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- PDB-2pk0: Structure of the S. agalactiae serine/threonine phosphatase at 2.... -

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Basic information

Entry
Database: PDB / ID: 2pk0
TitleStructure of the S. agalactiae serine/threonine phosphatase at 2.65 resolution
ComponentsSerine/threonine protein phosphatase Stp1
KeywordsSIGNALING PROTEIN / Streptococcus agalactiae / serine / threonine / phosphatase / signaling motif
Function / homology
Function and homology information


protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / metal ion binding
Similarity search - Function
Protein phosphatase 2C / Sigma factor PP2C-like phosphatases / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Protein phosphatase
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsRantanen, M.K. / Lehtio, L. / Rajagopal, L. / Rubens, C.E. / Goldman, A.
CitationJournal: Febs J. / Year: 2007
Title: Structure of Streptococcus agalactiae serine/threonine phosphatase. The subdomain conformation is coupled to the binding of a third metal ion
Authors: Rantanen, M.K. / Lehtio, L. / Rajagopal, L. / Rubens, C.E. / Goldman, A.
History
DepositionApr 17, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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.end_auth_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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine protein phosphatase Stp1
B: Serine/threonine protein phosphatase Stp1
C: Serine/threonine protein phosphatase Stp1
D: Serine/threonine protein phosphatase Stp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,98816
Polymers109,6184
Non-polymers37112
Water5,314295
1
A: Serine/threonine protein phosphatase Stp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4533
Polymers27,4041
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine protein phosphatase Stp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5454
Polymers27,4041
Non-polymers1413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine/threonine protein phosphatase Stp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4774
Polymers27,4041
Non-polymers733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serine/threonine protein phosphatase Stp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5135
Polymers27,4041
Non-polymers1084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.400, 92.100, 86.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALASERSERAA-4 - 2421 - 247
21ALAALASERSERBB-4 - 2421 - 247
12TYRTYRGLUGLUCC0 - 2415 - 246
22TYRTYRSERSERDD0 - 2425 - 247

NCS ensembles :
ID
1
2
DetailsBiological monomer

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Components

#1: Protein
Serine/threonine protein phosphatase Stp1


Mass: 27404.447 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Strain: A909 / Gene: stp / Plasmid: pGEX4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q3K363, UniProt: Q8VQA1*PLUS, protein-serine/threonine phosphatase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Mg acetate, 18% PEG 8000, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. all: 32931 / Num. obs: 32767 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 5.2 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 11.7
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.7 / Num. unique all: 7442 / Rsym value: 0.44 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Manually built model from SAD phasing = S.a. STP with 70% of residues built

Resolution: 2.65→19.65 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.87 / SU B: 12.859 / SU ML: 0.273 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 3.077 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27121 1651 5 %RANDOM
Rwork0.19667 ---
all0.20046 32000 --
obs0.2 31351 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.058 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.65→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7468 0 17 295 7780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0217566
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.95410268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1475975
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09726.297370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.979151300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7281532
X-RAY DIFFRACTIONr_chiral_restr0.0930.21210
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025714
X-RAY DIFFRACTIONr_nbd_refined0.1460.13317
X-RAY DIFFRACTIONr_nbtor_refined0.3130.55126
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.3582
X-RAY DIFFRACTIONr_metal_ion_refined0.10.310
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.156
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2760.317
X-RAY DIFFRACTIONr_mcbond_it1.82724936
X-RAY DIFFRACTIONr_mcangle_it2.90137750
X-RAY DIFFRACTIONr_scbond_it1.91522892
X-RAY DIFFRACTIONr_scangle_it2.91832518
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1862medium positional0.390.5
2C1810medium positional0.180.5
1A1862medium thermal0.842
2C1810medium thermal0.612
LS refinement shellResolution: 2.65→2.718 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 116 -
Rwork0.252 2193 -
obs--100 %

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