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- PDB-6gj9: PURPLE ACID PHYTASE FROM WHEAT ISOFORM B2 - REGENERATION COMPLEX -

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Basic information

Entry
Database: PDB / ID: 6gj9
TitlePURPLE ACID PHYTASE FROM WHEAT ISOFORM B2 - REGENERATION COMPLEX
ComponentsPurple acid phosphatase
KeywordsHYDROLASE / EC 3.1.3.26 / PURPLE ACID PHYTASE
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / metal ion binding
Similarity search - Function
Purple acid phosphatase-like / Purple acid phosphatase-like, N-terminal / Purple acid phosphatase, N-terminal / Iron/zinc purple acid phosphatase-like C-terminal domain / Purple acid phosphatase, metallophosphatase domain / Iron/zinc purple acid phosphatase-like protein C / Purple acid Phosphatase, N-terminal domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type ...Purple acid phosphatase-like / Purple acid phosphatase-like, N-terminal / Purple acid phosphatase, N-terminal / Iron/zinc purple acid phosphatase-like C-terminal domain / Purple acid phosphatase, metallophosphatase domain / Iron/zinc purple acid phosphatase-like protein C / Purple acid Phosphatase, N-terminal domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Purple acid phosphatase / Purple acid phosphatase
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsFaba-Rodriguez, R. / Brearley, C.A. / Hemmings, A.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M022978/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of a cereal purple acid phytase provides insights to phytate degradation in plants
Authors: Faba-Rodriguez, R. / Dionisio, G. / Brinch-Pedersen, H. / Brearley, C.A. / Hemmings, A.M.
History
DepositionMay 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Purple acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,67613
Polymers57,5491
Non-polymers2,12612
Water12,070670
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-4 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.971, 126.971, 107.518
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Purple acid phosphatase


Mass: 57549.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Tissue: aleurone vacuole / Gene: PAPhy / Plasmid: pGAPZalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71H(OCH1::G418R)
References: UniProt: C4PKL0, UniProt: F6MIW5*PLUS, acid phosphatase

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Sugars , 2 types, 7 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 675 molecules

#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57.56 % / Description: CUBIC
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2 M SODIUM THIOCYANATE; 20% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2016
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.76→48.3 Å / Num. obs: 63514 / % possible obs: 99 % / Redundancy: 3.5 % / Biso Wilson estimate: 14.2 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.09 / Rrim(I) all: 0.173 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.76-1.853.30.57892650.6930.3580.68498.7
5.56-48.33.60.06219920.9930.0360.07297.9

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Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GIT

6git


Resolution: 1.76→38.766 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 19.35
RfactorNum. reflection% reflection
Rfree0.1955 3160 4.98 %
Rwork0.1437 --
obs0.1463 63506 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.21 Å2 / Biso mean: 18.9717 Å2 / Biso min: 4.66 Å2
Refinement stepCycle: final / Resolution: 1.76→38.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3913 0 257 670 4840
Biso mean--36.92 31.37 -
Num. residues----504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064317
X-RAY DIFFRACTIONf_angle_d1.065924
X-RAY DIFFRACTIONf_chiral_restr0.067645
X-RAY DIFFRACTIONf_plane_restr0.005767
X-RAY DIFFRACTIONf_dihedral_angle_d14.6632490
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7597-1.7860.29331420.24112613275599
1.786-1.81390.29031450.22952676282199
1.8139-1.84360.29091580.21842518267698
1.8436-1.87540.25551350.21112608274399
1.8754-1.90950.2421450.20672626277199
1.9095-1.94630.27311360.20032615275198
1.9463-1.9860.227820.17982675275798
1.986-2.02920.24331530.1962571272499
2.0292-2.07640.24811290.17452600272999
2.0764-2.12830.21921310.13712648277999
2.1283-2.18580.19281480.12872615276399
2.1858-2.25010.21491710.13112615278699
2.2501-2.32280.18211290.130426552784100
2.3228-2.40580.20541470.129326352782100
2.4058-2.50210.21061450.13132600274599
2.5021-2.61590.18141380.13122647278599
2.6159-2.75380.19111310.133526232754100
2.7538-2.92630.18131210.12822679280099
2.9263-3.15210.17271470.131526102757100
3.1521-3.46920.17691100.12772647275799
3.4692-3.97070.16731270.11852633276099
3.9707-5.0010.13461490.111726272776100
5.001-38.7750.14851410.14462610275198

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