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- PDB-4jmj: Structure of dusp11 -

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Basic information

Entry
Database: PDB / ID: 4jmj
TitleStructure of dusp11
ComponentsRNA/RNP complex-1-interacting phosphatase
KeywordsHYDROLASE / alpha/beta hydrolase
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / polynucleotide 5'-phosphatase activity / phosphatase activity / RNA processing / protein dephosphorylation / intercellular bridge / protein tyrosine phosphatase activity / fibrillar center / nuclear speck / mitochondrion ...Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / polynucleotide 5'-phosphatase activity / phosphatase activity / RNA processing / protein dephosphorylation / intercellular bridge / protein tyrosine phosphatase activity / fibrillar center / nuclear speck / mitochondrion / RNA binding / nucleoplasm / nucleus
Similarity search - Function
: / 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 ...: / 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 / RNA/RNP complex-1-interacting phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.382 Å
AuthorsJeong, D.G. / Kim, S.J. / Ryu, S.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The family-wide structure and function of human dual-specificity protein phosphatases.
Authors: Jeong, D.G. / Wei, C.H. / Ku, B. / Jeon, T.J. / Chien, P.N. / Kim, J.K. / Park, S.Y. / Hwang, H.S. / Ryu, S.Y. / Park, H. / Kim, D.S. / Kim, S.J. / Ryu, S.E.
History
DepositionMar 14, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: RNA/RNP complex-1-interacting phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4403
Polymers21,3091
Non-polymers1302
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.779, 94.779, 44.304
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein RNA/RNP complex-1-interacting phosphatase / Dual specificity protein phosphatase 11 / Phosphatase that interacts with RNA/RNP complex 1


Mass: 21309.303 Da / Num. of mol.: 1 / Fragment: UNP residues 28-208 / Mutation: C125S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP11, PIR1 / Production host: Escherichia coli (E. coli)
References: UniProt: O75319, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 10, 2006
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→40 Å / Num. all: 9356 / Num. obs: 9276 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.38→2.47 Å / % possible all: 94

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Processing

Software
NameVersionClassification
HKL-3000data collection
AMoREphasing
CNS1.21refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YN9

1yn9


Resolution: 2.382→27.36 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.26 / σ(F): 1.32 / Phase error: 26.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.219 496 5.37 %
Rwork0.1781 8736 -
obs0.1804 9232 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.94 Å2 / Biso mean: 61.4401 Å2 / Biso min: 25.35 Å2
Refinement stepCycle: LAST / Resolution: 2.382→27.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 6 30 1540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071547
X-RAY DIFFRACTIONf_angle_d1.1522093
X-RAY DIFFRACTIONf_dihedral_angle_d16.032594
X-RAY DIFFRACTIONf_chiral_restr0.084217
X-RAY DIFFRACTIONf_plane_restr0.005276
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3821-2.62160.29581270.22742160228799
2.6216-3.00060.26921280.23052150227899
3.0006-3.77880.23861170.183821912308100
3.7788-27.36210.17971240.152122352359100
Refinement TLS params.Method: refined / Origin x: 35.9787 Å / Origin y: 11.8223 Å / Origin z: 3.0491 Å
111213212223313233
T0.4633 Å2-0.1166 Å20.0506 Å2-0.2656 Å2-0.0177 Å2--0.3359 Å2
L1.5096 °2-0.2733 °20.1176 °2-1.9898 °20.3033 °2--2.0453 °2
S-0.0018 Å °-0.0697 Å °-0.1367 Å °0.0092 Å °-0.126 Å °0.2468 Å °0.5406 Å °-0.3939 Å °-0.0043 Å °
Refinement TLS groupSelection details: all

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