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- PDB-4mbb: Cubic crystal form of PIR1 dual specificity phosphatase core -

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Basic information

Entry
Database: PDB / ID: 4mbb
TitleCubic crystal form of PIR1 dual specificity phosphatase core
ComponentsRNA/RNP complex-1-interacting phosphatase
KeywordsHYDROLASE / Atypical Dual Specificity Phosphatase / PIR1-core / RNA splicing / Helical hairpin / PTP-loop / deep catalytic cleft / Phosphate-binding loop (P-loop) / Acidic loop (WPD-loop) / RNA phosphatase / Dual specificity phosphatase / RNA-RNP complex-1 / dephosphorylation / nucleus
Function / homology
Function and homology information


protein tyrosine/serine/threonine phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / polynucleotide 5'-phosphatase activity / intercellular bridge / phosphatase activity / RNA processing / protein dephosphorylation / protein tyrosine phosphatase activity / fibrillar center / nuclear speck ...protein tyrosine/serine/threonine phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / polynucleotide 5'-phosphatase activity / intercellular bridge / phosphatase activity / RNA processing / protein dephosphorylation / protein tyrosine phosphatase activity / fibrillar center / nuclear speck / 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 / Dual specificity protein phosphatase domain profile. / 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 ...Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / 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 / Tyrosine specific protein phosphatases domain profile. / 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: 1.849 Å
AuthorsSankhala, R.S. / Lokareddy, R.K. / Cingolani, G.
CitationJournal: Biochemistry / Year: 2014
Title: Structure of Human PIR1, an Atypical Dual-Specificity Phosphatase.
Authors: Sankhala, R.S. / Lokareddy, R.K. / Cingolani, G.
History
DepositionAug 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: RNA/RNP complex-1-interacting phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6083
Polymers21,4771
Non-polymers1302
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: RNA/RNP complex-1-interacting phosphatase
hetero molecules

A: RNA/RNP complex-1-interacting phosphatase
hetero molecules

A: RNA/RNP complex-1-interacting phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8249
Polymers64,4323
Non-polymers3916
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_456z-1,x,y+11
crystal symmetry operation9_546y,z-1,x+11
Buried area4850 Å2
ΔGint-83 kcal/mol
Surface area25120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.740, 92.740, 92.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-513-

HOH

21A-516-

HOH

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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: 21477.498 Da / Num. of mol.: 1 / Fragment: UNP residues 29-207 / Mutation: C152S
Source method: isolated from a genetically manipulated source
Details: cell culture / Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP11, PIR1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O75319, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 3.09 Å3/Da / Density % sol: 60.26 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Bis-Tris 0.1M, NaCl 0.2M, polyethylene glycol 3350 22%, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1771
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X6A10.972
SYNCHROTRONNSLS X29A21.07
Detector
TypeIDDetectorDate
ADSC QUANTUM 2701CCDMar 19, 2013
ADSC QUANTUM 315r2CCDJun 19, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9721
21.071
ReflectionResolution: 1.85→15 Å / Num. obs: 22788 / % possible obs: 99.09 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.85→1.92 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YN9

1yn9


Resolution: 1.849→14.664 Å / SU ML: 0.19 / σ(F): 0.82 / Phase error: 18.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1875 1129 4.96 %RANDOM
Rwork0.1685 ---
obs0.1694 22769 99.09 %-
all-22788 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.849→14.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 6 181 1701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121572
X-RAY DIFFRACTIONf_angle_d1.3782129
X-RAY DIFFRACTIONf_dihedral_angle_d14.606609
X-RAY DIFFRACTIONf_chiral_restr0.109222
X-RAY DIFFRACTIONf_plane_restr0.007283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8485-1.93250.29141430.24022703X-RAY DIFFRACTION100
1.9325-2.03410.22521450.20892674X-RAY DIFFRACTION100
2.0341-2.16120.2131410.192710X-RAY DIFFRACTION100
2.1612-2.32740.19431390.17262706X-RAY DIFFRACTION100
2.3274-2.56060.19441380.17762716X-RAY DIFFRACTION100
2.5606-2.92850.21921400.17852716X-RAY DIFFRACTION100
2.9285-3.67990.20571430.16412721X-RAY DIFFRACTION99
3.6799-14.6640.14551400.15192694X-RAY DIFFRACTION95
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)
15.4903-3.0101-6.6361.80143.55458.0699-0.0975-1.07590.84170.9002-0.08850.6319-0.0191-0.0847-0.1750.5695-0.0439-0.00520.4435-0.18660.686311.615331.0366112.1285
23.5210.2956-0.80692.1791.33517.67740.2869-0.05280.4745-0.26660.1534-0.4859-0.89050.2791-0.24530.3832-0.08030.09890.2246-0.02710.424723.701529.070292.4934
32.74060.53920.75624.9821-1.99082.64560.0463-0.97060.63260.8954-0.07540.3349-1.5751-0.1635-0.43140.682-0.00210.05780.3321-0.12610.477715.89336.2435106.3712
42.90270.2027-0.61992.9740.02483.02870.36290.03730.8672-0.1259-0.0068-0.173-0.92640.0873-0.2730.5513-0.05680.11850.2448-0.00930.507617.325735.457796.2904
54.997-1.6332-1.2835.24171.35745.21460.10060.09510.5497-0.0690.01880.3418-0.8209-0.1478-0.06890.3482-0.00350.0210.30360.02680.26749.51227.192494.3572
63.35923.7687-3.72666.3114-5.54455.25930.24030.73880.3185-0.26390.64891.4379-0.424-0.9084-0.72570.36270.0561-0.00610.43660.02970.29098.856821.556782.8397
72.94740.9218-1.0323.4411.18121.09740.21470.29150.4011-0.47990.0907-0.1545-0.4463-0.2398-0.15790.32350.02050.08480.21330.06030.2317.504423.797586.08
83.7416-0.3128-0.06512.85480.85815.85030.00150.2517-0.0692-0.19010.0859-0.19820.06180.2647-0.09630.2459-0.02520.05390.27980.01030.263824.081414.84888.7288
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 53 )
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 64 )
4X-RAY DIFFRACTION4chain 'A' and (resid 65 through 101 )
5X-RAY DIFFRACTION5chain 'A' and (resid 102 through 123 )
6X-RAY DIFFRACTION6chain 'A' and (resid 124 through 140 )
7X-RAY DIFFRACTION7chain 'A' and (resid 141 through 171 )
8X-RAY DIFFRACTION8chain 'A' and (resid 172 through 207 )

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