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PDB | 3FXK | Crystal Structure of Human Protein phosphatase 1A (PPM1A) Bound with Phosphate at 10 mM of Mn2+

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Internal ID
64025
PDB Entry ID
3FXK
Title
Crystal Structure of Human Protein phosphatase 1A (PPM1A) Bound with Phosphate at 10 mM of Mn2+
Authors
Hu, T.,Wang, L.,Wang, K.,Jiang, H.,Shen, X.
Primary Citation
AuthorsHu, T., Wang, L., Wang, K., Chen, J., Jiang, H., Shen, X.
TitleStructural basis for the Mn2+-dependent activation of human PPM1A
JournalTo be published
AbstractView
 
History
Deposition: 2009-01-21Release: 2010-01-26Last Modified:
Experimental Method
TypeX-RAY DIFFRACTION
Parameters
Resolution [Å]R-Value (Obs.)R-Value (Work)R-FreeSpace Group
2.100.1980.1960.234P 31 2 1
Unit Cell
Length [Å]a90.76b90.76c105.71
Angles [°]alpha90.00beta90.00gamma120.00
Molecular Description
PolymerMoleculeMutationFragmentChainsEC NumberOther details
1Protein phosphatase 1AA3.1.3.16
Functional Class
Source
PolymerScientific NameCommon NameExpression System
1Homo sapienshumanEscherichia coli
Related PDB Entries
Chemical Component
IdentifierNameFormulaLigand StructureLigand Interaction
MNMANGANESE (II) IONMn2[View][View]
PO4PHOSPHATE IONO4P3[View][View]
SCOP Classification
CATH Classification
Structural Details
KeywordHydrolase
Textphosphatase, Hydrolase, Magnesium, Manganese, Metal-binding, Phosphoprotein, Protein phosphatase
 
Polymeric Molecules
Chain A
DescriptionProtein phosphatase 1A
Polymer typepolypeptide
Formula Weight43574.3
Source Methodgenetically manipulated
Entity NamePPM1A, Protein phosphatase 2C isoform alpha, PP2C-alpha, IA
Entity Name Sysn/a
 
Entity Poly
EntityChiralityLinkageMonomer# Mon.StrandTypeDetails
1n/anonon/aApolypeptide(L)n/a
Ligands And Prosthetic Groups
IDNameFormulaWeightLigand Structure
MNMANGANESE (II) IONMn254.938View
PO4PHOSPHATE IONO4P394.971View
EC and Associated Pathways
ChainsIUBMBKEGG EnzymeMetaCycReactome
A3.1.3.163.1.3.163.1.3.163.1.3.16
Natural/Genetically Modified Source
Common Namehuman
Scientific NameHomo sapiens
Source Genusn/a
Host Common Namen/a
Host Scientific NameEscherichia coli
Host Genusn/a
Host Cell Linen/a
Host StrainBL21(DE3)
Host Vector Typeplasmid
Host PlasmidpET-24a
 
Crystallization Experiments
Methodvapor diffusion, hanging drop
PH5.2
Temperature277.0
Details50mM potassium phosphate, 12%(w/v) PEG8000, 15%(v/v) glycerol, 2mM DTT, 10mM MnCl2, pH 5.2, vapor diffusion, hanging drop, temperature 277K
 
Unit Cell
Length a (Å)Length b Å)Length c (Å)
90.7690.76105.71
Angle Alpha (°)Angle Beta (°)Angle Gamma (°)
90.0090.00120.00
Space Group
P 31 2 1
Diffraction Detector
DetectorIMAGE PLATE
TypeRIGAKU RAXIS IV++
Detailsn/a
Collection Date2008-03-15
 
Diffraction Radiation
Monochromatorn/a
Diffraction ProtocolSINGLE WAVELENGTH
Wavelengthn/a
Wavelength List1.5418
 
Diffraction Source
SourceROTATING ANODE
TypeRIGAKU
Siten/a
Beamlinen/a
 
Reflection Details
Observed Criterion Sigma (F)n/a
Observed Criterion Sigma (I)n/a
Resolution (High)2.10
Resolution (Low)27.83
Number Reflections (All) n/a
Number Reflections (Observed)29451
Percent Possible (Observed)98.8
R Merge I (Observed)0.065
Net I Over Average Sigma (I)n/a
B (Isotropic) From Wilson Plotn/a
Redundancy9.6
 
High Resolution Shell Details
Resolution(High)2.10
Resolution(Low)2.21
Percent Possible(All) 98.30
R Merge I(Observed)0.353
Mean I Over Sigma(Observed)2.2
R Sym I(Observed)0.353
Redundancy9.7
Num Unique Reflections(All)4240
 
Resolution(High)2.21
Resolution(Low)2.35
Percent Possible(All) 98.20
R Merge I(Observed)0.270
Mean I Over Sigma(Observed)2.6
R Sym I(Observed)0.270
Redundancy9.7
Num Unique Reflections(All)3961
 
Resolution(High)2.35
Resolution(Low)2.51
Percent Possible(All) 98.60
R Merge I(Observed)0.182
Mean I Over Sigma(Observed)4.2
R Sym I(Observed)0.182
Redundancy9.7
Num Unique Reflections(All)3779
 
