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- PDB-9e9l: Vanadate-bound Putative Ancestral Protein Tyrosine Phosphatase Sh... -

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Basic information

Entry
Database: PDB / ID: 9e9l
TitleVanadate-bound Putative Ancestral Protein Tyrosine Phosphatase ShufPTP - Intermediate p-loop Conformation
ComponentsShufPTP
KeywordsHYDROLASE / phosphatase / inhibitor / ASR / CSO / Oxidized Cystine
Function / homologyVANADATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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)17,8285
Polymers17,4291
Non-polymers3994
Water32418
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)85.718, 85.718, 32.374
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.03 Å3/Da / Density % sol: 39.6 %
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, 5 mM sodium metavanadate 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.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 7921 / % possible obs: 97.4 % / Redundancy: 14.2 % / Biso Wilson estimate: 34.12 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.046 / Rrim(I) all: 0.18 / Χ2: 0.993 / Net I/σ(I): 11 / Num. measured all: 112232
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.1-2.1811.10.4516940.9420.9850.1250.4691.02386.1
2.18-2.2611.60.4067510.9560.9890.1120.4220.96593.9
2.26-2.3712.40.3627550.9690.9920.0970.3750.9794.8
2.37-2.49120.3458130.9710.9930.0950.3591.00898.9
2.49-2.6514.80.2977950.9770.9940.0770.3070.998100
2.65-2.8515.80.2658020.9840.9960.0680.2740.973100
2.85-3.1415.90.2258070.9830.9960.0570.2320.978100
3.14-3.5915.60.1848300.9910.9980.0480.1910.992100
3.59-4.5216.10.158140.9890.9970.0390.1561.028100
4.52-5015.60.1428600.9880.9970.0380.1470.993100

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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: 2.1→37.12 Å / SU ML: 0.1977 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.8607
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2238 392 4.97 %
Rwork0.1836 7501 -
obs0.1857 7893 96.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.38 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1190 0 21 18 1229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841233
X-RAY DIFFRACTIONf_angle_d1.05141668
X-RAY DIFFRACTIONf_chiral_restr0.0524185
X-RAY DIFFRACTIONf_plane_restr0.0075208
X-RAY DIFFRACTIONf_dihedral_angle_d15.593460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.40.25111190.20792317X-RAY DIFFRACTION91.13
2.4-3.030.25371360.21482551X-RAY DIFFRACTION99.59
3.03-37.120.20811370.16812633X-RAY DIFFRACTION99.93

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