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

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Basic information

Entry
Database: PDB / ID: 4fdt
TitleCrystal Structure of a Multiple Inositol Polyphosphate Phosphatase
ComponentsPutative multiple inositol polyphosphate histidine phosphatase 1
KeywordsHYDROLASE / Phosphatase
Function / homologyHistidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Phosphoglycerate mutase-like / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / PHOSPHATE ION / Multiple inositol polyphosphate histidine phosphatase 1
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 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)98,7216
Polymers98,4072
Non-polymers3144
Water8,125451
1
A: Putative multiple inositol polyphosphate histidine phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3603
Polymers49,2031
Non-polymers1572
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)49,3603
Polymers49,2031
Non-polymers1572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.720, 120.640, 76.070
Angle α, β, γ (deg.)90.00, 107.89, 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-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5
Details: 0.2M Ammonium acetate, pH5.0, 18% PEG 3350, Protein 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.93→62.07 Å / Num. all: 65891 / Num. obs: 65891 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9301→1.999 Å / % possible all: 82

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Processing

Software
NameVersionClassification
DNAdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.93→60.32 Å / SU ML: 0.24 / σ(F): 0 / Phase error: 20.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 3171 5.08 %RANDOM
Rwork0.1657 ---
all0.168 62399 --
obs0.168 62399 91.92 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.3784 Å2-0 Å2-2.6626 Å2
2--3.6572 Å2-0 Å2
3----1.7575 Å2
Refinement stepCycle: LAST / Resolution: 1.93→60.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6474 0 18 451 6943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076955
X-RAY DIFFRACTIONf_angle_d0.9769472
X-RAY DIFFRACTIONf_dihedral_angle_d14.0742702
X-RAY DIFFRACTIONf_chiral_restr0.0661016
X-RAY DIFFRACTIONf_plane_restr0.0051211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9301-1.9990.28182930.23495266X-RAY DIFFRACTION82
1.999-2.07910.28583200.21255488X-RAY DIFFRACTION86
2.0791-2.17370.25033040.18885732X-RAY DIFFRACTION89
2.1737-2.28830.22352900.17335851X-RAY DIFFRACTION91
2.2883-2.43170.24163240.16695865X-RAY DIFFRACTION92
2.4317-2.61940.21463220.166055X-RAY DIFFRACTION94
2.6194-2.8830.24323340.16866112X-RAY DIFFRACTION96
2.883-3.30020.22043290.16516201X-RAY DIFFRACTION96
3.3002-4.15780.183390.14796261X-RAY DIFFRACTION97
4.1578-60.34950.18113160.1576397X-RAY DIFFRACTION97

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