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- PDB-4kk3: YwlE arginine phosphatase - wildtype -

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Basic information

Entry
Database: PDB / ID: 4kk3
TitleYwlE arginine phosphatase - wildtype
ComponentsLow molecular weight protein-tyrosine-phosphatase YwlE
KeywordsHYDROLASE / protein modification / arginine phosphorylation / arginine dephosphorylation / phospho-proteome / LMW-PTP
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
PHOSPHATE ION / Protein-arginine-phosphatase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 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 27, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)17,2062
Polymers17,1111
Non-polymers951
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.131, 40.749, 41.056
Angle α, β, γ (deg.)90.000, 92.260, 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: 17110.943 Da / Num. of mol.: 1
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: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.08 Å3/Da / Density % sol: 40.84 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 25% PEG400, 50 mM Tris-HCl, pH 7.7, 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 16, 2010
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
ReflectionRedundancy: 5.8 % / Av σ(I) over netI: 4.4 / Number: 87309 / Rsym value: 0.067 / D res high: 1.7 Å / D res low: 28.962 Å / Num. obs: 15093 / % possible obs: 96.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.3828.9696.310.0720.0725.5
3.85.3894.310.0480.0485
3.13.897.610.0530.0535.8
2.693.197.710.0580.0585.7
2.42.6997.310.0670.0676
2.192.497.310.0810.0815.6
2.032.199810.0940.0946.2
1.92.039610.1320.1325.5
1.791.997.910.1920.1926.1
1.71.7995.210.2880.2885.7
ReflectionResolution: 1.7→28.962 Å / Num. all: 15093 / Num. obs: 15093 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rsym value: 0.067 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.795.70.2882.21226621460.28895.2
1.79-1.96.10.1923.11277320920.19297.9
1.9-2.035.50.1324.51073719350.13296
2.03-2.196.20.0946.41142318350.09498
2.19-2.45.60.0817.1953916960.08197.3
2.4-2.6960.0678.9904815170.06797.3
2.69-3.15.70.05810.2768613510.05897.7
3.1-3.85.80.05311.1667511500.05397.6
3.8-5.3850.0481343798690.04894.3
5.38-28.9625.50.0724.927835020.07296.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALA3.3.20data scaling
SHARPphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.7→19.968 Å / Occupancy max: 1 / Occupancy min: 0.32 / FOM work R set: 0.8453 / SU ML: 0.19 / σ(F): 1.42 / Phase error: 22.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 1497 9.99 %RANDOM
Rwork0.1857 ---
obs0.1889 15074 95.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.97 Å2 / Biso mean: 31.2993 Å2 / Biso min: 11.12 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1186 0 5 76 1267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071210
X-RAY DIFFRACTIONf_angle_d1.0681630
X-RAY DIFFRACTIONf_chiral_restr0.08184
X-RAY DIFFRACTIONf_plane_restr0.006211
X-RAY DIFFRACTIONf_dihedral_angle_d13.569455
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.72790.29331290.22941137126690
1.7279-1.75770.23061510.21611251140295
1.7577-1.78960.24121360.21781235137196
1.7896-1.8240.22881520.21111273142597
1.824-1.86120.25371360.18781306144297
1.8612-1.90170.26131490.19491196134597
1.9017-1.94590.26321270.21181272139997
1.9459-1.99450.23071440.21071193133793
1.9945-2.04840.25241500.19451262141296
2.0484-2.10860.2471430.18771220136397
2.1086-2.17660.21911390.18391256139598
2.1766-2.25430.19961310.17571301143297
2.2543-2.34440.19591380.18761253139197
2.3444-2.45090.23291290.17161227135694
2.4509-2.57990.20811330.1911273140697
2.5799-2.74110.23911480.19731286143497
2.7411-2.95220.2221430.1941241138497
2.9522-3.24810.20951360.19431233136995
3.2481-3.71550.18451400.18531283142398
3.7155-4.67120.19511230.1651196131991
4.6712-19.96950.22971250.17141260138596
Refinement TLS params.Method: refined / Origin x: 12.3711 Å / Origin y: 0.2362 Å / Origin z: 12.4044 Å
111213212223313233
T0.1243 Å20.0059 Å20.003 Å2-0.1175 Å2-0.0021 Å2--0.1525 Å2
L2.31 °2-0.4014 °20.7604 °2-1.7595 °20.3269 °2--2.535 °2
S-0.0147 Å °-0.0651 Å °-0.1472 Å °0.0403 Å °0.0534 Å °0.0718 Å °-0.0109 Å °0.009 Å °0.0046 Å °
Refinement TLS groupSelection details: all

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