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- PDB-3d1h: Structure of the PTP-Like Phytase Expressed by Selenomonas Rumina... -

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Basic information

Entry
Database: PDB / ID: 3d1h
TitleStructure of the PTP-Like Phytase Expressed by Selenomonas Ruminantium at an Ionic Strength of 500 mM
ComponentsMyo-inositol hexaphosphate phosphohydrolase
KeywordsHYDROLASE / PTP / PROTEIN TYROSINE PHOSPHATASE / PHYTASE / P-LOOP
Function / homology
Function and homology information


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
Myo-inositol hexaphosphate phosphohydrolase
Similarity search - Component
Biological speciesSelenomonas ruminantium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGruninger, R.J. / Selinger, L.B. / Mosimann, S.C.
CitationJournal: Febs J. / Year: 2008
Title: Effect of ionic strength and oxidation on the P-loop conformation of the protein tyrosine phosphatase-like phytase, PhyAsr.
Authors: Gruninger, R.J. / Brent Selinger, L. / Mosimann, S.C.
History
DepositionMay 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)78,4367
Polymers77,9762
Non-polymers4605
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-12.9 kcal/mol
Surface area27610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.858, 137.174, 79.839
Angle α, β, γ (deg.)90.00, 102.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myo-inositol hexaphosphate phosphohydrolase


Mass: 38987.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Selenomonas ruminantium (bacteria) / Gene: phyA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7WUJ1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 484 / 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: 3.14 Å3/Da / Density % sol: 60.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 10% P8K, 450 MM NACL, 50 MM NA-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: 1.1158 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 20, 2006
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 46736 / % possible obs: 91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.055 / Net I/σ(I): 16.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3133 / Rsym value: 0.19 / % possible all: 56.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
AMoREphasing
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2b4p

2b4p


Resolution: 2.1→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.5 / σ(I): 1.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2544 -random
Rwork0.184 ---
all0.187 ---
obs0.186 46736 91 %-
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5098 0 30 484 5612

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