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- PDB-2b4u: Structure of the C252S mutant of Selenomonas ruminantium PTP-like... -

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Basic information

Entry
Database: PDB / ID: 2b4u
TitleStructure of the C252S 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: 2 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_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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)77,9137
Polymers77,4812
Non-polymers4325
Water12,935718
1
A: myo-inositol hexaphosphate phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9744
Polymers38,7411
Non-polymers2343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: myo-inositol hexaphosphate phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9393
Polymers38,7411
Non-polymers1982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.837, 137.187, 79.954
Angle α, β, γ (deg.)90.00, 103.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein myo-inositol hexaphosphate phosphohydrolase


Mass: 38740.680 Da / Num. of mol.: 2 / Mutation: C252S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Selenomonas ruminantium (bacteria) / Gene: phyasr_C252S / 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.464
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2951vapor diffusion6.51.35 M ammonium sulfate, 0.90 M NaCl, 1 % 1,6 hexandiol, pH 6.5, VAPOR DIFFUSION, temperature 295K
2952vapor diffusion6.51.35 M ammonium sulfate, 0.90 M NaCl, 1 % 1,6 hexandiol, pH 6.5, VAPOR DIFFUSION, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)Wavelength
SYNCHROTRONALS 8.3.111.0206
ROTATING ANODEENRAF-NONIUS FR59121.5418
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDJul 29, 2004double crystal
Nonius Kappa CCD2CCDJul 30, 2004osmic mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystalSINGLE WAVELENGTHMx-ray1
2osmic mirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.02061
21.54181
ReflectionResolution: 2→50 Å / Num. all: 51554 / Num. obs: 48658 / % possible obs: 79 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.094 / Χ2: 1.07
Reflection shellResolution: 2→2.07 Å / % possible obs: 74.9 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.565 / Num. measured obs: 4849 / Χ2: 1.165 / % possible all: 64.9

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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: 2→40 Å / σ(F): 85 / Stereochemistry target values: CNS defalut
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1117 1.7 %random
Rwork0.197 ---
all-51554 --
obs-48658 79 %-
Solvent computationBsol: 50.738 Å2
Displacement parametersBiso mean: 19.207 Å2
Baniso -1Baniso -2Baniso -3
1-3.102 Å20 Å2-3.297 Å2
2--2.722 Å20 Å2
3----5.824 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5114 0 25 718 5857
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.054
X-RAY DIFFRACTIONc_bond_d0.006
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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