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- PDB-3o3l: Structure of the PTP-like phytase from Selenomonas ruminantium in... -

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Basic information

Entry
Database: PDB / ID: 3o3l
TitleStructure of the PTP-like phytase from Selenomonas ruminantium in complex with myo-inositol (1,3,4,5)tetrakisphosphate
ComponentsMyo-inositol hexaphosphate phosphohydrolase
KeywordsHYDROLASE / Phytase / Protein tyrosine phosphatase / Inositol phosphatase / phytate / inositol phosphate
Function / homology
Function and homology information


dephosphorylation / hydrolase activity
Similarity search - Function
Alpha-Beta Plaits - #1690 / Inositol hexakisphosphate / Inositol hexakisphosphate / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like ...Alpha-Beta Plaits - #1690 / Inositol hexakisphosphate / Inositol hexakisphosphate / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE / ACETATE ION / Myo-inositol hexaphosphate phosphohydrolase
Similarity search - Component
Biological speciesSelenomonas ruminantium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGruninger, R.J. / Selinger, L.B. / Mosimann, S.C.
CitationJournal: To be Published
Title: Structural analysis of substrate binding in PTPLPs
Authors: Gruninger, R.J. / Dobing, S. / Smith, A. / Weiden, H.J. / Selinger, L.B. / Mosimann, S.C.
History
DepositionJul 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myo-inositol hexaphosphate phosphohydrolase
B: Myo-inositol hexaphosphate phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,01118
Polymers77,9442
Non-polymers2,06816
Water13,799766
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-24 kcal/mol
Surface area27360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.130, 136.950, 79.910
Angle α, β, γ (deg.)90.000, 102.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Myo-inositol hexaphosphate phosphohydrolase / PTP-like phytase


Mass: 38971.848 Da / Num. of mol.: 2 / Mutation: C252S
Source method: isolated from a genetically manipulated source
Details: Construct consists of mature protein (aa 28-346) cloned into NdeI site of pET28b.
Source: (gene. exp.) Selenomonas ruminantium (bacteria) / Strain: JY35 / Gene: phyA, phyasr / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7WUJ1

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Non-polymers , 5 types, 782 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-4IP / INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE


Mass: 500.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H16O18P4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 766 / 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: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 10% P8K, 200 mM NaCl, 50 mM Na-acetate (pH 4.8), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 26, 2008 / Details: Double Crystal Si(111)
RadiationMonochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.85→77.947 Å / Num. all: 77167 / Num. obs: 77167 / % possible obs: 94.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.5 / Redundancy: 4.9 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.9550.7531.953141106340.75389.3
1.95-2.0750.483.150561101120.4889.5
2.07-2.214.90.3274.54729895940.32790.5
2.21-2.394.80.2256.14426792210.22593.2
2.39-2.624.70.1737.54108886980.17395.9
2.62-2.934.70.1210.23814280790.1297.6
2.93-3.384.70.08515.23390572140.08599
3.38-4.144.80.05621.62935161790.05699.6
4.14-5.855.60.03725.82652047760.037100
5.85-77.855.60.037251493626600.03799.9

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.5data scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→51.4 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8994 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1876 3894 4.7 %random
Rwork0.1626 ---
all0.172 77167 --
obs0.166 76792 93.5 %-
Solvent computationBsol: 42.6765 Å2
Displacement parametersBiso max: 73.85 Å2 / Biso mean: 20.6926 Å2 / Biso min: 7.12 Å2
Baniso -1Baniso -2Baniso -3
1--4.624 Å20 Å22.562 Å2
2---1.315 Å20 Å2
3---5.939 Å2
Refinement stepCycle: LAST / Resolution: 1.85→51.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5134 0 125 766 6025
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.554
X-RAY DIFFRACTIONc_mcbond_it1.5341.5
X-RAY DIFFRACTIONc_scbond_it2.6052
X-RAY DIFFRACTIONc_mcangle_it2.1722
X-RAY DIFFRACTIONc_scangle_it3.7832.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep_edit.paramwater_edit.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5GIP3_4IP_golact_tight.parGIP3_4IP_golact.top

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