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- PDB-4v0u: The crystal structure of ternary PP1G-PPP1R15B and G-actin complex -

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Basic information

Entry
Database: PDB / ID: 4v0u
TitleThe crystal structure of ternary PP1G-PPP1R15B and G-actin complex
Components
  • ACTIN, ALPHA SKELETAL MUSCLE
  • PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
  • SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
KeywordsMOTOR PROTEIN/HYDROLASE / MOTOR PROTEIN-HYDROLASE COMPLEX
Function / homology
Function and homology information


Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / RAF activation / PTW/PP1 phosphatase complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / protein phosphatase type 1 complex / regulation of nucleocytoplasmic transport / RHO GTPases Activate Formins / Separation of Sister Chromatids ...Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / RAF activation / PTW/PP1 phosphatase complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / protein phosphatase type 1 complex / regulation of nucleocytoplasmic transport / RHO GTPases Activate Formins / Separation of Sister Chromatids / protein phosphatase 1 binding / lamin binding / protein phosphatase regulator activity / cytoskeletal motor activator activity / glycogen metabolic process / ER overload response / myosin heavy chain binding / protein-serine/threonine phosphatase / tropomyosin binding / entrainment of circadian clock by photoperiod / actin filament bundle / negative regulation of PERK-mediated unfolded protein response / troponin I binding / filamentous actin / mesenchyme migration / negative regulation of protein phosphorylation / protein serine/threonine phosphatase activity / phosphatase activity / cleavage furrow / microtubule organizing center / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / blastocyst development / positive regulation of glial cell proliferation / protein dephosphorylation / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / response to endoplasmic reticulum stress / actin filament / filopodium / circadian regulation of gene expression / response to hydrogen peroxide / regulation of circadian rhythm / kinetochore / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / neuron differentiation / calcium-dependent protein binding / presynapse / lamellipodium / regulation of translation / cell body / midbody / spermatogenesis / dendritic spine / mitochondrial outer membrane / chromosome, telomeric region / hydrolase activity / nuclear speck / protein domain specific binding / cell division / calcium ion binding / positive regulation of gene expression / protein kinase binding / protein-containing complex binding / nucleolus / glutamatergic synapse / magnesium ion binding / endoplasmic reticulum / mitochondrion / ATP binding / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
Protein phosphatase 1, regulatory subunit 15B, N-terminal / eIF2-alpha phosphatase phosphorylation constitutive repressor / Protein phosphatase 1, regulatory subunit 15A/B, C-terminal / : / Phosphatase-1 catalytic subunit binding region / 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. ...Protein phosphatase 1, regulatory subunit 15B, N-terminal / eIF2-alpha phosphatase phosphorylation constitutive repressor / Protein phosphatase 1, regulatory subunit 15A/B, C-terminal / : / Phosphatase-1 catalytic subunit binding region / 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 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / LATRUNCULIN B / : / Serine/threonine-protein phosphatase PP1-gamma catalytic subunit / Actin, alpha skeletal muscle / Protein phosphatase 1 regulatory subunit 15B
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
ORYCTOLAGUS CUNICULUS (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.88 Å
AuthorsChen, R. / Yan, Y. / Casado, A.C. / Ron, D. / Read, R.J.
CitationJournal: Elife / Year: 2015
Title: G-actin provides substrate-specificity to eukaryotic initiation factor 2 alpha holophosphatases.
Authors: Chen, R. / Rato, C. / Yan, Y. / Crespillo-Casado, A. / Clarke, H.J. / Harding, H.P. / Marciniak, S.J. / Read, R.J. / Ron, D.
History
DepositionSep 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Other
Category: citation / pdbx_database_proc / pdbx_database_status
Item: _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.recvd_author_approval
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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_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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: ACTIN, ALPHA SKELETAL MUSCLE
B: ACTIN, ALPHA SKELETAL MUSCLE
C: ACTIN, ALPHA SKELETAL MUSCLE
D: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
E: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
F: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
G: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
H: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
I: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
J: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
K: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
L: ACTIN, ALPHA SKELETAL MUSCLE
M: ACTIN, ALPHA SKELETAL MUSCLE
N: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
O: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)450,45735
Polymers445,39415
Non-polymers5,06320
Water00
1
J: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
K: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3264
Polymers47,2162
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-24.1 kcal/mol
Surface area13220 Å2
MethodPISA
2
F: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
G: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3264
Polymers47,2162
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-24 kcal/mol
Surface area13220 Å2
MethodPISA
3
N: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
O: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3264
Polymers47,2162
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-24 kcal/mol
Surface area13230 Å2
MethodPISA
4
H: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
I: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3264
Polymers47,2162
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-24.2 kcal/mol
Surface area13230 Å2
MethodPISA
5
D: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
E: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3264
Polymers47,2162
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-23.9 kcal/mol
Surface area13200 Å2
MethodPISA
6
A: ACTIN, ALPHA SKELETAL MUSCLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7653
Polymers41,8631
Non-polymers9032
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
B: ACTIN, ALPHA SKELETAL MUSCLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7653
Polymers41,8631
Non-polymers9032
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
C: ACTIN, ALPHA SKELETAL MUSCLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7653
Polymers41,8631
Non-polymers9032
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
L: ACTIN, ALPHA SKELETAL MUSCLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7653
Polymers41,8631
Non-polymers9032
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
M: ACTIN, ALPHA SKELETAL MUSCLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7653
Polymers41,8631
Non-polymers9032
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.910, 149.930, 318.720
Angle α, β, γ (deg.)90.00, 91.03, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22C
13B
23L
14B
24M
15A
25C
16A
26L
17A
27M
18C
28L
19C
29M
110D
210F
111D
211H
112D
212J
113D
213N
114E
214G
115E
215I
116E
216K
117E
217O
118F
218H
119F
219J
120F
220N
121G
221I
122G
222K
123G
223O
124H
224J
125H
225N
126I
226K
127I
227O
128J
228N
129K
229O
130L
230M

