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- PDB-8brn: Crystal structure of red kidney bean purple acid phosphatase in c... -

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Basic information

Entry
Database: PDB / ID: 8brn
TitleCrystal structure of red kidney bean purple acid phosphatase in complex with an alpha-aminonaphthylmethylphosphonic acid inhibitor
ComponentsFe(3+)-Zn(2+) purple acid phosphatase
KeywordsMETAL BINDING PROTEIN / Metallohydrolase / Phosphatase
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / ferric iron binding / extracellular region / zinc 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 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
: / CITRATE ANION / TRIETHYLENE GLYCOL / Chem-R9X / Fe(3+)-Zn(2+) purple acid phosphatase
Similarity search - Component
Biological speciesPhaseolus vulgaris (common bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFeder, D. / Hussein, W.M. / Guddat, L.W. / Schenk, G.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP0986292 Australia
Australian Research Council (ARC)DP150104358 Australia
CitationJournal: Eur.J.Med.Chem. / Year: 2023
Title: Optimization of an alpha-aminonaphthylmethylphosphonic acid inhibitor of purple acid phosphatase using rational structure-based design approaches.
Authors: Feder, D. / Mohd-Pahmi, S.H. / Adibi, H. / Guddat, L.W. / Schenk, G. / McGeary, R.P. / Hussein, W.M.
History
DepositionNov 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Fe(3+)-Zn(2+) purple acid phosphatase
B: Fe(3+)-Zn(2+) purple acid phosphatase
C: Fe(3+)-Zn(2+) purple acid phosphatase
D: Fe(3+)-Zn(2+) purple acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,077152
Polymers199,0824
Non-polymers26,994148
Water47,9742663
1
A: Fe(3+)-Zn(2+) purple acid phosphatase
C: Fe(3+)-Zn(2+) purple acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,51875
Polymers99,5412
Non-polymers13,97773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9150 Å2
ΔGint-215 kcal/mol
Surface area33610 Å2
MethodPISA
2
B: Fe(3+)-Zn(2+) purple acid phosphatase
D: Fe(3+)-Zn(2+) purple acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,55977
Polymers99,5412
Non-polymers13,01775
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10050 Å2
ΔGint-249 kcal/mol
Surface area33830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.859, 125.859, 298.339
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-1225-

HOH

21A-1242-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Fe(3+)-Zn(2+) purple acid phosphatase / PAP / Iron(III)-zinc(II) purple acid phosphatase


Mass: 49770.602 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Phaseolus vulgaris (common bean) / References: UniProt: P80366, acid phosphatase

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Sugars , 10 types, 22 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.: 3
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
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-4/a3-b1_a4-c1_c4-d1_d2-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3/a3-b1_a4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-4/a3-b1_a4-c1_c4-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4/a3-b1_a4-c1_c4-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#8: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-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
DGlcpNAcb1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#9: Polysaccharide beta-D-mannopyranose-(5-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(5-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb5-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+5)][b-D-Lyxp]{}}}}LINUCSPDB-CARE
#10: Polysaccharide alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#15: 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.: 5
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 , 12 types, 2789 molecules

#11: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Zn
#12: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Fe
#13: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Formula: C6H5O7
#14: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C6H14O4
#16: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 32
Source method: isolated from a genetically manipulated source
Formula: SO4
#17: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#18: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 50
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#19: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#20: Chemical
ChemComp-R9X / [(R)-(decanoylamino)-naphthalen-1-yl-methyl]phosphonic acid


Mass: 391.441 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H30NO4P / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#22: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H6OS / Comment: DMSO, precipitant*YM
#23: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2663 / 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: 3.44 Å3/Da / Density % sol: 64.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 2.3 M ammonium sulfate, 0.1 M sodium acetate, pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→19.96 Å / Num. obs: 182773 / % possible obs: 99 % / Redundancy: 4.9 % / Biso Wilson estimate: 22.97 Å2 / CC1/2: 0.988 / Rsym value: 0.165 / Net I/σ(I): 9.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.9 % / Num. unique obs: 5833 / CC1/2: 0.489 / Rsym value: 1.03 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.96 Å / SU ML: 0.2367 / Cross valid method: FREE R-VALUE / σ(F): 0.07 / Phase error: 19.5387
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2062 9127 5.01 %
Rwork0.1568 173000 -
obs0.1593 182127 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.26 Å2
Refinement stepCycle: LAST / Resolution: 2→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14065 0 1716 2663 18444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007516501
X-RAY DIFFRACTIONf_angle_d0.919122393
X-RAY DIFFRACTIONf_chiral_restr0.05942391
X-RAY DIFFRACTIONf_plane_restr0.00762701
X-RAY DIFFRACTIONf_dihedral_angle_d15.70856179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.31272970.26295536X-RAY DIFFRACTION95.98
2.02-2.050.3222880.25615526X-RAY DIFFRACTION96.24
2.05-2.070.29932980.24435581X-RAY DIFFRACTION96.08
2.07-2.10.2852880.24575644X-RAY DIFFRACTION96.47
2.1-2.130.31332970.23695555X-RAY DIFFRACTION97.4
2.13-2.150.26192970.22385625X-RAY DIFFRACTION97.07
2.15-2.180.25653080.20645651X-RAY DIFFRACTION97.48
2.19-2.220.25842830.20275719X-RAY DIFFRACTION97.91
2.22-2.250.26243010.19715697X-RAY DIFFRACTION98.01
2.25-2.290.23153060.18795691X-RAY DIFFRACTION98.49
2.29-2.330.26163190.17885755X-RAY DIFFRACTION98.73
2.33-2.370.22362870.17585741X-RAY DIFFRACTION98.87
2.37-2.420.21972780.16525783X-RAY DIFFRACTION99.18
2.42-2.470.2383210.16695724X-RAY DIFFRACTION99.02
2.47-2.520.24893290.16735737X-RAY DIFFRACTION99.13
2.52-2.580.21423010.16135770X-RAY DIFFRACTION99.36
2.58-2.640.22823090.15955772X-RAY DIFFRACTION99.46
2.64-2.710.21853090.15995805X-RAY DIFFRACTION99.48
2.71-2.790.22953030.15615842X-RAY DIFFRACTION99.51
2.79-2.880.19772740.15345816X-RAY DIFFRACTION99.71
2.88-2.990.21043270.15375835X-RAY DIFFRACTION99.47
2.99-3.10.20422820.15525824X-RAY DIFFRACTION99.66
3.1-3.250.20813170.14825830X-RAY DIFFRACTION99.61
3.25-3.420.19393080.13915869X-RAY DIFFRACTION99.6
3.42-3.630.16453060.12995852X-RAY DIFFRACTION99.63
3.63-3.910.16693400.1185854X-RAY DIFFRACTION99.65
3.91-4.30.14853200.11485883X-RAY DIFFRACTION99.58
4.3-4.910.14142910.10295938X-RAY DIFFRACTION99.49
4.91-6.150.15133440.12475948X-RAY DIFFRACTION99.37
6.16-19.960.21552990.17686197X-RAY DIFFRACTION99.12

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