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- PDB-2wgp: Crystal structure of human dual specificity phosphatase 14 -

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Basic information

Entry
Database: PDB / ID: 2wgp
TitleCrystal structure of human dual specificity phosphatase 14
ComponentsDUAL SPECIFICITY PROTEIN PHOSPHATASE 14
KeywordsHYDROLASE / MKP6 / DUSP14 / PROTEIN PHOSPHATASE / DUAL SPECIFICITY PHOSPHATASE
Function / homology
Function and homology information


MAP kinase tyrosine/serine/threonine phosphatase activity / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / RNA binding
Similarity search - Function
: / Atypical dual specificity phosphatase, subfamily B / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. ...: / Atypical dual specificity phosphatase, subfamily B / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Dual specificity protein phosphatase 14
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsLountos, G.T. / Tropea, J.E. / Cherry, S. / Waugh, D.S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Overproduction, Purification and Structure Determination of Human Dual-Specificity Phosphatase 14.
Authors: Lountos, G.T. / Tropea, J.E. / Cherry, S. / Waugh, D.S.
#1: Journal: J.Immunol. / Year: 2001
Title: Negative-Feedback Regulation of Cd28 Costimulation by a Novel Mitogen-Activated Protein Kinase Phosphatase, Mkp6.
Authors: Marti, F. / Krause, A. / Post, N.H. / Lyddane, C. / Dupont, B. / Sadelain, M. / King, P.D.
History
DepositionApr 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 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

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Assembly

Deposited unit
A: DUAL SPECIFICITY PROTEIN PHOSPHATASE 14
B: DUAL SPECIFICITY PROTEIN PHOSPHATASE 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7754
Polymers42,5852
Non-polymers1902
Water6,251347
1
A: DUAL SPECIFICITY PROTEIN PHOSPHATASE 14
B: DUAL SPECIFICITY PROTEIN PHOSPHATASE 14
hetero molecules

A: DUAL SPECIFICITY PROTEIN PHOSPHATASE 14
B: DUAL SPECIFICITY PROTEIN PHOSPHATASE 14
hetero molecules

A: DUAL SPECIFICITY PROTEIN PHOSPHATASE 14
B: DUAL SPECIFICITY PROTEIN PHOSPHATASE 14
hetero molecules

A: DUAL SPECIFICITY PROTEIN PHOSPHATASE 14
B: DUAL SPECIFICITY PROTEIN PHOSPHATASE 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,10116
Polymers170,3428
Non-polymers7608
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545y,-x-1,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
Buried area16070 Å2
ΔGint-154.95 kcal/mol
Surface area51240 Å2
MethodPISA
2
A: DUAL SPECIFICITY PROTEIN PHOSPHATASE 14
hetero molecules

A: DUAL SPECIFICITY PROTEIN PHOSPHATASE 14
hetero molecules

A: DUAL SPECIFICITY PROTEIN PHOSPHATASE 14
hetero molecules

A: DUAL SPECIFICITY PROTEIN PHOSPHATASE 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5518
Polymers85,1714
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545y,-x-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation2_445-x-1,-y-1,z1
Buried area5760 Å2
ΔGint-49.9 kcal/mol
Surface area33130 Å2
MethodPQS
3
B: DUAL SPECIFICITY PROTEIN PHOSPHATASE 14
hetero molecules

B: DUAL SPECIFICITY PROTEIN PHOSPHATASE 14
hetero molecules

B: DUAL SPECIFICITY PROTEIN PHOSPHATASE 14
hetero molecules

B: DUAL SPECIFICITY PROTEIN PHOSPHATASE 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5518
Polymers85,1714
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545y,-x-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation2_445-x-1,-y-1,z1
Buried area5810 Å2
ΔGint-46.1 kcal/mol
Surface area33220 Å2
MethodPQS
Unit cell
Length a, b, c (Å)85.011, 85.011, 115.112
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein DUAL SPECIFICITY PROTEIN PHOSPHATASE 14 / DUAL SPECIFICITY PHOSPHATASE 14 / MITOGEN-ACTIVATED PROTEIN KINASE PHOSPHATASE 6 / MKP-1-LIKE ...DUAL SPECIFICITY PHOSPHATASE 14 / MITOGEN-ACTIVATED PROTEIN KINASE PHOSPHATASE 6 / MKP-1-LIKE PROTEIN TYROSINE PHOSPHATASE / MAP KINASE PHOSPHATASE 6 / MKP-6 / MKP-L