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPPHEPHEBB1 - 3751 - 375
21ASPASPPHEPHEAA1 - 3751 - 375
12ASPASPPHEPHEBB1 - 3751 - 375
22ASPASPPHEPHECC1 - 3751 - 375
13ASPASPPHEPHEBB1 - 3751 - 375
23ASPASPPHEPHELL1 - 3751 - 375
14ASPASPPHEPHEBB1 - 3751 - 375
24ASPASPPHEPHEMM1 - 3751 - 375
15ASPASPPHEPHEAA1 - 3751 - 375
25ASPASPPHEPHECC1 - 3751 - 375
16ASPASPPHEPHEAA1 - 3751 - 375
26ASPASPPHEPHELL1 - 3751 - 375
17ASPASPPHEPHEAA1 - 3751 - 375
27ASPASPPHEPHEMM1 - 3751 - 375
18ASPASPPHEPHECC1 - 3751 - 375
28ASPASPPHEPHELL1 - 3751 - 375
19ASPASPPHEPHECC1 - 3751 - 375
29ASPASPPHEPHEMM1 - 3751 - 375
110LEULEUGLUGLUDD7 - 3007 - 300
210LEULEUGLUGLUFF7 - 3007 - 300
111LEULEUGLUGLUDD7 - 3007 - 300
211LEULEUGLUGLUHH7 - 3007 - 300
112LEULEUGLUGLUDD7 - 3007 - 300
212LEULEUGLUGLUJJ7 - 3007 - 300
113LEULEUGLUGLUDD7 - 3007 - 300
213LEULEUGLUGLUNN7 - 3007 - 300
114LYSLYSARGARGEE639 - 65814 - 33
214LYSLYSARGARGGG639 - 65814 - 33
115LYSLYSARGARGEE639 - 65814 - 33
215LYSLYSARGARGII639 - 65814 - 33
116LYSLYSARGARGEE639 - 65814 - 33
216LYSLYSARGARGKK639 - 65814 - 33
117LYSLYSARGARGEE639 - 65814 - 33
217LYSLYSARGARGOO639 - 65814 - 33
118LEULEUGLUGLUFF7 - 3007 - 300
218LEULEUGLUGLUHH7 - 3007 - 300
119LEULEUGLUGLUFF7 - 3007 - 300
219LEULEUGLUGLUJJ7 - 3007 - 300
120LEULEUGLUGLUFF7 - 3007 - 300
220LEULEUGLUGLUNN7 - 3007 - 300
121LYSLYSARGARGGG639 - 65814 - 33
221LYSLYSARGARGII639 - 65814 - 33
122LYSLYSARGARGGG639 - 65814 - 33
222LYSLYSARGARGKK639 - 65814 - 33
123LYSLYSARGARGGG639 - 65814 - 33
223LYSLYSARGARGOO639 - 65814 - 33
124LEULEUGLUGLUHH7 - 3007 - 300
224LEULEUGLUGLUJJ7 - 3007 - 300
125LEULEUGLUGLUHH7 - 3007 - 300
225LEULEUGLUGLUNN7 - 3007 - 300
126LYSLYSARGARGII639 - 65814 - 33
226LYSLYSARGARGKK639 - 65814 - 33
127LYSLYSARGARGII639 - 65814 - 33
227LYSLYSARGARGOO639 - 65814 - 33
128LEULEUGLUGLUJJ7 - 3007 - 300
228LEULEUGLUGLUNN7 - 3007 - 300
129LYSLYSARGARGKK639 - 65814 - 33
229LYSLYSARGARGOO639 - 65814 - 33
130ASPASPPHEPHELL1 - 3751 - 375
230ASPASPPHEPHEMM1 - 3751 - 375

