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- PDB-7ov8: Crystal structure of pig purple acid phosphatase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7ov8
TitleCrystal structure of pig purple acid phosphatase in complex with 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) and glycerol
ComponentsTartrate-resistant acid phosphatase type 5
KeywordsHYDROLASE / Purple acid phosphatase / metallohydrolases / osteoporosis / fragment-based drug design / METAL BINDING PROTEIN
Function / homology
Function and homology information


Vitamin B2 (riboflavin) metabolism / acid phosphatase / acid phosphatase activity / ferric iron binding / iron ion transport / ferrous iron binding / extracellular region
Similarity search - Function
Purple acid phosphatase / : / 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
: / TRIETHYLENE GLYCOL / PHOSPHATE ION / Tartrate-resistant acid phosphatase type 5
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFeder, D. / McGeary, R.P. / Guddat, L.W. / Schenk, G.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP0986292 Australia
Australian Research Council (ARC)150104358 Australia
CitationJournal: Chemmedchem / Year: 2021
Title: Rational Design of Potent Inhibitors of a Metallohydrolase Using a Fragment-Based Approach.
Authors: Feder, D. / Mohd-Pahmi, S.H. / Hussein, W.M. / Guddat, L.W. / McGeary, R.P. / Schenk, G.
History
DepositionJun 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 2.0Apr 6, 2022Group: Atomic model / Data collection / Category: atom_site / pdbx_nonpoly_scheme
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.occupancy / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tartrate-resistant acid phosphatase type 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,91134
Polymers36,9321
Non-polymers3,97933
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-0 kcal/mol
Surface area13470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.382, 69.772, 75.309
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Tartrate-resistant acid phosphatase type 5 / TR-AP / Tartrate-resistant acid ATPase / TrATPase / Type 5 acid phosphatase / Uteroferrin / UF / ...TR-AP / Tartrate-resistant acid ATPase / TrATPase / Type 5 acid phosphatase / Uteroferrin / UF / Pig purple acid phosphatase


Mass: 36932.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P09889, acid phosphatase
#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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 8 types, 450 molecules

#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FE / FE (III) ION


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


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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.22 Å3/Da / Density % sol: 44.61 % / Description: Rod-shaped purple crystals
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 25% (W/V) PEG3350, 0.1 M LICL, 5% (V/V)ISOPROPANOL, 0.1 M SODIUM CITRATE PH 5.0, PROTEIN CONCENTRATION 38 MG/ML

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→48 Å / Num. obs: 15124 / % possible obs: 99.3 % / Redundancy: 3.64 % / Biso Wilson estimate: 28.69 Å2 / Rmerge(I) obs: 0.163 / Χ2: 0.95 / Net I/σ(I): 4.2
Reflection shellResolution: 2.3→2.48 Å / Redundancy: 3.64 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2 / Num. unique obs: 2896 / Χ2: 1.03 / % possible all: 94

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Processing

Software
NameVersionClassification
CrystalClear1.14_3260data collection
PHENIX1.14_3260refinement
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UTE

1ute


Resolution: 2.3→39.57 Å / SU ML: 0.3182 / Cross valid method: FREE R-VALUE / σ(F): 0.18 / Phase error: 27.1728 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2556 754 5.05 %
Rwork0.1618 14168 -
obs0.1665 14922 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.25 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2399 0 244 418 3061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00772945
X-RAY DIFFRACTIONf_angle_d1.06953974
X-RAY DIFFRACTIONf_chiral_restr0.0538390
X-RAY DIFFRACTIONf_plane_restr0.0056471
X-RAY DIFFRACTIONf_dihedral_angle_d22.9771170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.480.34561560.2132740X-RAY DIFFRACTION97.57
2.48-2.730.31311580.20532823X-RAY DIFFRACTION99.67
2.73-3.120.3621280.18982854X-RAY DIFFRACTION99.3
3.12-3.930.23281570.13382817X-RAY DIFFRACTION98.38
3.93-39.570.19021550.14212934X-RAY DIFFRACTION97.51

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