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- PDB-7ov2: Crystal structure of pig purple acid phosphatase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7ov2
TitleCrystal structure of pig purple acid phosphatase in complex with L-glutamine, (poly)ethylene glycol fragments 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 / : / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
CITRIC ACID / : / GLUTAMINE / TRIETHYLENE GLYCOL / PHOSPHATE ION / Tartrate-resistant acid phosphatase type 5
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.1Apr 6, 2022Group: Advisory / Derived calculations / Category: pdbx_validate_symm_contact / struct_conn
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 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)45,01878
Polymers35,1541
Non-polymers9,86477
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12290 Å2
ΔGint54 kcal/mol
Surface area13840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.447, 68.668, 77.007
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


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
#2: Polysaccharide beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 12 types, 276 molecules

#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical...
ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C5H10N2O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: PO4
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O4
#10: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#12: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#13: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.44 Å3/Da / Density % sol: 49.51 % / Description: Rod-shaped purple crystals
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting 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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→77.01 Å / Num. obs: 20575 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 19.98 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.052 / Rrim(I) all: 0.141 / Net I/σ(I): 12.8
Reflection shellResolution: 2.1→2.21 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 2938 / CC1/2: 0.905 / Rpim(I) all: 0.193 / Rrim(I) all: 0.528 / % possible all: 100

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Processing

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

1ute


Resolution: 2.1→51.25 Å / SU ML: 0.1711 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.7341
RfactorNum. reflection% reflectionSelection details
Rfree0.1957 1050 5.12 %5
Rwork0.1424 ---
obs0.1451 20497 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.55 Å2
Refinement stepCycle: LAST / Resolution: 2.1→51.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2585 0 447 200 3232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083225
X-RAY DIFFRACTIONf_angle_d0.9784232
X-RAY DIFFRACTIONf_chiral_restr0.054432
X-RAY DIFFRACTIONf_plane_restr0.0055533
X-RAY DIFFRACTIONf_dihedral_angle_d21.70731920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.210.22711560.162715X-RAY DIFFRACTION99.97
2.21-2.350.19271510.14742722X-RAY DIFFRACTION99.9
2.35-2.530.2351450.1452742X-RAY DIFFRACTION99.97
2.53-2.790.22341580.14732748X-RAY DIFFRACTION99.83
2.79-3.190.20791670.13522750X-RAY DIFFRACTION99.86
3.19-4.020.15561160.12162848X-RAY DIFFRACTION99.73
4.02-51.250.1791570.15372922X-RAY DIFFRACTION99.58

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