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- PDB-9e9u: Vanadate-bound Putative Ancestral Protein Tyrosine Phosphatase Sh... -

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Basic information

Entry
Database: PDB / ID: 9e9u
TitleVanadate-bound Putative Ancestral Protein Tyrosine Phosphatase ShufPTP - Highest p-loop Conformation
ComponentsShufPTP
KeywordsHYDROLASE / phosphatase / inhibitor / ASR / CSO / OCS / Oxidized Cystine
Function / homologyVANADATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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)17,5762
Polymers17,4611
Non-polymers1151
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.050, 86.050, 32.225
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: 17461.180 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-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.04 Å3/Da / Density % sol: 39.8 %
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: 1.8→50 Å / Num. obs: 12747 / % possible obs: 99.1 % / Redundancy: 16.8 % / Biso Wilson estimate: 25.47 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.039 / Rrim(I) all: 0.173 / Χ2: 1.016 / Net I/σ(I): 9.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.8-1.866.60.64111570.7430.9230.230.6881.02591.9
1.86-1.9410.30.59412510.8290.9520.1830.6241.02499.4
1.94-2.0314.60.47412920.9420.9850.1250.4911.00799.9
2.03-2.1317.70.40312730.9720.9930.0970.4150.98699.9
2.13-2.2719.70.31112670.9820.9950.0720.3191.035100
2.27-2.4419.40.25712900.9840.9960.060.2641.035100
2.44-2.6919.30.21612900.990.9980.050.2221.02399.9
2.69-3.0819.90.1812770.9920.9980.0410.1851.011100
3.08-3.8819.70.14812980.9940.9990.0340.1521.012100
3.88-50190.13313520.9940.9990.0310.1371.004100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACTdata extraction
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→37.26 Å / SU ML: 0.1017 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.2297
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2138 641 5.04 %
Rwork0.1781 12068 -
obs0.1799 12709 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.8 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1221 0 5 52 1278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00771252
X-RAY DIFFRACTIONf_angle_d1.00821695
X-RAY DIFFRACTIONf_chiral_restr0.0627186
X-RAY DIFFRACTIONf_plane_restr0.0084214
X-RAY DIFFRACTIONf_dihedral_angle_d16.3031480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.940.30461250.2442269X-RAY DIFFRACTION95.11
1.94-2.140.26761310.18552424X-RAY DIFFRACTION99.61
2.14-2.440.20861260.19062428X-RAY DIFFRACTION99.88
2.44-3.080.23341290.20592437X-RAY DIFFRACTION99.92
3.08-37.260.18461300.1522510X-RAY DIFFRACTION99.96

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