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- PDB-2vsw: The structure of the rhodanese domain of the human dual specifici... -

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Basic information

Entry
Database: PDB / ID: 2vsw
TitleThe structure of the rhodanese domain of the human dual specificity phosphatase 16
ComponentsDUAL SPECIFICITY PROTEIN PHOSPHATASE 16
KeywordsHYDROLASE / NUCLEUS / CASP8
Function / homology
Function and homology information


: / MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / Suppression of autophagy / Signaling by MAPK mutants / negative regulation of JUN kinase activity / RAF-independent MAPK1/3 activation / JUN kinase binding / mitogen-activated protein kinase binding ...: / MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / Suppression of autophagy / Signaling by MAPK mutants / negative regulation of JUN kinase activity / RAF-independent MAPK1/3 activation / JUN kinase binding / mitogen-activated protein kinase binding / myosin phosphatase activity / mitogen-activated protein kinase p38 binding / negative regulation of MAPK cascade / protein-serine/threonine phosphatase / phosphatase activity / phosphoprotein phosphatase activity / dephosphorylation / protein dephosphorylation / protein-tyrosine-phosphatase / Negative regulation of MAPK pathway / cytoplasmic vesicle / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase phosphatase / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Rhodanese-like domain ...Mitogen-activated protein (MAP) kinase phosphatase / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Dual specificity protein phosphatase 16
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMurray, J.W. / Barr, A. / Pike, A.C.W. / Elkins, J. / Phillips, C. / Wang, J. / Savitsky, P. / Roos, A. / Bishop, S. / Wickstroem, M. ...Murray, J.W. / Barr, A. / Pike, A.C.W. / Elkins, J. / Phillips, C. / Wang, J. / Savitsky, P. / Roos, A. / Bishop, S. / Wickstroem, M. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Burgess-Brown, N. / Pantic, N. / Bray, J. / von Delft, F. / Gileadi, O. / Knapp, S.
CitationJournal: To be Published
Title: The Structure of the Rhodanese Domain of the Human Dual Specifity Phosphatase 16
Authors: Murray, J.W. / Barr, A. / Pike, A.C.W. / Elkins, J. / Phillips, C. / Wang, J. / Salah, E. / Niesen, F. / Savitsky, P. / Roos, A. / Bishop, S. / Wickstroem, M. / Bountra, C. / Edwards, A.M. / ...Authors: Murray, J.W. / Barr, A. / Pike, A.C.W. / Elkins, J. / Phillips, C. / Wang, J. / Salah, E. / Niesen, F. / Savitsky, P. / Roos, A. / Bishop, S. / Wickstroem, M. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Burgess-Brown, N. / Pantic, N. / Bray, J. / von Delft, F. / Gileadi, O. / Knapp, S.
History
DepositionApr 30, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUAL SPECIFICITY PROTEIN PHOSPHATASE 16
B: DUAL SPECIFICITY PROTEIN PHOSPHATASE 16


Theoretical massNumber of molelcules
Total (without water)34,1492
Polymers34,1492
Non-polymers00
Water1,63991
1
A: DUAL SPECIFICITY PROTEIN PHOSPHATASE 16
B: DUAL SPECIFICITY PROTEIN PHOSPHATASE 16

A: DUAL SPECIFICITY PROTEIN PHOSPHATASE 16
B: DUAL SPECIFICITY PROTEIN PHOSPHATASE 16


Theoretical massNumber of molelcules
Total (without water)68,2994
Polymers68,2994
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5550 Å2
ΔGint-39.7 kcal/mol
Surface area28720 Å2
MethodPQS
2
A: DUAL SPECIFICITY PROTEIN PHOSPHATASE 16

A: DUAL SPECIFICITY PROTEIN PHOSPHATASE 16


Theoretical massNumber of molelcules
Total (without water)34,1492
Polymers34,1492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1580 Å2
ΔGint-10.6 kcal/mol
Surface area15550 Å2
MethodPQS
3
B: DUAL SPECIFICITY PROTEIN PHOSPHATASE 16

B: DUAL SPECIFICITY PROTEIN PHOSPHATASE 16


Theoretical massNumber of molelcules
Total (without water)34,1492
Polymers34,1492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1610 Å2
ΔGint-10.2 kcal/mol
Surface area15590 Å2
MethodPQS
Unit cell
Length a, b, c (Å)70.451, 69.128, 61.017
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2003-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.02783, -0.9996, -0.008519), (-0.9996, 0.02778, 0.006586), (-0.006346, 0.008699, -0.9999)
Vector: -0.0232, 0.09575, -31.1)

