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- PDB-4fdu: Crystal Structure of a Multiple Inositol Polyphosphate Phosphatase -

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Basic information

Entry
Database: PDB / ID: 4fdu
TitleCrystal Structure of a Multiple Inositol Polyphosphate Phosphatase
ComponentsPutative multiple inositol polyphosphate histidine phosphatase 1
KeywordsHYDROLASE / Phosphatase
Function / homology
Function and homology information


multiple inositol-polyphosphate phosphatase / 2,3-bisphosphoglycerate 3-phosphatase / hydrolase activity / membrane
Similarity search - Function
Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Phosphoglycerate mutase-like / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-MYO-INOSITOL-HEXASULPHATE / Multiple inositol polyphosphate phosphatase 1
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.293 Å
AuthorsLi, A.W.H. / Hemmings, A.M.
CitationJournal: Cell Rep / Year: 2014
Title: A Bacterial Homolog of a Eukaryotic Inositol Phosphate Signaling Enzyme Mediates Cross-kingdom Dialog in the Mammalian Gut.
Authors: Stentz, R. / Osborne, S. / Horn, N. / Li, A.W. / Hautefort, I. / Bongaerts, R. / Rouyer, M. / Bailey, P. / Shears, S.B. / Hemmings, A.M. / Brearley, C.A. / Carding, S.R.
History
DepositionMay 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: 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

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Assembly

Deposited unit
A: Putative multiple inositol polyphosphate histidine phosphatase 1
B: Putative multiple inositol polyphosphate histidine phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9147
Polymers98,4072
Non-polymers1,5075
Water2,468137
1
A: Putative multiple inositol polyphosphate histidine phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9263
Polymers49,2031
Non-polymers7232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative multiple inositol polyphosphate histidine phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9884
Polymers49,2031
Non-polymers7853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.160, 117.300, 75.510
Angle α, β, γ (deg.)90.00, 107.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative multiple inositol polyphosphate histidine phosphatase 1


Mass: 49203.426 Da / Num. of mol.: 2 / Fragment: UNP residues 21-425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_4744 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-RIL / References: UniProt: Q89YI8
#2: Chemical ChemComp-IHS / D-MYO-INOSITOL-HEXASULPHATE


Mass: 660.535 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O24S6
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5
Details: 0.2M Ammonium acetate pH5.0 18% PEG 3350 Protein conc.=1mg/ml, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2011
RadiationMonochromator: Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.29→39.1 Å / Num. all: 38461 / Num. obs: 38461 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2928→2.3747 Å / % possible all: 82

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.293→37.942 Å / SU ML: 0.32 / σ(F): 0 / Phase error: 25.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 1810 5.03 %RANDOM
Rwork0.168 ---
all0.1712 35979 --
obs0.1712 35979 92.65 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.0219 Å20 Å2-4.8826 Å2
2--15.3553 Å2-0 Å2
3----5.8022 Å2
Refinement stepCycle: LAST / Resolution: 2.293→37.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6468 0 84 137 6689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086799
X-RAY DIFFRACTIONf_angle_d1.1369232
X-RAY DIFFRACTIONf_dihedral_angle_d15.6332582
X-RAY DIFFRACTIONf_chiral_restr0.078999
X-RAY DIFFRACTIONf_plane_restr0.0051159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.293-2.37470.34641610.23163022X-RAY DIFFRACTION82
2.3747-2.46980.30331420.22973150X-RAY DIFFRACTION85
2.4698-2.58220.31541780.21593189X-RAY DIFFRACTION87
2.5822-2.71830.31881720.20453349X-RAY DIFFRACTION91
2.7183-2.88850.30971930.19533415X-RAY DIFFRACTION93
2.8885-3.11150.25521880.1753504X-RAY DIFFRACTION95
3.1115-3.42440.23591780.17273591X-RAY DIFFRACTION97
3.4244-3.91950.22831860.16293638X-RAY DIFFRACTION99
3.9195-4.93640.17991990.12513660X-RAY DIFFRACTION99
4.9364-37.94740.18042130.15963651X-RAY DIFFRACTION98

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