Resolution(High)2.51
Resolution(Low)2.71
Percent Possible(All) 98.70
R Merge I(Observed)0.130
Mean I Over Sigma(Observed)5.9
R Sym I(Observed)0.130
Redundancy9.7
Num Unique Reflections(All)3527
 
Resolution(High)2.71
Resolution(Low)2.97
Percent Possible(All) 99.10
R Merge I(Observed)0.086
Mean I Over Sigma(Observed)8.8
R Sym I(Observed)0.086
Redundancy9.6
Num Unique Reflections(All)3271
 
Resolution(High)2.97
Resolution(Low)3.32
Percent Possible(All) 99.10
R Merge I(Observed)0.056
Mean I Over Sigma(Observed)12.9
R Sym I(Observed)0.056
Redundancy9.6
Num Unique Reflections(All)2979
 
Resolution(High)3.32
Resolution(Low)3.83
Percent Possible(All) 99.40
R Merge I(Observed)0.038
Mean I Over Sigma(Observed)17.8
R Sym I(Observed)0.038
Redundancy9.5
Num Unique Reflections(All)2624
 
Resolution(High)3.83
Resolution(Low)4.70
Percent Possible(All) 99.60
R Merge I(Observed)0.031
Mean I Over Sigma(Observed)19.7
R Sym I(Observed)0.031
Redundancy9.4
Num Unique Reflections(All)2270
 
Resolution(High)4.70
Resolution(Low)6.64
Percent Possible(All) 99.70
R Merge I(Observed)0.030
Mean I Over Sigma(Observed)18.8
R Sym I(Observed)0.030
Redundancy9.3
Num Unique Reflections(All)1782
 
Resolution(High)6.64
Resolution(Low)27.83
Percent Possible(All) 98.30
R Merge I(Observed)0.029
Mean I Over Sigma(Observed)18.6
R Sym I(Observed)0.029
Redundancy8.7
Num Unique Reflections(All)1018
 
Refinement Statistics
Structure Solution Methodn/a
Resolution (High)2.10
Resolution (Low)15.00
Cut-off Sigma (F)0.0
Cut-off Sigma (I)n/a
Number of Reflections (All)n/a
Number of Reflections (Observed)29362
Number of Reflections (R-Free) 1486
Percent Reflections (Observed)98.55
R-Factor (All)n/a
R-Factor (Observed)0.198
R-Work0.196
R-Free0.234
R-Free Selection DetailsRANDOM
 
Temperature Factor Modeling
Isotropic Thermal Modeln/a
Mean Isotropic B Value27.384
Anisotropic B[1][1]-0.10
Anisotropic B[1][2]-0.05
Anisotropic B[1][3]0.00
Anisotropic B[2][2]-0.10
Anisotropic B[2][3]0.00
Anisotropic B[3][3]0.15
 
Resolution Shells
Shell Resol (High)2.10
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)86
Number of Reflections (R-Work)2015
R-Factor (R-Work)0.217
R-Factor (R-Free)0.271
R-Free Errorn/a
Percent Reflections (Observed)97.77
 
RMS Deviations
First|Previous|1 of 2|Next|Last|
Parameter TypeDeviation From Ideal
r_bond_refined_d0.010
r_angle_refined_deg1.272
r_dihedral_angle_1_deg5.726
r_dihedral_angle_2_deg30.588
r_dihedral_angle_3_deg15.927
r_dihedral_angle_4_deg21.988
r_chiral_restr0.093
r_gen_planes_refined0.004
r_nbd_refined0.206
r_nbtor_refined0.299
First|Previous|1 of 2|Next|Last|
Number of Non-Hydrogen Atoms Used in Refinement
Protein Atoms2821
Nucleic Acid Atoms0
Heterogen Atoms12
Solvent Atoms313
 
Programs
Data Collectionn/a
Data Reduction (intensity integration)n/a
Data Reduction (data scaling)SCALA
Structure Solutionn/a
Structure RefinementREFMAC 5.2.0019
 
Software
Classificationdata processing
Software NameSCALA
Software Version 3.2.25
 
Classificationrefinement
Software NameREFMAC5
Software Version 5.2.0019
 
Classificationdata extraction
Software Namepdb_extract
Software Version 3.006
 
Sequence Chain
A
Sequence
  1   MGAFLDKPKM  EKHNAQGQGN  GLRYGLSSMQ  GWRVEMEDAH  TAVIGLPSGL  ESWSFFAVYD

 61   GHAGSQVAKY  CCEHLLDHIT  NNQDFKGSAG  APSVENVKNG  IRTGFLEIDE  HMRVMSEKKH

121   GADRSGSTAV  GVLISPQHTY  FINCGDSRGL  LCRNRKVHFF  TQDHKPSNPL  EKERIQNAGG

181   SVMIQRVNGS  LAVSRALGDF  DYKCVHGKGP  TEQLVSPEPE  VHDIERSEED  DQFIILACDG

241   IWDVMGNEEL  CDFVRSRLEV  TDDLEKVCNE  VVDTCLYKGS  RDNMSVILIC  FPNAPKVSPE

301   AVKKEAELDK  YLECRVEEII  KKQGEGVPDL  VHVMRTLASE  NIPSLPPGGE  LASKRNVIEA

361   VYNRLNPYKN  DDTDSTSTDD  MWLEHHHHHH