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- PDB-1qfc: STRUCTURE OF RAT PURPLE ACID PHOSPHATASE -

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Basic information

Entry
Database: PDB / ID: 1qfc
TitleSTRUCTURE OF RAT PURPLE ACID PHOSPHATASE
ComponentsPROTEIN (PURPLE ACID PHOSPHATASE)
KeywordsHYDROLASE / METAL PHOSPHATASE
Function / homology
Function and homology information


Vitamin B2 (riboflavin) metabolism / negative regulation of superoxide anion generation / cellular response to zinc ion starvation / response to macrophage colony-stimulating factor / negative regulation of macrophage cytokine production / acid phosphatase / acid phosphatase activity / response to L-ascorbic acid / negative regulation of nitric oxide biosynthetic process / negative regulation of interleukin-12 production ...Vitamin B2 (riboflavin) metabolism / negative regulation of superoxide anion generation / cellular response to zinc ion starvation / response to macrophage colony-stimulating factor / negative regulation of macrophage cytokine production / acid phosphatase / acid phosphatase activity / response to L-ascorbic acid / negative regulation of nitric oxide biosynthetic process / negative regulation of interleukin-12 production / negative regulation of cell adhesion / response to cholesterol / bone morphogenesis / superoxide anion generation / negative regulation of interleukin-1 beta production / response to zinc ion / negative regulation of tumor necrosis factor production / bone resorption / response to mechanical stimulus / multicellular organismal response to stress / response to cytokine / nitric oxide biosynthetic process / ferric iron binding / ossification / osteoclast differentiation / ferrous iron binding / response to insulin / negative regulation of inflammatory response / response to ethanol / response to lipopolysaccharide / lysosome / hydrolase activity / defense response to Gram-positive bacterium / positive regulation of cell migration / extracellular space
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
: / PHOSPHATE ION / Tartrate-resistant acid phosphatase type 5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.7 Å
AuthorsUppenberg, J. / Lindqvist, F. / Svensson, C. / Ek-Rylander, B. / Andersson, G.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of a mammalian purple acid phosphatase.
Authors: Uppenberg, J. / Lindqvist, F. / Svensson, C. / Ek-Rylander, B. / Andersson, G.
History
DepositionApr 8, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 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: PROTEIN (PURPLE ACID PHOSPHATASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8215
Polymers34,3931
Non-polymers4284
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.380, 116.380, 63.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein PROTEIN (PURPLE ACID PHOSPHATASE) / TARTRATE RESISTANT ACID PHOSPHATASE / TRAP


Mass: 34392.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29288, acid phosphatase
#2: 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
#3: Chemical ChemComp-FE / FE (III) ION


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


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
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: 3.1 Å3/Da / Density % sol: 61 %
Crystal growpH: 7 / Details: pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 6.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 %(w/v)PEG80001reservoir
20.1 MHEPES1reservoir
30.1 Mpotassium phosphate1reservoir
45 mg/mlprotein1drop
510 mMammonium acetate1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 15, 1998 / Details: YALE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 10486 / % possible obs: 90.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 57.9 Å2 / Rsym value: 0.107 / Net I/σ(I): 8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.52 / % possible all: 70.1
Reflection
*PLUS
Rmerge(I) obs: 0.107

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
SHARPphasing
CNS0.4refinement
RefinementMethod to determine structure: MAD / Resolution: 2.7→15 Å / Rfactor Rfree error: 0.009 / Data cutoff high rms absF: 1607036.24 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1058 10.3 %RANDOM
Rwork0.234 ---
obs-10276 89 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.13 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso mean: 57.3 Å2
Baniso -1Baniso -2Baniso -3
1--17 Å20 Å20 Å2
2---17 Å20 Å2
3---34.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2269 0 21 0 2290
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.851.5
X-RAY DIFFRACTIONc_mcangle_it6.482
X-RAY DIFFRACTIONc_scbond_it8.062
X-RAY DIFFRACTIONc_scangle_it11.112.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.382 132 10.8 %
Rwork0.331 1088 -
obs--62.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1MYTOP:PROTEIN_REP.PARAMMYTOP:PROTEIN.TOP
X-RAY DIFFRACTION2MYTOP:ION_JONAS.PARAMMYTOP:ION_JONAS.TOP
X-RAY DIFFRACTION3MYTOP:CARBOHYDRATE.PARAMMYTOP:CARBOHYDRATE.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.3 % / Rfactor obs: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 57.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.382 / % reflection Rfree: 10.8 % / Rfactor Rwork: 0.331

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