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

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Basic information

Entry
Database: PDB / ID: 3mmj
TitleStructure of the PTP-like phytase from Selenomonas ruminantium in complex with myo-inositol hexakisphosphate
ComponentsMyo-inositol hexaphosphate phosphohydrolase
KeywordsHYDROLASE / phytase / protein tyrosine phosphatase / inositol phosphate / inositol phosphatase
Function / homology
Function and homology information


phosphatase activity / dephosphorylation
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 profile. / Tyrosine-specific protein phosphatases domain / 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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / INOSITOL HEXAKISPHOSPHATE / PHOSPHATE ION / Myo-inositol hexaphosphate phosphohydrolase
Similarity search - Component
Biological speciesSelenomonas ruminantium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGruninger, R.J. / Selinger, L.B. / Mosimann, S.C.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Substrate binding in protein-tyrosine phosphatase-like inositol polyphosphatases.
Authors: Gruninger, R.J. / Dobing, S. / Smith, A.D. / Bruder, L.M. / Selinger, L.B. / Wieden, H.J. / Mosimann, S.C.
History
DepositionApr 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 17, 2013Group: Database references
Revision 1.3Oct 14, 2020Group: Derived calculations / Structure summary / Category: chem_comp / struct_site
Item: _chem_comp.pdbx_synonyms / _struct_site.pdbx_auth_asym_id ..._chem_comp.pdbx_synonyms / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 6, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Sep 6, 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: Myo-inositol hexaphosphate phosphohydrolase
B: Myo-inositol hexaphosphate phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,58616
Polymers72,3432
Non-polymers2,24214
Water15,943885
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-64 kcal/mol
Surface area27030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.130, 136.950, 79.910
Angle α, β, γ (deg.)90.00, 102.95, 90.00
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


Mass: 36171.738 Da / Num. of mol.: 2 / Mutation: C252S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Selenomonas ruminantium (bacteria) / Strain: JY35 / Gene: phyA / Plasmid: pet28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7WUJ1

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Non-polymers , 6 types, 899 molecules

#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 885 / 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: 3.4 Å3/Da / Density % sol: 63.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 8-10% PEG8000, 200-300 NaCl, 50 mM Sodium Acetate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 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: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.6→51 Å / Num. all: 120565 / Num. obs: 120565 / % possible obs: 92.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.7
Reflection shellResolution: 1.6→1.68 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 1.5 / Num. unique all: 14414 / % possible all: 77

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B4U
Resolution: 1.6→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 6015 -random
Rwork0.177 ---
all0.182 120565 --
obs0.177 120565 92.9 %-
Displacement parametersBiso mean: 16 Å2
Baniso -1Baniso -2Baniso -3
1--1.298 Å20 Å21.461 Å2
2---2.743 Å20 Å2
3---4.042 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5103 0 129 885 6117

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