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- PDB-6hkw: Crystal structure of human SDS22 -

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Basic information

Entry
Database: PDB / ID: 6hkw
TitleCrystal structure of human SDS22
ComponentsProtein phosphatase 1 regulatory subunit 7
KeywordsSIGNALING PROTEIN / LRR protein / PP1 regulator
Function / homology
Function and homology information


protein phosphatase regulator activity / enzyme regulator activity / positive regulation of protein dephosphorylation / chromosome / extracellular exosome / nucleus / cytoplasm
Similarity search - Function
Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / Leucine-rich repeat / Leucine-rich repeat, SDS22-like subfamily / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Protein phosphatase 1 regulatory subunit 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsHeroes, E. / Choy, M.S. / Page, R. / Peti, W. / Ulens, C. / Van Meervelt, L. / Nys, M. / Bollen, M.
Funding support United States, Belgium, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1R01NS091336 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098482 United States
GOA/15/016 Belgium
G065515N Belgium
CitationJournal: Structure / Year: 2019
Title: Structure-Guided Exploration of SDS22 Interactions with Protein Phosphatase PP1 and the Splicing Factor BCLAF1.
Authors: Heroes, E. / Van der Hoeven, G. / Choy, M.S. / Garcia, J.D.P. / Ferreira, M. / Nys, M. / Derua, R. / Beullens, M. / Ulens, C. / Peti, W. / Van Meervelt, L. / Page, R. / Bollen, M.
History
DepositionSep 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein phosphatase 1 regulatory subunit 7
B: Protein phosphatase 1 regulatory subunit 7
C: Protein phosphatase 1 regulatory subunit 7
D: Protein phosphatase 1 regulatory subunit 7
E: Protein phosphatase 1 regulatory subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,66925
Polymers209,7475
Non-polymers1,92120
Water45025
1
A: Protein phosphatase 1 regulatory subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5267
Polymers41,9491
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein phosphatase 1 regulatory subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2384
Polymers41,9491
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein phosphatase 1 regulatory subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3345
Polymers41,9491
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein phosphatase 1 regulatory subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3345
Polymers41,9491
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Protein phosphatase 1 regulatory subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2384
Polymers41,9491
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)177.764, 81.153, 191.958
Angle α, β, γ (deg.)90.000, 104.370, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain Q
21chain G
31chain H
41chain I
51chain J
61chain K
71chain M
81chain N
91chain O
101chain P
12(chain A and (resseq 55:57 or (resid 58 and (name...
22(chain B and (resseq 55:57 or (resid 58 and (name...
32(chain C and (resseq 55:57 or (resid 58 and (name...
42(chain D and (resseq 55:57 or (resid 58 and (name...
52(chain E and (resseq 55:57 or (resid 58 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain QQ1
211chain GG1
311chain HH1
411chain II1
511chain JJ1
611chain KK1
711chain MM1
811chain NN1
911chain OO1
1011chain PP1
112(chain A and (resseq 55:57 or (resid 58 and (name...A0
212(chain B and (resseq 55:57 or (resid 58 and (name...B0
312(chain C and (resseq 55:57 or (resid 58 and (name...C0
412(chain D and (resseq 55:57 or (resid 58 and (name...D0
512(chain E and (resseq 55:57 or (resid 58 and (name...E0

NCS ensembles :
ID
1
2

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Components

#1: Protein
Protein phosphatase 1 regulatory subunit 7 / Protein phosphatase 1 regulatory subunit 22


Mass: 41949.465 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1R7, SDS22 / Cell line (production host): HKB11 / Production host: Homo sapiens (human) / References: UniProt: Q15435
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.76 Å3/Da / Density % sol: 67.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: ammonium sulfate, PEG 4000, glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 3.09→47.79 Å / Num. obs: 94224 / % possible obs: 99 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.7
Reflection shellResolution: 3.09→3.13 Å / Rmerge(I) obs: 0.733

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AW4

4aw4


Resolution: 3.09→46.863 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 24.47
RfactorNum. reflection% reflection
Rfree0.2388 4557 4.84 %
Rwork0.2098 --
obs0.2112 94223 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.17 Å2 / Biso mean: 47.1663 Å2 / Biso min: 17.53 Å2
Refinement stepCycle: final / Resolution: 3.09→46.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12475 0 100 25 12600
Biso mean--71.51 32.02 -
Num. residues----1530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512675
X-RAY DIFFRACTIONf_angle_d1.02117095
X-RAY DIFFRACTIONf_chiral_restr0.0642015
X-RAY DIFFRACTIONf_plane_restr0.0052200
X-RAY DIFFRACTIONf_dihedral_angle_d15.9867925
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
21A7254X-RAY DIFFRACTION10.544TORSIONAL
22B7254X-RAY DIFFRACTION10.544TORSIONAL
23C7254X-RAY DIFFRACTION10.544TORSIONAL
24D7254X-RAY DIFFRACTION10.544TORSIONAL
25E7254X-RAY DIFFRACTION10.544TORSIONAL
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 (%)
3.09-3.12520.38891750.34692976315199
3.1252-3.16190.37171480.3373041318999
3.1619-3.20050.38771430.33462940308399
3.2005-3.2410.31771160.31153083319999
3.241-3.28360.30081530.30542944309799
3.2836-3.32860.33991350.28782955309099
3.3286-3.37610.33981550.28323096325199
3.3761-3.42650.27931440.28032950309499
3.4265-3.480.29161580.28313033319199
3.48-3.53710.28561490.26572978312799
3.5371-3.5980.2691650.25322997316299
3.598-3.66340.26551460.24442988313499
3.6634-3.73390.25921670.21912943311099
3.7339-3.810.21151450.19513035318099
3.81-3.89280.21921610.19073006316799
3.8928-3.98340.21671750.18472933310899
3.9834-4.08290.23821750.19093060323599
4.0829-4.19320.22481480.18452917306599
4.1932-4.31650.21381460.17812990313699
4.3165-4.45580.21921430.19023037318098
4.4558-4.61490.19351110.19022923303497
4.6149-4.79950.21141490.16313008315799
4.7995-5.01770.21021340.15223008314299
5.0177-5.28190.18861810.1712957313899
5.2819-5.61230.19041720.181229983170100
5.6123-6.04480.23951400.191430313171100
6.0448-6.65160.25061340.20362979311398
6.6516-7.61050.20781560.19922982313899
7.6105-9.5750.22771400.18273012315299
9.575-46.8680.17371930.14772866305996

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