Mass: 21292.689 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PJT92 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA 2 (DE3)
References: UniProt: O95147, protein-tyrosine-phosphatase, protein-serine/threonine phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.46 Å3/Da / Density % sol: 49.6 % / Description: NONE
Crystal growpH: 5.4
Details: 0.1M SODIUM CITRATE PH 5.4, 1.1 M AMMONIUM PHOSPHATE MONOBASIC,0.1 M NDSB-256 CRYOPROTECTED WITH 20% GLYCEROL

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 16, 2008 / Details: MSC OSMIC MIRROR SYSTEM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 32950 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.8
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.9 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.4.0057refinement
HKL-3000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ESB

2esb


Resolution: 1.88→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.695 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NO ELECTRON DENSITY WAS PRESENT FOR RESIDUES 2-23 AND THUS ARE NOT INCLUDED IN THE FINAL MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.22058 1670 5.1 %RANDOM
Rwork0.17548 ---
obs0.17775 31259 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.187 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.88→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2651 0 10 347 3008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222741
X-RAY DIFFRACTIONr_bond_other_d0.0050.021866
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.9423729
X-RAY DIFFRACTIONr_angle_other_deg1.03134523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8775337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55822.203118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91415448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8761522
X-RAY DIFFRACTIONr_chiral_restr0.0940.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213019
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02589
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_it0.661.51675
X-RAY DIFFRACTIONr_mcbond_other0.1921.5674
X-RAY DIFFRACTIONr_mcangle_it1.16222719
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.84831066
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9434.51008
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: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 122 -
Rwork0.275 2118 -
obs--91.69 %
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)
11.72590.00020.1550.92690.22981.4584-0.0785-0.16980.1850.0609-0.00620.0187-0.0513-0.03480.0847-0.10420.0098-0.0218-0.1079-0.03170.073-38.071-21.967.174
20.7543-0.09480.06841.04050.06550.8019-0.02520.0540.1099-0.0717-0.0451-0.1084-0.05550.08560.0704-0.0883-0.0152-0.0084-0.08170.01910.0745-28.953-25.388-6.3
340.5697-2.8051-1.81955.56190.95868.15920.62580.56131.2397-1.7467-0.5903-1.6275-0.17911.0562-0.0355-0.13290.00560.0866-0.08220.06860.0667-17.045-35.851-10.826
41.81430.417-0.86680.88230.38941.1771-0.0730.296-0.0644-0.11360.0619-0.0329-0.04050.02540.011-0.0799-0.0209-0.0109-0.0529-0.00010.026-34.266-24.405-52.233
50.73130.0701-0.040.7021-0.07241.30210.0075-0.02120.0478-0.0234-0.01360.034-0.07540.02390.0061-0.0698-0.00740.0097-0.08770.01170.0425-38.213-20.361-38.17
63.95532.1291.11371.39011.13911.50630.1041-0.37710.15510.1389-0.17150.0827-0.0963-0.1120.0674-0.04230.00560.0285-0.0609-0.00310.0504-49.583-22.444-26.76
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 103
2X-RAY DIFFRACTION2A104 - 185
3X-RAY DIFFRACTION3A186 - 191
4X-RAY DIFFRACTION4B26 - 80
5X-RAY DIFFRACTION5B81 - 162
6X-RAY DIFFRACTION6B163 - 190

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