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30

NCS oper:
IDCodeMatrixVector
1given(0.253283, -0.62016, -0.742461), (-0.616221, -0.695062, 0.370351), (-0.745734, 0.363717, -0.558203)157.756, -62.9053, 319.872
2given(-0.357962, 0.552242, 0.752922), (-0.480153, -0.80044, 0.358816), (0.800822, -0.233075, 0.551688)150.394, -84.1798, 4.60396
3given(-0.552648, -0.78661, -0.275363), (-0.77894, 0.370026, 0.506293), (-0.296364, 0.494293, -0.817216)108.916, 7.62283, 176.162
4given(-0.44035, 0.781556, -0.441886), (0.839478, 0.183879, -0.511336), (-0.318384, -0.59612, -0.73707)248.8, -90.1695, 168.491
5given(0.129235, -0.499968, -0.856347), (-0.532237, -0.763626, 0.365512), (-0.836673, 0.408542, -0.364789)191.502, -76.3136, 311.747
6given(-0.152449, 0.558474, 0.815393), (-0.4881, -0.759942, 0.429238), (0.85937, -0.332556, 0.388444)123.255, -87.7376, 4.99855
7given(0.563868, -0.656766, 0.500711), (0.804794, 0.300893, -0.511634), (0.185364, 0.691463, 0.698225)53.4284, -78.0983, 167.607
8given(-0.536937, 0.665099, -0.518981), (0.826588, 0.291767, -0.481273), (-0.168673, -0.687397, -0.706424)251.33, -82.022, 149.727
9given(0.131613, -0.497661, -0.857328), (-0.528488, -0.766921, 0.364051), (-0.838677, 0.405174, -0.363945)191.405, -76.5921, 311.843
10given(-0.152893, 0.563352, 0.811947), (-0.494287, -0.755046, 0.430797), (0.855748, -0.335469, 0.393899)123.843, -86.6609, 4.97868
11given(0.562751, -0.657403, 0.501131), (0.804593, 0.296581, -0.51446), (0.189582, 0.69272, 0.695843)53.4441, -78.0947, 167.638
12given(-0.539318, 0.665523, -0.515961), (0.825769, 0.297872, -0.478934), (-0.165051, -0.684362, -0.710216)251.371, -81.4234, 150.009

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Components

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Protein , 3 types, 15 molecules ABCLMDFHJNEGIKO

