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- PDB-6ihw: Crystal structure of bacterial serine phosphatase bearing R161K m... -

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Basic information

Entry
Database: PDB / ID: 6ihw
TitleCrystal structure of bacterial serine phosphatase bearing R161K 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: 1.55 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

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Assembly

Deposited unit
A: Phosphorylated protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2075
Polymers30,1101
Non-polymers974
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-16 kcal/mol
Surface area11990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.578, 38.958, 65.409
Angle α, β, γ (deg.)90.00, 102.08, 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: 30109.648 Da / Num. of mol.: 1 / Mutation: R161K
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.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 1.93 Å3/Da / Density % sol: 36.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.05 M MgCl2, 0.1 M HEPES (pH=7.5), 30% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9375 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9375 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 32616 / % possible obs: 97.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 12.7
Reflection shellResolution: 1.55→1.61 Å / Rmerge(I) obs: 0.198 / Num. unique obs: 3033

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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: 1.55→29.606 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.54 / Phase error: 15.98
RfactorNum. reflection% reflection
Rfree0.1741 1595 4.91 %
Rwork0.1511 --
obs0.1522 32513 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→29.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 0 4 173 2139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092016
X-RAY DIFFRACTIONf_angle_d0.9772732
X-RAY DIFFRACTIONf_dihedral_angle_d15.5741213
X-RAY DIFFRACTIONf_chiral_restr0.067306
X-RAY DIFFRACTIONf_plane_restr0.006362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5495-1.59950.1881240.15492475X-RAY DIFFRACTION86
1.5995-1.65670.18761300.14892797X-RAY DIFFRACTION96
1.6567-1.7230.17431540.14372775X-RAY DIFFRACTION97
1.723-1.80140.21051600.14352766X-RAY DIFFRACTION96
1.8014-1.89640.17881470.14122822X-RAY DIFFRACTION98
1.8964-2.01520.17131450.14052865X-RAY DIFFRACTION99
2.0152-2.17070.17981440.14252841X-RAY DIFFRACTION98
2.1707-2.38910.18031310.14792860X-RAY DIFFRACTION99
2.3891-2.73460.18081570.15132897X-RAY DIFFRACTION99
2.7346-3.44450.18181610.15442876X-RAY DIFFRACTION99
3.4445-29.6110.14791420.16192944X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -3.6519 Å / Origin y: 2.8494 Å / Origin z: 79.3242 Å
111213212223313233
T0.0816 Å20.0099 Å2-0.0003 Å2-0.0987 Å20.0144 Å2--0.0779 Å2
L1.1896 °20.0415 °2-0.0383 °2-1.1637 °20.0415 °2--1.3881 °2
S-0.012 Å °-0.2888 Å °-0.0646 Å °0.1028 Å °-0.0094 Å °-0.011 Å °0.0432 Å °0.0547 Å °0.0033 Å °
Refinement TLS groupSelection details: all

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