAY DIFFRACTIONr_mcangle_it2.8451421
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.7658600
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.65110572
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 107 -
Rwork0.276 1548 -
obs--99.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2123-0.13270.14940.1057-0.06630.14340.00760.0104-0.0143-0.0053-0.03720.02330.0001-0.01650.02950.119-0.0095-0.00010.11040.01520.0981-0.5785-13.371215.5836
21.4958-1.4861-0.53042.60711.1850.5725-0.1798-0.2127-0.09310.1520.150.10780.04630.03250.02980.12080.01120.02480.14580.03490.0982-6.6157-12.562820.1466
30.4398-0.3574-0.12750.7447-0.11430.2633-0.0197-0.0310.01590.06270.0146-0.0462-0.0180.06740.00510.099-0.0048-0.02140.13010.00790.09536.3997-11.91099.8558
40.5097-0.2167-0.02550.3099-0.01921.0130.04170.0231-0.0767-0.0008-0.00980.06830.0712-0.0564-0.03190.1046-0.0095-0.01040.10950.00180.1131-2.9084-22.54684.9512
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-7 - 43
2X-RAY DIFFRACTION2A44 - 57
3X-RAY DIFFRACTION3A58 - 119
4X-RAY DIFFRACTION4A120 - 162

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