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- PDB-6iht: Crystal structure of bacterial serine phosphatase bound with phos... -

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Basic information

Entry
Database: PDB / ID: 6iht
TitleCrystal structure of bacterial serine phosphatase bound with phosphorylated peptide
Components
  • His12
  • Phosphorylated 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)
Peptide display vector fth1 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.569 Å
AuthorsYang, C.-G. / yang, T.
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 / struct_conn_type
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_asym_id / _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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphorylated protein phosphatase
X: His12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7058
Polymers30,4372
Non-polymers2686
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-43 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.693, 38.609, 65.003
Angle α, β, γ (deg.)90.00, 101.89, 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: 30137.660 Da / Num. of mol.: 1
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: Protein/peptide His12


Mass: 299.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Peptide display vector fth1 (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.88 Å3/Da / Density % sol: 34.7 %
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: BL18U1 / Wavelength: 0.9735 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9735 Å / Relative weight: 1
ReflectionResolution: 1.569→50 Å / Num. obs: 31706 / % possible obs: 99.2 % / Redundancy: 6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 39.5
Reflection shellResolution: 1.57→1.63 Å / Rmerge(I) obs: 0.37 / Num. unique obs: 3198

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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: 1.569→45.692 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 19.1
RfactorNum. reflection% reflection
Rfree0.1834 1630 5.15 %
Rwork0.1589 --
obs0.1602 31676 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.569→45.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 0 6 153 2110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131996
X-RAY DIFFRACTIONf_angle_d1.292701
X-RAY DIFFRACTIONf_dihedral_angle_d14.9251191
X-RAY DIFFRACTIONf_chiral_restr0.084300
X-RAY DIFFRACTIONf_plane_restr0.009357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5688-1.61490.20911170.16442427X-RAY DIFFRACTION95
1.6149-1.66710.21171360.15872513X-RAY DIFFRACTION100
1.6671-1.72670.18481550.15072468X-RAY DIFFRACTION100
1.7267-1.79580.18551380.14672527X-RAY DIFFRACTION100
1.7958-1.87750.1791340.14492499X-RAY DIFFRACTION100
1.8775-1.97650.15811380.14592507X-RAY DIFFRACTION100
1.9765-2.10030.17571390.14582530X-RAY DIFFRACTION100
2.1003-2.26250.18631400.15442502X-RAY DIFFRACTION99
2.2625-2.49020.2111400.15732494X-RAY DIFFRACTION99
2.4902-2.85050.17211140.16682545X-RAY DIFFRACTION99
2.8505-3.59110.17691430.1572524X-RAY DIFFRACTION98
3.5911-45.71090.1841360.17132510X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4024-0.11260.05690.9001-0.09191.7153-0.0124-0.1825-0.03860.08690.0038-0.02620.0281-0.01170.00340.09760.0027-0.00020.09970.00140.1023-3.88752.701779.0197
22.75511.24590.95031.32441.38161.5184-0.8187-1.24480.00241.65481.18532.9679-0.8007-2.15-0.35530.30110.130.07260.49680.04680.4396-17.45342.543781.679
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:241)
2X-RAY DIFFRACTION2(chain X and resseq 1:3)

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