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Components

#1: Protein DUAL SPECIFICITY PROTEIN PHOSPHATASE 16 / MITOGEN-ACTIVATED PROTEIN KINASE PHOSPHATASE 7 / MAP KINASE PHOSPHATASE 7 / MKP-7 / DUSP16


Mass: 17074.695 Da / Num. of mol.: 2 / Fragment: RHODANESE DOMAIN, RESIDUES 5-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-R3-PRARE2 / References: UniProt: Q9BY84
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 50.1 % / Description: NONE
Crystal growDetails: 0.2 M NANO3, 0.1 M BIS-TRIS-PROPANE PH 8.5, 20% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9828
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9828 Å / Relative weight: 1
Reflection twinOperator: -K,H,L / Fraction: 0.207
ReflectionResolution: 2.2→49.22 Å / Num. obs: 15465 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 5.09 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 4.94
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.11 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.63 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OUC

2ouc


Resolution: 2.2→38.37 Å / Phase error: 26.71 / Stereochemistry target values: TWIN_LSQ_F
Details: DATA ARE PSEUDOMEROHEDRALLY TWINNED. REFINED AGAINST A TWIN TARGET IN PHENIX.
RfactorNum. reflection% reflection
Rfree0.227 774 5.15 %
Rwork0.169 --
obs0.172 15036 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.68 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 50.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.2216 Å20 Å20 Å2
2--6.128 Å20 Å2
3----7.8775 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 0 91 2123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042055
X-RAY DIFFRACTIONf_angle_d0.8132775
X-RAY DIFFRACTIONf_dihedral_angle_d13.686745
X-RAY DIFFRACTIONf_chiral_restr0.053341
X-RAY DIFFRACTIONf_plane_restr0.002352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2002-2.30030.3255800.27481694X-RAY DIFFRACTION98
2.3003-2.42150.2876920.24931729X-RAY DIFFRACTION98
2.4215-2.57320.2642990.22441745X-RAY DIFFRACTION98
2.5732-2.77190.2896870.23041778X-RAY DIFFRACTION98
2.7719-3.05070.26021060.20051791X-RAY DIFFRACTION98
3.0507-3.49190.2458720.16921829X-RAY DIFFRACTION98
3.4919-4.39840.17541030.12241842X-RAY DIFFRACTION98
4.3984-38.37270.20261060.13151883X-RAY DIFFRACTION98
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)
10.7015-0.3881-0.52970.4280.11130.4225-0.18050.3644-0.0425-0.3215-0.00380.1246-0.2081-0.27940.16170.3054-0.0538-0.08620.36910.0120.1541-13.69741.5639-31.8908
21.8708-1.79731.21250.9207-0.83221.9346-0.4102-0.30060.48690.17640.0770.106-0.3794-0.75090.34850.45950.1916-0.15440.4422-0.02190.455-14.843916.3858-23.813
31.7820.1176-0.23111.14230.4077-2.3723-0.38630.55410.0841-0.61750.33340.17280.00280.02320.00170.4649-0.1338-0.08770.34060.02470.1435-9.01365.2708-32.5221
41.0874-0.5361-0.16820.6572-0.22351.1958-0.06440.00530.2870.139-0.0509-0.2155-0.24410.05120.1260.1911-0.0169-0.03610.1593-0.01890.2636-0.972213.73040.8492
52.8118-0.9518-1.02950.7878-0.2190.75560.11790.3335-0.08170.1718-0.02640.2397-0.2512-0.3362-0.11060.20440.0911-0.01340.196-0.05540.3749-16.079515.1114-6.9814
60.7862-0.41110.14441.4616-0.08730.7542-0.08280.03710.03390.1942-0.00170.2156-0.05780.090.05760.203-0.00680.03590.2073-0.03570.192-5.05189.06781.5536
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN B AND RESID 5:48
2X-RAY DIFFRACTION2CHAIN B AND RESID 49:78
3X-RAY DIFFRACTION3CHAIN B AND RESID 79:138
4X-RAY DIFFRACTION4CHAIN A AND RESID 5:48
5X-RAY DIFFRACTION5CHAIN A AND RESID 49:78
6X-RAY DIFFRACTION6CHAIN A AND RESID 79:138

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