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- PDB-6rxe: Crystal Structure of Bifidobacterium longum Multiple Inositol Pol... -

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Basic information

Entry
Database: PDB / ID: 6rxe
TitleCrystal Structure of Bifidobacterium longum Multiple Inositol Polyphosphate Phosphatase Complex with Inositol Hexasulfate
ComponentsHistidine acid phosphatase
KeywordsHYDROLASE / phytase / histidine phosphatase / MINPP / Bifidobacterium
Function / homology
Function and homology information


multiple inositol-polyphosphate phosphatase / 2,3-bisphosphoglycerate 3-phosphatase / hydrolase activity / membrane / metal ion binding
Similarity search - Function
Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily
Similarity search - Domain/homology
D-MYO-INOSITOL-HEXASULPHATE / PHOSPHATE ION / Multiple inositol polyphosphate phosphatase 1
Similarity search - Component
Biological speciesBifidobacterium longum subsp. infantis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsAcquistapace, I.M. / Brearley, C.A. / Hemmings, A.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M022978/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Snapshots during the catalytic cycle of a histidine acid phytase reveal an induced-fit structural mechanism.
Authors: Acquistapace, I.M. / Zi Etek, M.A. / Li, A.W.H. / Salmon, M. / Kuhn, I. / Bedford, M.R. / Brearley, C.A. / Hemmings, A.M.
History
DepositionJun 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine acid phosphatase
B: Histidine acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,6676
Polymers112,1562
Non-polymers1,5114
Water25,8151433
1
A: Histidine acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8343
Polymers56,0781
Non-polymers7562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histidine acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8343
Polymers56,0781
Non-polymers7562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.829, 106.411, 76.462
Angle α, β, γ (deg.)90.00, 112.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histidine acid phosphatase


Mass: 56078.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum subsp. infantis (strain ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12) (bacteria)
Strain: ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12
Gene: Blon_0263 / Plasmid: pOPINF / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta 2 (DE3) pLysS / References: UniProt: B7GTV0
#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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1433 / 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: 2.32 Å3/Da / Density % sol: 47.1 % / Description: large needle
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 10 mM HEPES, 75 mM NaCl, 10% (w/v) PEG 1000, 10% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.84→70.57 Å / Num. obs: 90353 / % possible obs: 99.7472 % / Redundancy: 3.3 % / Biso Wilson estimate: 10.9 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 3.6
Reflection shellResolution: 1.84→1.97 Å / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4482 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RXD

6rxd


Resolution: 1.84→70.569 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.93
RfactorNum. reflection% reflection
Rfree0.2388 4453 4.93 %
Rwork0.2074 --
obs0.209 90352 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.84→70.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7719 0 82 1433 9234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048113
X-RAY DIFFRACTIONf_angle_d0.68911051
X-RAY DIFFRACTIONf_dihedral_angle_d7.0946485
X-RAY DIFFRACTIONf_chiral_restr0.0421137
X-RAY DIFFRACTIONf_plane_restr0.0041457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.86090.36831210.34242915X-RAY DIFFRACTION100
1.8609-1.88280.37711530.33652791X-RAY DIFFRACTION99
1.8828-1.90580.33751390.32222901X-RAY DIFFRACTION100
1.9058-1.92990.38971240.3132839X-RAY DIFFRACTION100
1.9299-1.95530.32091460.29872854X-RAY DIFFRACTION100
1.9553-1.98210.30331430.29092832X-RAY DIFFRACTION99
1.9821-2.01040.35331590.28132842X-RAY DIFFRACTION99
2.0104-2.04040.30281500.27762822X-RAY DIFFRACTION99
2.0404-2.07230.30851670.26882839X-RAY DIFFRACTION99
2.0723-2.10630.33241310.25832855X-RAY DIFFRACTION100
2.1063-2.14260.30041620.24672841X-RAY DIFFRACTION100
2.1426-2.18160.29111280.23432874X-RAY DIFFRACTION100
2.1816-2.22350.26691270.22952880X-RAY DIFFRACTION100
2.2235-2.26890.23721330.21562890X-RAY DIFFRACTION100
2.2689-2.31820.2521350.20672854X-RAY DIFFRACTION100
2.3182-2.37220.24961380.21722874X-RAY DIFFRACTION100
2.3722-2.43150.27181310.20792874X-RAY DIFFRACTION100
2.4315-2.49730.20741660.20982852X-RAY DIFFRACTION100
2.4973-2.57070.26971440.20262873X-RAY DIFFRACTION100
2.5707-2.65370.2591780.19892840X-RAY DIFFRACTION100
2.6537-2.74860.2341580.19572848X-RAY DIFFRACTION100
2.7486-2.85860.20121610.18662859X-RAY DIFFRACTION100
2.8586-2.98870.22151520.18932863X-RAY DIFFRACTION100
2.9887-3.14630.2381410.17922911X-RAY DIFFRACTION100
3.1463-3.34340.20311520.17132845X-RAY DIFFRACTION100
3.3434-3.60160.19741440.15872888X-RAY DIFFRACTION100
3.6016-3.9640.17571380.14422905X-RAY DIFFRACTION100
3.964-4.53750.17071350.14312906X-RAY DIFFRACTION100
4.5375-5.71630.162230.15732791X-RAY DIFFRACTION100
5.7163-70.6210.2011740.19072941X-RAY DIFFRACTION100

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