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- PDB-2b4p: Structure of the D223N mutant of Selenomonas ruminantium PTP-like... -

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Basic information

Entry
Database: PDB / ID: 2b4p
TitleStructure of the D223N mutant of Selenomonas ruminantium PTP-like phytase
Componentsmyo-inositol hexaphosphate phosphohydrolase
KeywordsHYDROLASE / PTP-like / ionic strength
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
MALONATE ION / Myo-inositol hexaphosphate phosphohydrolase
Similarity search - Component
Biological speciesSelenomonas ruminantium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsGruninger, R.J. / Selinger, L.B. / Mosimann, S.C.
CitationJournal: Protein Sci. / Year: 2007
Title: Kinetic and structural analysis of a bacterial protein tyrosine phosphatase-like myo-inositol polyphosphatase.
Authors: Puhl, A.A. / Gruninger, R.J. / Greiner, R. / Janzen, T.W. / Mosimann, S.C. / Selinger, L.B.
History
DepositionSep 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)76,9976
Polymers76,7222
Non-polymers2754
Water10,989610
1
A: myo-inositol hexaphosphate phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4632
Polymers38,3611
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: myo-inositol hexaphosphate phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5344
Polymers38,3611
Non-polymers1733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.200, 137.420, 79.610
Angle α, β, γ (deg.)90.00, 102.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein myo-inositol hexaphosphate phosphohydrolase


Mass: 38361.234 Da / Num. of mol.: 2 / Mutation: D223N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Selenomonas ruminantium (bacteria) / Gene: phyasr_R252K / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7WUJ1, EC: 3.1.3.72
#2: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 610 / 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: 64 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.5
Details: 1.35 M ammonium sulfate, 0.90 M NaCl, 1 % 1,6 hexandiol, pH 6.5, vapor diffusion, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1166 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2004
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1166 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. all: 77249 / Num. obs: 77204 / % possible obs: 87.9 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.074 / Χ2: 2.346
Reflection shellResolution: 1.81→1.86 Å / % possible obs: 70.9 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.411 / Num. measured obs: 6208 / Χ2: 1.453 / % possible all: 63.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.7data extraction
XFITdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→40 Å / σ(F): 44 / Stereochemistry target values: CNS defalut
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2346 2.6 %Random
Rwork0.196 ---
all-77249 --
obs-74855 86.3 %-
Solvent computationBsol: 42.765 Å2
Displacement parametersBiso mean: 18.648 Å2
Baniso -1Baniso -2Baniso -3
1-3.973 Å20 Å2-2.228 Å2
2--2.959 Å20 Å2
3----6.933 Å2
Refinement stepCycle: LAST / Resolution: 1.81→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5103 0 16 610 5729
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.139
X-RAY DIFFRACTIONc_bond_d0.008
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2malonate.parmalonate.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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