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- PDB-8dhi: Crystal Structure of Clostridioides difficile Protein Tyrosine Ph... -

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Basic information

Entry
Database: PDB / ID: 8dhi
TitleCrystal Structure of Clostridioides difficile Protein Tyrosine Phosphatase at pH 8.5
ComponentsTYR_PHOSPHATASE_2 domain-containing protein
KeywordsHYDROLASE / phosphatase
Function / homologyTyrosine/serine-protein phosphatase IphP-type / Tyrosine phosphatase family / phosphoprotein phosphatase activity / dephosphorylation / 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: 1.588 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 8.5
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


Theoretical massNumber of molelcules
Total (without water)57,9382
Polymers57,9382
Non-polymers00
Water10,052558
1
A: TYR_PHOSPHATASE_2 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)28,9691
Polymers28,9691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TYR_PHOSPHATASE_2 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)28,9691
Polymers28,9691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.250, 42.736, 86.859
Angle α, β, γ (deg.)90.000, 106.530, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris, pH 8,.5, 0.2 M magnesium chloride, 25% (w/v) polyethylene glycol

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Data collection

DiffractionMean temperature: 293 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: 1.588→50 Å / Num. obs: 67967 / % possible obs: 99.9 % / Redundancy: 3.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.04 / Net I/σ(I): 25.4
Reflection shellResolution: 1.59→1.62 Å / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2 / Num. unique obs: 3352 / CC1/2: 0.79 / Rpim(I) all: 0.354

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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: 1.588→38.021 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2042 3321 4.89 %
Rwork0.1738 64629 -
obs0.1753 67950 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.76 Å2 / Biso mean: 26.9477 Å2 / Biso min: 11.1 Å2
Refinement stepCycle: final / Resolution: 1.588→38.021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3924 0 0 558 4482
Biso mean---36.7 -
Num. residues----478
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.588-1.6110.31621270.2585257796
1.611-1.63510.2431310.2362683100
1.6351-1.66060.22511230.22312695100
1.6606-1.68780.28921400.2342652100
1.6878-1.71690.22261350.21822697100
1.7169-1.74820.25161520.19462635100
1.7482-1.78180.2211410.19052702100
1.7818-1.81820.20811380.18342658100
1.8182-1.85770.21131310.17742735100
1.8577-1.90090.20221660.1792629100
1.9009-1.94840.22051330.17872698100
1.9484-2.00110.23241420.18512652100
2.0011-2.060.1851370.17532716100
2.06-2.12650.21221320.16942718100
2.1265-2.20250.1931240.16752658100
2.2025-2.29060.20621330.16782712100
2.2906-2.39490.20261360.16772712100
2.3949-2.52110.22941420.18042699100
2.5211-2.6790.21921450.18042707100
2.679-2.88580.20311370.17842709100
2.8858-3.17610.2251520.18142691100
3.1761-3.63540.17361390.1562732100
3.6354-4.5790.15961370.142757100
4.579-38.020.21071480.1796280599
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)
11.66050.37710.07324.1434-4.60158.65260.01120.0288-0.0469-0.07530.13730.2297-0.0148-0.1835-0.1790.0523-0.0163-0.00310.14590.00550.16036.9557-4.176230.7225
22.74350.3546-0.63883.2344-1.15542.7404-0.05550.13030.321-0.06610.09010.0781-0.448-0.1477-0.06430.188-0.0015-0.03630.10730.00730.155113.458812.927126.396
30.7973-0.073-0.02011.04930.54843.019-0.00970.14350.0432-0.15430.047-0.1225-0.08870.1555-0.03070.1294-0.02980.01490.13640.01230.157421.73551.375919.0235
40.5066-0.17780.32842.7578-3.40416.0374-0.07110.0616-0.0146-0.17990.23270.18190.0494-0.4135-0.18040.1071-0.0267-0.0060.1286-0.00640.124510.4064-1.777517.7466
51.8067-1.19912.34972.2584-2.53135.5920.11150.1742-0.1023-0.33050.00740.04840.3021-0.0168-0.15840.1349-0.0240.02160.1345-0.01740.127218.247-7.147915.8234
63.9033-4.82240.14226.5529-0.23856.8551-0.0957-0.1751-0.04560.40790.1424-0.13420.06480.1116-0.03840.1321-0.0429-0.00110.09240.0220.130616.2473-9.062941.4757
73.2207-0.38830.10742.8758-0.02882.51990.13150.1815-0.4766-0.3231-0.0299-0.0940.47340.3223-0.0640.22840.071-0.02890.1722-0.02380.2033-13.1516-7.735923.4759
81.12380.6472-1.15464.7505-3.96156.1122-0.13140.5897-0.1867-0.54880.35530.11410.3996-0.5223-0.25070.2626-0.0803-0.08510.4062-0.07260.2986-26.3025-2.45767.3766
92.568-0.00260.53030.6378-0.32433.32860.08910.1377-0.1468-0.1322-0.00310.070.23480.0338-0.10550.12980.0095-0.0160.10040.00250.1462-23.07260.798922.8817
102.579-3.5649-3.15198.2464.70264.26750.0366-0.04720.1148-0.11120.1789-0.2198-0.24710.3202-0.34810.1095-0.0364-0.01650.20820.01320.1637-11.20653.99079.7887
112.0955-0.4595-3.13050.59431.24746.20090.14150.29110.1024-0.1904-0.07040.0076-0.4207-0.346-0.1030.16070.0374-0.01670.16910.02160.1473-23.28688.428215.0989
128.8124-3.11211.26267.15820.53463.6847-0.2158-0.63090.06820.4330.2697-0.00580.07810.3342-0.04520.14750.0069-0.02640.1993-0.03240.1112-17.46736.798940.7796
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )A1 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 68 )A21 - 68
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 144 )A69 - 144
4X-RAY DIFFRACTION4chain 'A' and (resid 145 through 185 )A145 - 185
5X-RAY DIFFRACTION5chain 'A' and (resid 186 through 233 )A186 - 233
6X-RAY DIFFRACTION6chain 'A' and (resid 234 through 246 )A234 - 246
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 68 )B1 - 68
8X-RAY DIFFRACTION8chain 'B' and (resid 69 through 101 )B69 - 101
9X-RAY DIFFRACTION9chain 'B' and (resid 102 through 160 )B102 - 160
10X-RAY DIFFRACTION10chain 'B' and (resid 161 through 185 )B161 - 185
11X-RAY DIFFRACTION11chain 'B' and (resid 186 through 233 )B186 - 233
12X-RAY DIFFRACTION12chain 'B' and (resid 234 through 246 )B234 - 246

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