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- PDB-6ihr: Crystal structure of bacterial serine phosphatase with His tag -

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Basic information

Entry
Database: PDB / ID: 6ihr
TitleCrystal structure of bacterial serine phosphatase with His tag
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
PHOSPHATE ION / protein-serine/threonine phosphatase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.348 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.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_label_atom_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_symmetry

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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)30,3065
Polymers30,1381
Non-polymers1684
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-25 kcal/mol
Surface area12240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.468, 86.694, 39.186
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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, NCTC10654_01263, NCTC10702_01924, NCTC11940_01141, NCTC13131_00423, NCTC13196_02843, ...Gene: prpC, prpC_1, BN1321_240063, BTN44_06615, CSC83_01010, CSC87_08725, EP54_08495, EQ90_08165, ERS072840_01404, NCTC10654_01263, NCTC10702_01924, NCTC11940_01141, NCTC13131_00423, NCTC13196_02843, NCTC13812_01250, 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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M LiSO4, 0.1 M Tris-HCl (pH=8.0), 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: 0.9735 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9735 Å / Relative weight: 1
ReflectionResolution: 1.348→29.1 Å / Num. obs: 59431 / % possible obs: 99.3 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 26.1
Reflection shellResolution: 1.35→1.4 Å / Rmerge(I) obs: 0.37 / Num. unique obs: 5623

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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: 1.348→29.088 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 15.38
RfactorNum. reflection% reflectionSelection details
Rfree0.1807 3119 5.25 %RANDOM
Rwork0.1612 ---
obs0.1622 59379 99.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.348→29.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 8 300 2346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072115
X-RAY DIFFRACTIONf_angle_d0.9772869
X-RAY DIFFRACTIONf_dihedral_angle_d16.008784
X-RAY DIFFRACTIONf_chiral_restr0.089319
X-RAY DIFFRACTIONf_plane_restr0.005381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3481-1.36920.28511370.2632316X-RAY DIFFRACTION92
1.3692-1.39170.25131480.22582459X-RAY DIFFRACTION98
1.3917-1.41560.26591240.21342498X-RAY DIFFRACTION99
1.4156-1.44140.22441450.18732558X-RAY DIFFRACTION100
1.4414-1.46910.21271360.18012537X-RAY DIFFRACTION100
1.4691-1.49910.17321550.17132513X-RAY DIFFRACTION100
1.4991-1.53170.19461400.16682537X-RAY DIFFRACTION100
1.5317-1.56730.20141320.15142574X-RAY DIFFRACTION100
1.5673-1.60650.18711530.14822522X-RAY DIFFRACTION100
1.6065-1.64990.17491350.15132533X-RAY DIFFRACTION100
1.6499-1.69850.16951530.14712560X-RAY DIFFRACTION100
1.6985-1.75330.18391290.1532558X-RAY DIFFRACTION100
1.7533-1.8160.16861320.15452556X-RAY DIFFRACTION100
1.816-1.88870.15891270.14982577X-RAY DIFFRACTION100
1.8887-1.97460.1821540.14412577X-RAY DIFFRACTION100
1.9746-2.07870.18441370.14892573X-RAY DIFFRACTION100
2.0787-2.20890.17031500.15012577X-RAY DIFFRACTION100
2.2089-2.37930.17671600.14992562X-RAY DIFFRACTION100
2.3793-2.61870.17751330.15742623X-RAY DIFFRACTION100
2.6187-2.99720.17321580.16472605X-RAY DIFFRACTION100
2.9972-3.77490.16721380.1522648X-RAY DIFFRACTION100
3.7749-29.09510.1711430.17112797X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -18.8775 Å / Origin y: 12.3855 Å / Origin z: -10.5982 Å
111213212223313233
T0.0725 Å20.0195 Å20.0091 Å2-0.0737 Å20.0084 Å2--0.0562 Å2
L1.2527 °20.0803 °2-0.1417 °2-0.9925 °20.1006 °2--0.8897 °2
S-0.0211 Å °-0.0974 Å °-0.0199 Å °0.0604 Å °0.0021 Å °-0.0111 Å °0.0645 Å °0.0554 Å °0.0008 Å °
Refinement TLS groupSelection details: (chain A and resseq -11:245)

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