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- PDB-7ov3: Crystal structure of pig purple acid phosphatase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7ov3
TitleCrystal structure of pig purple acid phosphatase in complex with Maybridge fragment CC063346, dimethyl sulfoxide and citrate
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 / bone resorption / ferric iron binding / ferrous iron binding / iron ion transport / extracellular region
Similarity search - Function
Purple acid phosphatase / : / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
CITRIC ACID / : / TRIETHYLENE GLYCOL / PHOSPHATE ION / N-methyl-1-(1-methyl-1H-indazol-3-yl)methanamine / Tartrate-resistant acid phosphatase type 5
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 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)39,29734
Polymers35,1541
Non-polymers4,14333
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint1 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.085, 71.325, 77.553
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 , 1 types, 1 molecules A

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


Mass: 35154.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P09889, acid phosphatase

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Sugars , 2 types, 2 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
#6: 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.: 1
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 , 11 types, 442 molecules

#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-R2J / N-methyl-1-(1-methyl-1H-indazol-3-yl)methanamine


Mass: 175.230 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H13N3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H8O7
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#11: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#12: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#13: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.52 Å3/Da / Density % sol: 51.21 % / 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→40.61 Å / Num. obs: 21574 / % possible obs: 87.5 % / Redundancy: 5.81 % / Biso Wilson estimate: 29.13 Å2 / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.131 / Χ2: 0.95 / Net I/σ(I): 7.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.32 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1450 / Rrim(I) all: 0.442 / Χ2: 1.02 / % possible all: 46

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
CrystalCleardata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UTE

1ute


Resolution: 2→34.07 Å / SU ML: 0.2499 / Cross valid method: FREE R-VALUE / σ(F): 0.86 / Phase error: 25.7662
RfactorNum. reflection% reflection
Rfree0.2316 1100 5.14 %
Rwork0.1649 --
obs0.1683 21388 86.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.4 Å2
Refinement stepCycle: LAST / Resolution: 2→34.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 252 411 3049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752891
X-RAY DIFFRACTIONf_angle_d1.02363916
X-RAY DIFFRACTIONf_chiral_restr0.0538403
X-RAY DIFFRACTIONf_plane_restr0.0054484
X-RAY DIFFRACTIONf_dihedral_angle_d9.44752680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.3212730.24291377X-RAY DIFFRACTION47.84
2.09-2.20.3094990.20481893X-RAY DIFFRACTION65.7
2.2-2.340.26751510.19862457X-RAY DIFFRACTION85.62
2.34-2.520.29261640.19112832X-RAY DIFFRACTION98.36
2.52-2.770.27911610.19182858X-RAY DIFFRACTION98.76
2.77-3.170.24781470.17452884X-RAY DIFFRACTION98.96
3.17-40.20331460.14122935X-RAY DIFFRACTION98.81
4-34.070.1821590.14393052X-RAY DIFFRACTION98.65

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