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

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Basic information

Entry
Database: PDB / ID: 6rxf
TitleCrystal Structure of Bifidobacterium longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate
Components(Histidine acid phosphatase) x 2
KeywordsHYDROLASE / phytase / histidine phosphatase / MINPP / Bifidobacterium
Function / homologyinositol phosphate phosphatase activity / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / acid phosphatase activity / Histidine phosphatase superfamily / membrane / metal ion binding / Histidine acid phosphatase
Function and homology information
Biological speciesBifidobacterium longum subsp. infantis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.397 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 / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)114,18019
Polymers113,0682
Non-polymers1,11217
Water5,999333
1
A: Histidine acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0189
Polymers56,4951
Non-polymers5238
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histidine acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,16210
Polymers56,5741
Non-polymers5899
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.508, 73.118, 88.987
Angle α, β, γ (deg.)71.300, 72.990, 78.990
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

#1: Protein Histidine acid phosphatase


Mass: 56494.695 Da / Num. of mol.: 1
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)
Gene: Blon_0263
Variant: ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta 2 (DE3) pLysS / References: UniProt: B7GTV0
#2: Protein Histidine acid phosphatase


Mass: 56573.672 Da / Num. of mol.: 1
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)
Gene: Blon_0263
Variant: ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta 2 (DE3) pLysS / References: UniProt: B7GTV0
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.88 Å3/Da / Density % sol: 57.24 % / Description: needle
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES, 0.01 M zinc chloride, 18 % PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 30, 2018
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.397→68.86 Å / Num. obs: 46820 / % possible obs: 94.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.233 / Net I/σ(I): 2.3
Reflection shellResolution: 2.397→2.48 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4365

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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: 2.397→52.774 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2346 --
Rwork0.1824 --
obs-46808 94.53 %
Refinement stepCycle: LAST / Resolution: 2.397→52.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7808 0 17 333 8158

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