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- PDB-1ute: PIG PURPLE ACID PHOSPHATASE COMPLEXED WITH PHOSPHATE -

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Basic information

Entry
Database: PDB / ID: 1ute
TitlePIG PURPLE ACID PHOSPHATASE COMPLEXED WITH PHOSPHATE
ComponentsPROTEIN (II PURPLE ACID PHOSPHATASE)
KeywordsHYDROLASE / PURPLE ACID PHOSPHATASE / TARTRATE RESISTANT ACID PHOSPHATASE / METALLOENZYME / UTEROFERRIN
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 / 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
MU-OXO-DIIRON / ISOPROPYL ALCOHOL / PHOSPHATE ION / Tartrate-resistant acid phosphatase type 5
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.55 Å
AuthorsGuddat, L.W. / Mcalpine, A. / Hume, D. / Hamilton, S. / De Jersey, J. / Martin, J.L.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: Crystal structure of mammalian purple acid phosphatase.
Authors: Guddat, L.W. / McAlpine, A.S. / Hume, D. / Hamilton, S. / de Jersey, J. / Martin, J.L.
#1: Journal: Science / Year: 1995
Title: Crystal Structure of a Purple Acid Phosphatase Containing a Dinuclear Fe(III)- Zn(II) Active Site
Authors: Strater, N. / Klabunde, T. / Tucker, P. / Witzel, H. / Krebs, B.
History
DepositionJan 18, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 1, 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_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _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.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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (II PURPLE ACID PHOSPHATASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8615
Polymers35,1541
Non-polymers7074
Water6,107339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.610, 70.010, 77.110
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 (II PURPLE ACID PHOSPHATASE) / E.C.3.1.3.2 HYDROLASE / UTEROFERRIN / TRAP / PAP / TARTRATE RESISTANT ACID PHOSPHATASE


Mass: 35154.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: PO4 PHOSPHATE FE+3 BINUCLEAR METAL CENTRE OXO OXYGEN BRIDGE BETWEEN TWO FE+3. IPA ISOPROPANOL
Source: (natural) Sus scrofa (pig) / Secretion: UTERUS / References: UniProt: P09889, 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, 342 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2O
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 53 %
Crystal growpH: 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. PROTEIN CONCENTRATION 38MG/ML.
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 Msodium citrate1reservoir
225 %(w/v)PEG33001reservoir
30.1 M1reservoirLiCl
410 %(v/v)isopropanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 15, 1998 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→100 Å / Num. obs: 140370 / % possible obs: 89.4 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 9.6
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.1 / % possible all: 57
Reflection
*PLUS
Num. obs: 46161 / Num. measured all: 140370
Reflection shell
*PLUS
% possible obs: 57.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MIR / Resolution: 1.55→100 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.257 4432 10 %RANDOM
Rwork0.213 ---
obs0.213 43833 85.5 %-
Displacement parametersBiso mean: 20 Å2
Refinement stepCycle: LAST / Resolution: 1.55→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 40 339 2749
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.31
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.151.06
X-RAY DIFFRACTIONx_mcangle_it1.741.23
X-RAY DIFFRACTIONx_scbond_it2.211.06
X-RAY DIFFRACTIONx_scangle_it3.381.23
LS refinement shellResolution: 1.55→1.62 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.354 294 9.4 %
Rwork0.324 2838 -
obs--54 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3.CHOTOPH3.CHO
X-RAY DIFFRACTION3ISO.PARISO.TOP
X-RAY DIFFRACTION4PARAMETERS.ELEMENTSTOPOLOGY.ELEMENTS
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 1 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONx_mcbond_it1.06
X-RAY DIFFRACTIONx_scbond_it1.06
X-RAY DIFFRACTIONx_mcangle_it1.23
X-RAY DIFFRACTIONx_scangle_it1.23
LS refinement shell
*PLUS
Rfactor Rfree: 0.354 / % reflection Rfree: 9.4 % / Rfactor Rwork: 0.324

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