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- PDB-9e9n: Ligand Free Putative Ancestral Protein Tyrosine Phosphatase ShufP... -

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Basic information

Entry
Database: PDB / ID: 9e9n
TitleLigand Free Putative Ancestral Protein Tyrosine Phosphatase ShufPTP - Lowest p-loop Conformation
ComponentsShufPTP
KeywordsHYDROLASE / phosphatase / inhibitor / ASR / CSO / Oxidized Cystine
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsDenson, J.M. / Shen, R. / Hengge, A.C. / Johnson, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: To Be Published
Title: A Putative Ancestral Protein Tyrosine Phosphatase Probes the Evolutionary Origin of PTP Loop Motions
Authors: Shen, R. / Denson, J.M. / Hengge, A.C. / Johnson, S.J.
History
DepositionNov 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ShufPTP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6273
Polymers17,4291
Non-polymers1982
Water77543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.637, 85.637, 32.191
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein ShufPTP


Mass: 17429.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.02 Å3/Da / Density % sol: 39.1 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 8 mg/mL protein, 0.1 M CAPS, 30% PEG 400 at a 1:1:0.2 protein/well/additive screen. The additive screen contains 0.2 M (NH4)2SO4, 20-30% PEG 4000, and 10-35% glycerol. Soaked in 5mM Tris-HCl pH 7.5 for 24hrs

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 19, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 10049 / % possible obs: 98.5 % / Redundancy: 18.1 % / Biso Wilson estimate: 34.64 Å2 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.023 / Rrim(I) all: 0.102 / Χ2: 1.016 / Net I/σ(I): 13.9 / Num. measured all: 182280
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsRpim(I) allRrim(I) allΧ2% possible all
1.94-2.014.90.9838690.4340.0011.03985.7
2.01-2.0912.60.8359920.2360.871.02599.6
2.09-2.1818.50.61710090.1460.6340.992100
2.18-2.319.60.43810090.1010.450.991100
2.3-2.4419.80.31310030.0720.3211.034100
2.44-2.6320.40.23510170.0530.2411.04100
2.63-2.920.80.16810200.0380.1721.031100
2.9-3.3221.20.11410200.0250.1170.997100
3.32-4.1821.40.07410320.0160.0751.034100
4.18-50200.04910780.0110.050.995100

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Processing

Software
NameVersionClassification
PDB_EXTRACTdata extraction
PHENIX1.20.1_4487refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→37.08 Å / SU ML: 0.1302 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2843
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2312 505 5.04 %
Rwork0.1778 9519 -
obs0.1805 10024 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.85 Å2
Refinement stepCycle: LAST / Resolution: 1.94→37.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1183 0 13 43 1239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681238
X-RAY DIFFRACTIONf_angle_d0.91271674
X-RAY DIFFRACTIONf_chiral_restr0.0502185
X-RAY DIFFRACTIONf_plane_restr0.0076212
X-RAY DIFFRACTIONf_dihedral_angle_d14.5148175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-2.130.34821230.25742227X-RAY DIFFRACTION92.52
2.13-2.440.26681270.17632385X-RAY DIFFRACTION99.8
2.44-3.080.26331250.21162414X-RAY DIFFRACTION99.92
3.08-37.080.19461300.15372493X-RAY DIFFRACTION99.96

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