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- PDB-8dhj: Crystal structure of Clostridioides difficile Protein Tyrosine Ph... -

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Basic information

Entry
Database: PDB / ID: 8dhj
TitleCrystal structure of Clostridioides difficile Protein Tyrosine Phosphatase at pH 7.5
ComponentsTYR_PHOSPHATASE_2 domain-containing protein
KeywordsHYDROLASE / phosphatase
Function / homologyTyrosine/serine-protein phosphatase IphP-type / Tyrosine phosphatase family / phosphoprotein phosphatase activity / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Tyrosine specific protein phosphatases domain-containing protein
Function and homology information
Biological speciesClostridioides difficile 6050 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.483 Å
AuthorsLountos, G.T. / Tropea, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Crystal structure of Clostridioides difficile Protein Tyrosine Phosphatase at pH 7.5
Authors: Lountos, G.T. / Tropea, J.E.
History
DepositionJun 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYR_PHOSPHATASE_2 domain-containing protein
B: TYR_PHOSPHATASE_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,66311
Polymers57,9382
Non-polymers7259
Water9,692538
1
A: TYR_PHOSPHATASE_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3496
Polymers28,9691
Non-polymers3805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TYR_PHOSPHATASE_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3145
Polymers28,9691
Non-polymers3454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.459, 42.677, 86.739
Angle α, β, γ (deg.)90.000, 106.420, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TYR_PHOSPHATASE_2 domain-containing protein


Mass: 28969.008 Da / Num. of mol.: 2
Mutation: First three glycine residues are non-native, remnants of linker
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile 6050 (bacteria)
Plasmid: pJT510 / Production host: Escherichia coli (E. coli) / References: UniProt: Q185E4
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 0.2 magnesium chloride, 25% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 82376 / % possible obs: 98.8 % / Redundancy: 2.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.035 / Net I/σ(I): 19.5
Reflection shellResolution: 1.48→1.5 Å / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4129 / CC1/2: 0.679 / Rpim(I) all: 0.41

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YWF

1ywf


Resolution: 1.483→36.229 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1993 3962 5.08 %
Rwork0.1563 74099 -
obs0.1585 78061 93.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.47 Å2 / Biso mean: 21.2777 Å2 / Biso min: 5.77 Å2
Refinement stepCycle: final / Resolution: 1.483→36.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3858 0 34 538 4430
Biso mean--30.96 33.62 -
Num. residues----473
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4831-1.50120.2852740.193128446
1.5012-1.52020.2037830.1823167959
1.5202-1.54020.24941080.1758203172
1.5402-1.56130.2581320.1625230383
1.5613-1.58360.21231270.1548260992
1.5836-1.60730.21861470.1528271898
1.6073-1.63240.18941330.1506282099
1.6324-1.65910.19271440.14882792100
1.6591-1.68780.18131510.13922792100
1.6878-1.71840.21461540.13942831100
1.7184-1.75150.18851590.14192763100
1.7515-1.78720.17641400.13672861100
1.7872-1.82610.18141640.14342780100
1.8261-1.86860.1971540.14512810100
1.8686-1.91530.19551590.14612785100
1.9153-1.96710.18941430.1483281999
1.9671-2.0250.21531480.1444283599
2.025-2.09030.20281670.1484278099
2.0903-2.1650.20751420.145281199
2.165-2.25170.1731440.1419283899
2.2517-2.35420.18851450.1411278199
2.3542-2.47830.18121480.1544281999
2.4783-2.63350.1811390.1601278998
2.6335-2.83670.21411480.166282098
2.8367-3.12210.22851670.1652275197
3.1221-3.57350.19661380.1532280997
3.5735-4.50090.16371520.1463273195
4.5009-36.220.24181520.2105265889

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