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- PDB-6ihu: Crystal structure of bacterial serine phosphatase bearing R161A m... -

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Basic information

Entry
Database: PDB / ID: 6ihu
TitleCrystal structure of bacterial serine phosphatase bearing R161A mutation
ComponentsPhosphorylated protein phosphatase
KeywordsHYDROLASE / bacteria / phosphatase / metal binding
Function / homology
Function and homology information


protein-serine/threonine phosphatase / protein serine/threonine 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-serine/threonine phosphatase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsYang, C.-G. / yang, T.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Acs Infect Dis. / Year: 2019
Title: Structural Insight into the Mechanism of Staphylococcus aureus Stp1 Phosphatase.
Authors: Yang, T. / Liu, T. / Gan, J. / Yu, K. / Chen, K. / Xue, W. / Lan, L. / Yang, S. / Yang, C.G.
History
DepositionOct 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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
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_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphorylated protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1244
Polymers30,0521
Non-polymers733
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-19 kcal/mol
Surface area9960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.998, 37.745, 65.575
Angle α, β, γ (deg.)90.00, 102.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphorylated protein phosphatase / Protein phosphatase / Protein serine/threonine phosphatase PrpC / regulation of stationary phase / ...Protein phosphatase / Protein serine/threonine phosphatase PrpC / regulation of stationary phase / Protein-serine/threonine phosphatase Stp1 / Serine/threonine-protein phosphatase


Mass: 30051.547 Da / Num. of mol.: 1 / Mutation: R161A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: prpC, prpC_1, BN1321_240063, BTN44_06615, CSC83_01010, CSC87_08725, EP54_08495, EQ90_08165, ERS072840_01404, NCTC11940_01141, NCTC13131_00423, NCTC13196_02843, NCTC9944_01222, RK64_06500, ...Gene: prpC, prpC_1, BN1321_240063, BTN44_06615, CSC83_01010, CSC87_08725, EP54_08495, EQ90_08165, ERS072840_01404, NCTC11940_01141, NCTC13131_00423, NCTC13196_02843, NCTC9944_01222, RK64_06500, SAMEA1469870_01594, SAMEA1531701_01402
Production host: Escherichia coli (E. coli)
References: UniProt: Q9RL81, protein-serine/threonine phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 1.89 Å3/Da / Density % sol: 34.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaCl, 0.1 M HEPES (pH=7.5), 25% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9735 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9735 Å / Relative weight: 1
ReflectionResolution: 1.84→30 Å / Num. obs: 18646 / % possible obs: 95.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.3
Reflection shellResolution: 1.84→1.92 Å / Rmerge(I) obs: 0.272 / Num. unique obs: 1702

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F1M

5f1m


Resolution: 1.84→29.475 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.51 / Phase error: 19.59
RfactorNum. reflection% reflection
Rfree0.2004 868 4.89 %
Rwork0.1689 --
obs0.1705 17765 89.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.84→29.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1735 0 3 161 1899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031762
X-RAY DIFFRACTIONf_angle_d0.5932378
X-RAY DIFFRACTIONf_dihedral_angle_d14.2511048
X-RAY DIFFRACTIONf_chiral_restr0.048264
X-RAY DIFFRACTIONf_plane_restr0.003315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8381-1.95320.20931070.17321999X-RAY DIFFRACTION64
1.9532-2.1040.23091340.16892742X-RAY DIFFRACTION88
2.104-2.31560.22421650.1752911X-RAY DIFFRACTION94
2.3156-2.65050.2241340.17313027X-RAY DIFFRACTION97
2.6505-3.33870.19681590.16313074X-RAY DIFFRACTION97
3.3387-29.47920.17731690.1683144X-RAY DIFFRACTION98

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