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- PDB-6ihl: Crystal structure of bacterial serine phosphatase -

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Basic information

Entry
Database: PDB / ID: 6ihl
TitleCrystal structure of bacterial serine phosphatase
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: 1.573 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
DepositionSep 30, 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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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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)28,2266
Polymers28,1041
Non-polymers1225
Water2,090116
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 area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.669, 38.160, 64.891
Angle α, β, γ (deg.)90.00, 101.47, 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: 28104.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: prpC, BN1321_240063, BTN44_06615, CSC83_01010, CSC87_08725, EP54_08495, EQ90_08165, ERS072840_01404, RK64_06500
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.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.01 Å3/Da / Density % sol: 38.96 %
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
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9735 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9735 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 31074 / % possible obs: 99.4 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 32.7
Reflection shellResolution: 1.57→1.63 Å / Rmerge(I) obs: 0.496 / Num. unique obs: 2993

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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: 1.573→45.738 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.24
RfactorNum. reflection% reflection
Rfree0.2046 1607 5.18 %
Rwork0.1697 --
obs0.1715 31039 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.573→45.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 5 116 2070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051994
X-RAY DIFFRACTIONf_angle_d0.7522702
X-RAY DIFFRACTIONf_dihedral_angle_d13.9471193
X-RAY DIFFRACTIONf_chiral_restr0.056304
X-RAY DIFFRACTIONf_plane_restr0.004359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5735-1.62420.26511420.23112420X-RAY DIFFRACTION90
1.6242-1.68230.23961360.21432675X-RAY DIFFRACTION99
1.6823-1.74970.22811560.19992667X-RAY DIFFRACTION100
1.7497-1.82930.21771450.18762682X-RAY DIFFRACTION100
1.8293-1.92570.19831500.17072677X-RAY DIFFRACTION100
1.9257-2.04640.2191470.16912679X-RAY DIFFRACTION100
2.0464-2.20440.19071610.16032676X-RAY DIFFRACTION100
2.2044-2.42620.21081250.16752728X-RAY DIFFRACTION100
2.4262-2.77730.19831430.16722709X-RAY DIFFRACTION100
2.7773-3.49890.2131450.16442733X-RAY DIFFRACTION100
3.4989-45.75710.19381570.16562786X-RAY DIFFRACTION99

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