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

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Basic information

Entry
Database: PDB / ID: 6rxg
TitleCrystal Structure of Bifidobacterium longum Multiple Inositol Polyphosphate Phosphatase Complex with Phosphate
Components(Histidine acid phosphatase) x 2
KeywordsHYDROLASE / phytase / histidine phosphatase / MINPP / Bifidobacterium
Function / homology
Function and homology information


multiple inositol-polyphosphate phosphatase / 2,3-bisphosphoglycerate 3-phosphatase / hydrolase activity / metal ion binding / membrane
Similarity search - Function
Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Multiple inositol polyphosphate phosphatase 1
Similarity search - Component
Biological speciesBifidobacterium longum subsp. infantis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsZietek, M.A.Z. / 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_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.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: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)113,68010
Polymers113,0682
Non-polymers6128
Water14,502805
1
A: Histidine acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8155
Polymers56,4951
Non-polymers3214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histidine acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8655
Polymers56,5741
Non-polymers2914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.600, 72.760, 87.330
Angle α, β, γ (deg.)71.43, 72.21, 76.75
Int Tables number1
Space group name H-MP1

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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)
Strain: ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12
Gene: Blon_0263 / 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)
Strain: ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12
Gene: Blon_0263 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta 2 (DE3) pLysS / References: UniProt: B7GTV0
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 805 / 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: 2.74 Å3/Da / Density % sol: 55.11 % / 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: May 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.71→68.231 Å / Num. obs: 123847 / % possible obs: 95.5 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 7
Reflection shellResolution: 1.71→1.74 Å / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6108 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RXD

6rxd


Resolution: 1.71→68.231 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 18.97
RfactorNum. reflection% reflection
Rfree0.1936 6116 4.94 %
Rwork0.1466 --
obs0.1489 123841 95.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.71→68.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7816 0 20 805 8641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098014
X-RAY DIFFRACTIONf_angle_d0.92710869
X-RAY DIFFRACTIONf_dihedral_angle_d14.7314741
X-RAY DIFFRACTIONf_chiral_restr0.051117
X-RAY DIFFRACTIONf_plane_restr0.0061463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.72940.27932090.23993892X-RAY DIFFRACTION95
1.7294-1.74980.29762130.23173924X-RAY DIFFRACTION95
1.7498-1.77110.28211920.22593866X-RAY DIFFRACTION95
1.7711-1.79350.28031960.21483898X-RAY DIFFRACTION95
1.7935-1.81710.27062100.20373928X-RAY DIFFRACTION94
1.8171-1.8420.27132020.20173801X-RAY DIFFRACTION95
1.842-1.86840.24762280.19113976X-RAY DIFFRACTION95
1.8684-1.89620.2842080.19633838X-RAY DIFFRACTION94
1.8962-1.92590.24031990.17953855X-RAY DIFFRACTION94
1.9259-1.95750.23812090.16253906X-RAY DIFFRACTION94
1.9575-1.99120.22232010.15443834X-RAY DIFFRACTION95
1.9912-2.02740.2281910.14743910X-RAY DIFFRACTION94
2.0274-2.06640.20492050.1373878X-RAY DIFFRACTION95
2.0664-2.10860.18182080.13143921X-RAY DIFFRACTION95
2.1086-2.15450.19271820.12623916X-RAY DIFFRACTION95
2.1545-2.20460.18211980.12833996X-RAY DIFFRACTION96
2.2046-2.25970.17032120.12283885X-RAY DIFFRACTION95
2.2597-2.32080.1711920.11783933X-RAY DIFFRACTION96
2.3208-2.38910.16741900.11813932X-RAY DIFFRACTION95
2.3891-2.46620.17442160.11613965X-RAY DIFFRACTION96
2.4662-2.55440.15922160.11093924X-RAY DIFFRACTION96
2.5544-2.65670.1491840.11294011X-RAY DIFFRACTION96
2.6567-2.77760.15382090.11513971X-RAY DIFFRACTION97
2.7776-2.9240.17781760.12744022X-RAY DIFFRACTION97
2.924-3.10720.17391920.13743959X-RAY DIFFRACTION97
3.1072-3.34710.18192320.13924001X-RAY DIFFRACTION97
3.3471-3.68390.1582150.13543910X-RAY DIFFRACTION96
3.6839-4.21690.1872200.14384005X-RAY DIFFRACTION97
4.2169-5.31260.19612040.15423941X-RAY DIFFRACTION96
5.3126-68.28570.22382070.19773927X-RAY DIFFRACTION96

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