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- PDB-1qhw: PURPLE ACID PHOSPHATASE FROM RAT BONE -

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Basic information

Entry
Database: PDB / ID: 1qhw
TitlePURPLE ACID PHOSPHATASE FROM RAT BONE
ComponentsPROTEIN (PURPLE ACID PHOSPHATASE)
KeywordsHYDROLASE / METAL PHOSPHATASE
Function / homology
Function and homology information


Vitamin B2 (riboflavin) metabolism / negative regulation of superoxide anion generation / response to macrophage colony-stimulating factor / negative regulation of macrophage cytokine production / response to L-ascorbic acid / acid phosphatase / acid phosphatase activity / cellular response to zinc ion starvation / negative regulation of nitric oxide biosynthetic process / negative regulation of interleukin-12 production ...Vitamin B2 (riboflavin) metabolism / negative regulation of superoxide anion generation / response to macrophage colony-stimulating factor / negative regulation of macrophage cytokine production / response to L-ascorbic acid / acid phosphatase / acid phosphatase activity / cellular response to zinc ion starvation / negative regulation of nitric oxide biosynthetic process / negative regulation of interleukin-12 production / negative regulation of cell adhesion / response to cholesterol / superoxide anion generation / bone morphogenesis / negative regulation of interleukin-1 beta production / response to zinc ion / negative regulation of tumor necrosis factor production / bone resorption / multicellular organismal response to stress / response to mechanical stimulus / nitric oxide biosynthetic process / ossification / ferric iron binding / osteoclast differentiation / response to cytokine / ferrous iron binding / response to insulin / response to organic cyclic compound / 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
: / Tartrate-resistant acid phosphatase type 5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLindqvist, Y. / Johansson, E. / Kaija, H. / Vihko, P. / Schneider, G.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Three-dimensional structure of a mammalian purple acid phosphatase at 2.2 A resolution with a mu-(hydr)oxo bridged di-iron center.
Authors: Lindqvist, Y. / Johansson, E. / Kaija, H. / Vihko, P. / Schneider, G.
#1: Journal: J.Bone Miner.Res. / Year: 1999
Title: Tartrate-Resistant Bone Acid Phosphatase: Large-Scale Production and Purification of the Recombinant Enzyme, Characterization, and Crystallization
Authors: Kaija, H. / Jia, J. / Lindqvist, Y. / Andersson, G. / Vihko, P.
History
DepositionMar 26, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Sep 15, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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 / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)37,6298
Polymers36,7701
Non-polymers8597
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.980, 88.120, 57.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 36769.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GLYCOSIDIC LINK BETWEEN ASN 118 AND NAG 344 GLYCOSIDIC LINK BETWEEN NAG 344 AND NAG 345
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: BONE / Cell: OSTEOCLAST / Gene: ACP5 / Organelle: LYSOSOME / Plasmid: PVL1392 / Gene (production host): ACP5 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P29288, 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-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

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Non-polymers , 4 types, 109 molecules

#3: Chemical ChemComp-FE / FE (III) ION


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 45 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Kaija, H., (1999) J.Bone Miner.Res., 14, 424.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
20.1 MHEPES1reservoir
32.24 Mammonium sulfate1reservoir
410 %PEG4001reservoir
50.05 Mzinc sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.7816
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7816 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 17244 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 6.2
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.2 / % possible all: 84.4
Reflection
*PLUS
Num. measured all: 63605
Reflection shell
*PLUS
% possible obs: 84.4 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BASED ON PDB ENTRY 4KBP

4kbp


Resolution: 2.2→40 Å / Rfactor Rfree error: 0.009 / Data cutoff high rms absF: 1502012.17 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.265 880 5.1 %RANDOM
Rwork0.213 ---
obs0.213 17201 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 35.3 Å2
Baniso -1Baniso -2Baniso -3
1--7.71 Å20 Å20 Å2
2---4.48 Å20 Å2
3---12.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati sigma a0.24 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2383 0 42 103 2528
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
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_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.952
X-RAY DIFFRACTIONc_scbond_it1.72
X-RAY DIFFRACTIONc_scangle_it2.542.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 150 5.9 %
Rwork0.264 2408 -
obs--84.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71
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
Highest resolution: 2.2 Å / Rfactor Rfree: 0.317 / % reflection Rfree: 5.9 % / Rfactor Rwork: 0.264 / Rfactor obs: 0.264

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