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- PDB-4kk4: YwlE arginine phosphatase - C7S mutant with phosphorylated active... -

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Basic information

Entry
Database: PDB / ID: 4kk4
TitleYwlE arginine phosphatase - C7S mutant with phosphorylated active site serine
ComponentsLow molecular weight protein-tyrosine-phosphatase YwlE
KeywordsHYDROLASE / protein modification / arginine phosphorylation / arginine dephosphorylation / phosphatase reaction intermediate / LMW PTP / phosphorylation at Ser6
Function / homology
Function and homology information


protein arginine phosphatase / protein arginine phosphatase activity / protein tyrosine phosphatase activity
Similarity search - Function
: / Protein-tyrosine phosphatase, low molecular weight / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein-arginine-phosphatase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFuhrmann, J. / Clausen, T.
CitationJournal: Cell Rep / Year: 2013
Title: Structural basis for recognizing phosphoarginine and evolving residue-specific protein phosphatases in gram-positive bacteria.
Authors: Fuhrmann, J. / Mierzwa, B. / Trentini, D.B. / Spiess, S. / Lehner, A. / Charpentier, E. / Clausen, T.
History
DepositionMay 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Low molecular weight protein-tyrosine-phosphatase YwlE


Theoretical massNumber of molelcules
Total (without water)17,1161
Polymers17,1161
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.840, 39.340, 40.670
Angle α, β, γ (deg.)90.000, 89.700, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Low molecular weight protein-tyrosine-phosphatase YwlE / LMPTP


Mass: 17116.391 Da / Num. of mol.: 1 / Mutation: C7S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: ywlE, BSU36930, ipc-31d / Production host: Escherichia coli (E. coli) / References: UniProt: P39155, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.01 Å3/Da / Density % sol: 38.68 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 30% PEG400, 50 mM Tris-HCl, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2011
RadiationMonochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→42.919 Å / Num. all: 12470 / Num. obs: 12470 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.053 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.93.30.3951.8602918500.39599.7
1.9-2.013.20.2522.6562017360.25299.6
2.01-2.153.20.1454.5530916510.14599.7
2.15-2.323.20.0966.4484815230.09699.6
2.32-2.553.10.0639.9437413890.06399.3
2.55-2.853.20.04912.6403012640.04998.8
2.85-3.2930.04611.3333011000.04697.8
3.29-4.022.80.04412.224658710.04491.2
4.02-5.693.30.03119.125307580.03199.1
5.69-21.462.90.03517.79563280.03578.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALA3.3.16data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→18.414 Å / Occupancy max: 1 / Occupancy min: 0.49 / FOM work R set: 0.8579 / SU ML: 0.2 / σ(F): 1.36 / Phase error: 21.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2154 571 4.96 %RANDOM
Rwork0.1725 ---
all0.1756 ---
obs0.1745 12465 92.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.5 Å2 / Biso mean: 36.7686 Å2 / Biso min: 14.35 Å2
Refinement stepCycle: LAST / Resolution: 1.8→18.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 0 0 59 1258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071227
X-RAY DIFFRACTIONf_angle_d1.0311653
X-RAY DIFFRACTIONf_chiral_restr0.071186
X-RAY DIFFRACTIONf_plane_restr0.004214
X-RAY DIFFRACTIONf_dihedral_angle_d14.545465
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.88190.26351600.24162764292493
1.8819-1.9810.25711300.21812699282993
1.981-2.10490.28151440.18892752289694
2.1049-2.26720.23231600.17152764292494
2.2672-2.49480.2291410.1642749289093
2.4948-2.85470.20281370.16712729286694
2.8547-3.59220.21961390.16622677281691
3.5922-18.41480.1811230.16292587271088
Refinement TLS params.Method: refined / Origin x: 12.7906 Å / Origin y: -18.2339 Å / Origin z: 12.347 Å
111213212223313233
T0.1606 Å2-0.0101 Å20.0092 Å2-0.1686 Å2-0.0002 Å2--0.1886 Å2
L1.6484 °2-0.2945 °20.6852 °2-1.7475 °2-0.2731 °2--2.7752 °2
S0.0328 Å °-0.0202 Å °-0.0556 Å °0.0603 Å °0.0218 Å °0.0773 Å °0.0564 Å °-0.1196 Å °0.0014 Å °
Refinement TLS groupSelection details: all

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