#1: Protein
ACTIN, ALPHA SKELETAL MUSCLE / ALPHA-ACTIN-1 / ACTIN


Mass: 41862.613 Da / Num. of mol.: 5 / Fragment: RESIDUES 3-377 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: MUSCLE / References: UniProt: P68135
#2: Protein
SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT / PP-1G / PROTEIN PHOSPHATASE 1C CATALYTIC SUBUNIT / PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT


Mass: 37030.777 Da / Num. of mol.: 5 / Fragment: RESIDUES 1-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P63087, protein-serine/threonine phosphatase
#3: Protein
PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B


Mass: 10185.355 Da / Num. of mol.: 5 / Fragment: RESIDUES 631-701
Source method: isolated from a genetically manipulated source
Details: TRUNCATED HUMAN PPP1R15B INCLUDING RESIDUES OF 631-701G
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q5SWA1

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Non-polymers , 3 types, 20 molecules

#4: Chemical
ChemComp-LAB / LATRUNCULIN B


Mass: 395.513 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C20H29NO5S
#5: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mn

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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: 2.8 Å3/Da / Density % sol: 56.17 % / Description: NONE
Crystal growpH: 7 / Details: 0.2M CACL2, 0.1 M HEPES, PH7.0, 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.979
DetectorType: PILATUS 2M / Detector: PIXEL / Date: May 18, 2014 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 7.88→82.79 Å / Num. obs: 5111 / % possible obs: 98 % / Observed criterion σ(I): 1.6 / Redundancy: 3.4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.2
Reflection shellResolution: 7.88→8.08 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.6 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
CCP4Iphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BIY AND STRUCTURE OF MOUSE PP1G IN COMPLEX WITH TRUNCATED HUMAN PPP1R15B INCLUDING 631-660

