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- PDB-4mov: 1.45 A Resolution Crystal Structure of Protein Phosphatase 1 -

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Basic information

Entry
Database: PDB / ID: 4mov
Title1.45 A Resolution Crystal Structure of Protein Phosphatase 1
ComponentsSerine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE / catalytic subunit / Serine/threonine phosphatase / nucleus
Function / homology
Function and homology information


regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / glycogen granule / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / cadherin binding involved in cell-cell adhesion / protein phosphatase 1 binding / regulation of translational initiation in response to stress ...regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / glycogen granule / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / cadherin binding involved in cell-cell adhesion / protein phosphatase 1 binding / regulation of translational initiation in response to stress / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / dephosphorylation / regulation of canonical Wnt signaling pathway / glycogen metabolic process / protein dephosphorylation / protein-serine/threonine phosphatase / entrainment of circadian clock by photoperiod / branching morphogenesis of an epithelial tube / Triglyceride catabolism / protein serine/threonine phosphatase activity / Maturation of hRSV A proteins / phosphatase activity / telomere maintenance in response to DNA damage / negative regulation of transcription elongation by RNA polymerase II / transition metal ion binding / DARPP-32 events / positive regulation of glycogen biosynthetic process / ribonucleoprotein complex binding / : / phosphoprotein phosphatase activity / lung development / Downregulation of TGF-beta receptor signaling / adherens junction / circadian regulation of gene expression / positive regulation of transcription elongation by RNA polymerase II / regulation of circadian rhythm / response to lead ion / presynapse / dendritic spine / perikaryon / protein stabilization / iron ion binding / cell division / nucleolus / glutamatergic synapse / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase ...Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4503 Å
AuthorsChoy, M.S. / Peti, W. / Page, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Understanding the antagonism of retinoblastoma protein dephosphorylation by PNUTS provides insights into the PP1 regulatory code.
Authors: Choy, M.S. / Hieke, M. / Kumar, G.S. / Lewis, G.R. / Gonzalez-Dewhitt, K.R. / Kessler, R.P. / Stein, B.J. / Hessenberger, M. / Nairn, A.C. / Peti, W. / Page, R.
History
DepositionSep 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,80510
Polymers68,3242
Non-polymers4818
Water11,187621
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4386
Polymers34,1621
Non-polymers2765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3674
Polymers34,1621
Non-polymers2053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.724, 77.600, 133.035
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / PP-1A


Mass: 34162.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CA, PPP1A / Production host: Escherichia coli (E. coli)
References: UniProt: P62136, protein-serine/threonine phosphatase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES, 1.0 M Lithium Chloride, 20% PEG 6000, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.45→46.929 Å / Num. all: 120975 / Num. obs: 120264 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Biso Wilson estimate: 11.81 Å2
Reflection shellResolution: 1.45→1.48 Å / % possible all: 93.1

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3E7A

3e7a


Resolution: 1.4503→46.929 Å / Occupancy max: 1 / Occupancy min: 0.24 / SU ML: 0.11 / σ(F): 0 / Phase error: 14.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1665 6022 5.01 %Random
Rwork0.1501 ---
obs0.1509 120168 99.38 %-
all-120918 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.63 Å2 / Biso mean: 16.7662 Å2 / Biso min: 1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.4503→46.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4607 0 16 621 5244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134906
X-RAY DIFFRACTIONf_angle_d1.5366681
X-RAY DIFFRACTIONf_chiral_restr0.107731
X-RAY DIFFRACTIONf_plane_restr0.008872
X-RAY DIFFRACTIONf_dihedral_angle_d12.4491838
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4503-1.46680.22041790.17923498367792
1.4668-1.48410.17812000.1673545374595
1.4841-1.50220.19912040.16593649385397
1.5022-1.52120.19271890.16353766395599
1.5212-1.54120.19341960.155337753971100
1.5412-1.56230.15662330.148137543987100
1.5623-1.58470.17221970.145937943991100
1.5847-1.60830.16531930.140537943987100
1.6083-1.63340.14651950.138737823977100
1.6334-1.66020.16772060.138137853991100
1.6602-1.68890.15731810.136938504031100
1.6889-1.71960.16281810.141137973978100
1.7196-1.75260.17671850.144638234008100
1.7526-1.78840.15671700.145938243994100
1.7884-1.82730.17092110.145138114022100
1.8273-1.86980.16131930.144837963989100
1.8698-1.91660.18462050.148338154020100
1.9166-1.96840.17212030.145637984001100
1.9684-2.02630.15312030.142638184021100
2.0263-2.09170.1682090.146938214030100
2.0917-2.16650.15592150.141438064021100
2.1665-2.25320.15812000.144238494049100
2.2532-2.35580.16442240.150738314055100
2.3558-2.480.16932150.151338024017100
2.48-2.63530.16941920.155738754067100
2.6353-2.83880.19172010.160538674068100
2.8388-3.12440.16162230.159638584081100
3.1244-3.57640.17622160.148938814097100
3.5764-4.50530.13541830.137639744157100
4.5053-46.95340.17142200.166441084328100
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)
10.0014-0.00010.00020.0003-0.00050.001-0.00250.00340.0073-0.00190.0014-0.0018-0.00910.0091-0.00050.0456-0.01280.00580.07910.00810.082642.825428.557758.9214
20.07240.01960.04520.03440.01290.02870.0233-0.0672-0.00230.03860.00640.00960.0193-0.04670.0836-0.048-0.0306-0.00050.02430.00070.008934.005223.385375.9364
30.0110.00450.00250.01320.00870.0063-0.017-0.07140.0330.0351-0.0268-0.0063-0.0259-0.0581-0.00980.10330.012-0.00370.11-0.02320.071536.81433.425288.6364
40.00110.0001-0.00050.00120.00020.00110.0015-0.00440.00310.00220.00030.0060.0162-0.00950.00040.1005-0.0287-0.00230.0603-0.0050.079761.072542.5818113.4912
50.0230.00690.01910.04540.02620.02820.0010.0338-0.0101-0.04150.0294-0.046-0.03450.03950.03140.1129-0.04020.03130.0266-0.03920.063867.581348.490697.6596
60.0128-0.00310.0080.0036-0.00490.0071-0.02310.0569-0.0226-0.0684-0.00120.0346-0.061-0.0038-0.00420.1742-0.0178-0.00280.0901-0.0160.069158.705350.55482.7702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 7:32A7 - 32
2X-RAY DIFFRACTION2chain A and resid 33:216A33 - 216
3X-RAY DIFFRACTION3chain A and resid 217:299A217 - 299
4X-RAY DIFFRACTION4chain B and resid 7:32B7 - 32
5X-RAY DIFFRACTION5chain B and resid 33:198B33 - 198
6X-RAY DIFFRACTION6chain B and resid 199:299B199 - 299

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