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- PDB-3qc1: Protein Phosphatase Subunit: Alpha4 -

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Basic information

Entry
Database: PDB / ID: 3qc1
TitleProtein Phosphatase Subunit: Alpha4
ComponentsImmunoglobulin-binding protein 1
KeywordsSIGNALING PROTEIN / PP2A
Function / homology
Function and homology information


regulation of dephosphorylation / : / positive regulation of dephosphorylation / mitogen-activated protein kinase kinase binding / B cell activation / negative regulation of apoptotic signaling pathway / protein phosphatase 2A binding / microtubule / protein domain specific binding / protein-containing complex binding ...regulation of dephosphorylation / : / positive regulation of dephosphorylation / mitogen-activated protein kinase kinase binding / B cell activation / negative regulation of apoptotic signaling pathway / protein phosphatase 2A binding / microtubule / protein domain specific binding / protein-containing complex binding / enzyme binding / positive regulation of transcription by RNA polymerase II / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1140 / TAP42-like family / TAP46-like protein / TAP42/TAP46-like superfamily / TAP42-like family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Special / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Immunoglobulin-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å
AuthorsSpiller, B.W. / LeNoue-Newton, M.L. / Watkins, G.R. / Germane, K.L. / Zhou, P. / McCorvey, L.R. / Wadzinski, B.E.
CitationJournal: TO BE PUBLISHED
Title: The Mid1 and PP2Ac binding domains of Alpha4 are both required for Alpha4 to inhibit PP2Ac degradation
Authors: Spiller, B.W. / LeNoue-Newton, M.L. / Watkins, G.R. / Germane, K.L. / Zhou, P. / McCorvey, L.R. / Wadzinski, B.E.
History
DepositionJan 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin-binding protein 1


Theoretical massNumber of molelcules
Total (without water)27,6931
Polymers27,6931
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.600, 76.600, 72.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Immunoglobulin-binding protein 1 / Alpha4 phosphoprotein / CD79a-binding protein 1 / Lymphocyte signal transduction molecule alpha 4 / p52


Mass: 27693.416 Da / Num. of mol.: 1 / Fragment: UNP residues 1-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Igbp1, Pc52 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q61249
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 25% PEG 1500, pH 7.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 13159 / Num. obs: 12891 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 19.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1230 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.35→26.362 Å / SU ML: 0.42 / σ(F): 0 / Phase error: 30.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.267 1016 9.96 %
Rwork0.2088 --
obs0.2148 10200 96.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.597 Å2 / ksol: 0.313 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.5021 Å20 Å2-0 Å2
2--5.5021 Å20 Å2
3----11.0042 Å2
Refine analyzeLuzzati sigma a obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.35→26.362 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1543 0 0 42 1585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071567
X-RAY DIFFRACTIONf_angle_d1.0222104
X-RAY DIFFRACTIONf_dihedral_angle_d19.603614
X-RAY DIFFRACTIONf_chiral_restr0.07238
X-RAY DIFFRACTIONf_plane_restr0.004270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.47390.37181390.30611238X-RAY DIFFRACTION92
2.4739-2.62870.34161370.2731258X-RAY DIFFRACTION94
2.6287-2.83150.31021450.2491306X-RAY DIFFRACTION97
2.8315-3.1160.30671460.23931328X-RAY DIFFRACTION99
3.116-3.5660.31461500.22131349X-RAY DIFFRACTION99
3.566-4.48910.24971460.19091320X-RAY DIFFRACTION95
4.4891-26.36360.20631530.17431385X-RAY DIFFRACTION96
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)
10.3654-0.26450.4053.6722-0.5821.0741-0.1931-0.91180.10670.9390.383-1.06480.14770.37070.05520.39660.0787-0.1010.6369-0.00230.544727.570718.342519.3101
21.9271-0.0309-0.53742.2320.80441.3814-0.1034-0.5714-0.88420.5373-0.01120.5360.4891-0.06190.05690.44550.05980.01050.5019-0.02330.267517.214217.85618.9792
30.1703-1.3203-1.37444.03394.19043.63240.31460.2193-0.0704-0.2871-0.93970.4957-0.2289-0.61890.48480.25730.1341-0.0750.4478-0.07780.317117.12822.13779.3004
48.08486.9399-7.8998.7696-6.21817.8630.2099-3.0089-0.00611.0943-2.55230.5038-1.1779-0.05341.40820.4868-0.1111-0.01791.402-0.33830.224236.007543.9387-20.121
51.9774-0.53911.32780.1622-0.41031.00180.48590.8783-0.38170.1744-0.4381-0.76350.3872-0.9152-0.34350.74910.05-0.00271.48190.03840.375835.796136.9238-2.9033
60.13962.18880.76762.45731.84782.1881-0.05580.0824-0.0524-0.32220.08670.0207-0.28140.2015-0.0760.23640.0934-0.06650.4725-0.03090.34625.025128.09068.466
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(resid 10:36)
2X-RAY DIFFRACTION2(resid 37:65)
3X-RAY DIFFRACTION3(resid 67:122)
4X-RAY DIFFRACTION4(resid 143:155)
5X-RAY DIFFRACTION5(resid 156:168)
6X-RAY DIFFRACTION6(resid 169:222)

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