4biy


Resolution: 7.88→82.79 Å / Cor.coef. Fo:Fc: 0.647 / SU ML: 7.58 / Cross valid method: THROUGHOUT / ESU R Free: 7.443 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.39976 290 5.4 %RANDOM
Rwork0.37024 ---
obs0.3718 5111 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 388.064 Å2
Baniso -1Baniso -2Baniso -3
1-4.46 Å20 Å2-19.35 Å2
2---1.83 Å20 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 7.88→82.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26765 0 300 0 27065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01927695
X-RAY DIFFRACTIONr_bond_other_d0.0240.0226035
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.9837560
X-RAY DIFFRACTIONr_angle_other_deg4.337360145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.43253380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65824.0081260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.608154730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.99915175
X-RAY DIFFRACTIONr_chiral_restr0.080.24145
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02130935
X-RAY DIFFRACTIONr_gen_planes_other0.0120.026255
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.10114.96913550
X-RAY DIFFRACTIONr_mcbond_other2.10114.96913549
X-RAY DIFFRACTIONr_mcangle_it3.88822.44916905
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.75114.66114145
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B236150.02
12A236150.02
21B236110.02
22C236110.02
31B236120.02
32L236120.02
41B236080.02
42M236080.02
51A236120.02
52C236120.02
61A236160.02
62L236160.02
71A236090.02
72M236090.02
81C236220.02
82L236220.02
91C236160.02
92M236160.02
101D194630
102F194630
111D194600
112H194600
121D194620
122J194620
131D194640
132N194640
141E8180.02
142G8180.02
151E8180.02
152I8180.02
161E8170.02
162K8170.02
171E8170.01
172O8170.01
181F194620
182H194620
191F194600
192J194600
201F194610
202N194610
211G8190
212I8190
221G8180
222K8180
231G8180
232O8180
241H194600
242J194600
251H194560
252N194560
261I8180
262K8180
271I8180
272O8180
281J194610
282N194610
291K8170
292O8170
301L236190.02
302M236190.02
LS refinement shellResolution: 7.88→8.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 15 -
Rwork0.372 371 -
obs--98.72 %
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)
15.8641-0.06562.80922.51832.74596.30170.53890.68121.581-0.0397-0.14110.17670.6136-0.5469-0.39781.70340.0516-0.24872.4212-0.08281.7246128.3236-33.3945140.1785
23.55092.50760.3724.00663.43035.4230.2784-0.0919-0.19940.3281-0.69970.35440.12190.51120.42140.3376-0.0423-0.48392.91930.24361.8095108.3632-67.6153133.0862
32.0271-0.30832.980.1852-0.18648.163-0.47490.5778-0.75970.0106-0.73220.0318-0.1110.05961.20723.13470.0254-0.53263.19220.60462.805792.0923-84.443476.3979
45.59282.6481-1.73586.2246-3.34423.88330.35090.22-0.1645-0.3054-0.3114-0.357-0.6936-0.1423-0.03940.9719-0.28470.24151.8639-0.13651.9309143.1195-69.6653176.3877
5196.2292-75.921190.569229.9011-79.7306257.6356-13.455110.69093.8294.3931-3.3173-2.8168-3.3485-0.517816.77244.329-2.47072.1542.4775-1.16694.6895139.3919-86.6912173.588
67.56740.5432-2.07498.556.29788.14790.02190.39790.76390.40920.32090.6377-0.69040.0754-0.34281.8323-0.0857-0.26822.43610.37032.3799103.4577-36.186893.2407
753.8604-35.1874119.205365.6156-56.356281.2037-1.7721.4081-2.81990.64724.8718-1.6647-6.90865.802-3.09981.92820.9097-0.90872.07320.55415.5749114.4381-22.393791.2354
80.7973-1.1887-0.274310.51880.92823.70950.11050.8312-0.42680.0182-0.1263-0.51180.95820.68880.01581.84080.291-0.09083.4812-0.49742.5859135.4437-59.643490.5279
9124.0512-20.48224.65856.2398-13.257635.59665.38033.5526-14.2467-1.7961-1.97381.70852.34084.3936-3.40655.0763-0.99552.84934.41382.15247.834141.9271-47.792279.0307
108.53441.3477-0.233510.9911-2.662611.1258-0.46360.6645-0.1090.18120.1537-0.4007-1.4592-0.75630.30991.89990.2342-0.72971.9065-0.13932.38658.9905-50.29346.7247
114.5653-12.123-10.015838.976710.899190.00140.2776-0.605-1.95551.89394.44924.8426-11.3848-1.5546-4.72683.5814-1.36481.25053.6143-1.08173.903142.5887-54.92651.6303
121.01452.5863-1.13647.3326-3.71872.26050.1704-0.45840.7291.8760.23161.2153-1.5727-1.4591-0.4023.96671.4919-1.31385.11620.03192.790131.8902-48.22743.2933
133.3704-3.1922.00133.2992-1.80611.5049-0.30621.06911.2568-0.4857-0.7409-1.7803-1.12770.38751.04714.2942-1.55570.29616.5541-0.52772.5764109.7307-66.846745.0708
149.6876-2.7049-1.17975.8122-1.06813.70770.03940.7271-1.0717-0.7734-0.39190.58140.52140.15790.35262.9671-0.2923-0.49682.36-0.43051.937363.8244-86.699531.3752
156.0991-9.0445-4.38213.71646.58753.205-0.4806-0.15911.34260.28621.1385-0.69520.01090.7931-0.6584.4349-5.3022-1.088.91562.61676.050552.1609-92.233243.5458
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 1377
2X-RAY DIFFRACTION2A1 - 1377
3X-RAY DIFFRACTION3C1 - 1377
4X-RAY DIFFRACTION4D7 - 302
5X-RAY DIFFRACTION5E639 - 658
6X-RAY DIFFRACTION6F7 - 302
7X-RAY DIFFRACTION7G639 - 658
8X-RAY DIFFRACTION8H7 - 302
9X-RAY DIFFRACTION9I639 - 658
10X-RAY DIFFRACTION10J7 - 302
11X-RAY DIFFRACTION11K639 - 658
12X-RAY DIFFRACTION12L1 - 1377
13X-RAY DIFFRACTION13M1 - 1377
14X-RAY DIFFRACTION14N7 - 302
15X-RAY DIFFRACTION15O639 - 658

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