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- PDB-3f41: Structure of the tandemly repeated protein tyrosine phosphatase l... -

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Basic information

Entry
Database: PDB / ID: 3f41
TitleStructure of the tandemly repeated protein tyrosine phosphatase like phytase from Mitsuokella multacida
ComponentsPhytase
KeywordsHYDROLASE / phytase / tandem repeat / protein tyrosine phosphatase / inositol phosphatase
Function / homology
Function and homology information


3-phytase / 3-phytase activity / dephosphorylation / cytosol
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
PHOSPHATE ION / Phytase
Similarity search - Component
Biological speciesMitsuokella multacida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsGruninger, R.J. / Selinger, L.B. / Mosimann, S.C.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural analysis of a multifunctional, tandemly repeated inositol polyphosphatase.
Authors: Gruninger, R.J. / Selinger, L.B. / Mosimann, S.C.
History
DepositionOct 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Phytase
B: Phytase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,29613
Polymers144,4822
Non-polymers81411
Water12,935718
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-21 kcal/mol
Surface area50850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.391, 73.304, 161.310
Angle α, β, γ (deg.)90.000, 93.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phytase


Mass: 72240.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Expression construct encodes residues 35-640 of PhyAmm and excludes the signal peptide (residues 1-34). The first 23 residues in the construct (residues 12-34) are an artifact of cloning. ...Details: Expression construct encodes residues 35-640 of PhyAmm and excludes the signal peptide (residues 1-34). The first 23 residues in the construct (residues 12-34) are an artifact of cloning. Residues 47-636 are visible in the model.
Source: (gene. exp.) Mitsuokella multacida (bacteria) / Strain: O32 / Gene: phyA, phyAmm / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3QMF6, 3-phytase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 718 / 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: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 10% PEG 8000, 2% ethylene glycol, 100 mM Tris, pH 8.5, vapor diffusion, temperature 298 K, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.2150,1.2146,1.1579
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 21, 2006
RadiationMonochromator: Double crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.2151
21.21461
31.15791
ReflectionResolution: 2.3→66 Å / Num. all: 77330 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 42.7 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 2.2 / Num. measured all: 28896 / Num. unique all: 10243 / Rsym value: 0.293 / % possible all: 91.4

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength11.2153.8-20.02
13 wavelength21.214610.49-23.83
13 wavelength31.15799.44-9.06
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1W31.930.7540.0010.0640.69
2W36.5070.2660.0190.4270.705
3W32.8330.7050.9930.2980.56
4W34.3260.3170.9850.1940.524
Phasing dmFOM : 0.76 / FOM acentric: 0.76 / FOM centric: 0.69 / Reflection: 43236 / Reflection acentric: 40894 / Reflection centric: 2342
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8-37.0450.880.890.819051636269
5-80.880.890.7458005351449
4-50.880.880.7772746854420
3.5-40.830.830.7172556901354
3-3.50.720.720.611296712420547
2.8-30.550.550.580357732303

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
SOLVE2.12phasing
RESOLVE2.12phasing
CNSrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.812 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2256 2.9 %Random
Rwork0.208 ---
all0.229 77195 --
obs0.23 74651 96.7 %-
Solvent computationBsol: 46.993 Å2
Displacement parametersBiso max: 80.59 Å2 / Biso mean: 39.618 Å2 / Biso min: 11.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.273 Å20 Å20.463 Å2
2--0.869 Å20 Å2
3----0.596 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9613 0 48 718 10379
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.462
X-RAY DIFFRACTIONc_mcbond_it1.8531.5
X-RAY DIFFRACTIONc_scbond_it2.7772
X-RAY DIFFRACTIONc_mcangle_it2.9272
X-RAY DIFFRACTIONc_scangle_it4.0092.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION3CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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