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- PDB-2bq8: Crystal structure of human purple acid phosphatase with an inhibi... -

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Basic information

Entry
Database: PDB / ID: 2bq8
TitleCrystal structure of human purple acid phosphatase with an inhibitory conformation of the repression loop
ComponentsTARTRATE-RESISTANT ACID PHOSPHATASE TYPE 5
KeywordsHYDROLASE / METALLOPHOSPHATASE / DINUCLEAR METAL SITE / TRAP
Function / homology
Function and homology information


negative regulation of superoxide anion generation / Vitamin B2 (riboflavin) metabolism / negative regulation of macrophage cytokine production / acid phosphatase / acid phosphatase activity / negative regulation of nitric oxide biosynthetic process / negative regulation of interleukin-12 production / bone morphogenesis / superoxide anion generation / negative regulation of interleukin-1 beta production ...negative regulation of superoxide anion generation / Vitamin B2 (riboflavin) metabolism / negative regulation of macrophage cytokine production / acid phosphatase / acid phosphatase activity / negative regulation of nitric oxide biosynthetic process / negative regulation of interleukin-12 production / bone morphogenesis / superoxide anion generation / negative regulation of interleukin-1 beta production / dephosphorylation / negative regulation of tumor necrosis factor production / bone resorption / nitric oxide biosynthetic process / ferric iron binding / response to cytokine / ferrous iron binding / negative regulation of inflammatory response / response to lipopolysaccharide / lysosome / defense response to Gram-positive bacterium / membrane / cytosol
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 speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsStraeter, N. / Jasper, B. / Krebs, B.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structures of Recombinant Human Purple Acid Phosphatase with and without an Inhibitory Conformation of the Repression Loop.
Authors: Strater, N. / Jasper, B. / Scholte, M. / Krebs, B. / Duff, A.P. / Langley, D.B. / Han, R. / Averill, B.A. / Freeman, H.C. / Guss, J.M.
History
DepositionApr 27, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_dist_value / _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_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
Revision 1.5Oct 23, 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
X: TARTRATE-RESISTANT ACID PHOSPHATASE TYPE 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6505
Polymers34,3771
Non-polymers2734
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)94.756, 94.756, 144.007
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11X-2014-

HOH

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Components

#1: Protein TARTRATE-RESISTANT ACID PHOSPHATASE TYPE 5 / PURPLE ACID PHOSPHATASE / TR-AP / TRATPASE / TARTRATE-RESISTANT ACID ATPASE


Mass: 34376.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P13686, acid phosphatase
#2: Chemical ChemComp-FE2 / FE (II) ION


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
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: 2.71 Å3/Da / Density % sol: 45.1 %
Crystal growpH: 6
Details: 0.05 M HEPES PH6.0, 2 M AMMONIUM SULFATE, 10% PEG400, 0.05M ZINC SULFATE, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8122
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8122 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 1988 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 19.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 28.7
Reflection shellResolution: 2.2→2.23 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 6.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UTE

1ute


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.698 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1014 5.1 %RANDOM
Rwork0.181 ---
obs0.182 18826 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å2-0.59 Å20 Å2
2---1.19 Å20 Å2
3---1.78 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2429 0 8 147 2584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222501
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.9263396
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7455303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43222.869122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90215398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7761520
X-RAY DIFFRACTIONr_chiral_restr0.0960.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021943
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21115
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21685
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2171
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8591.51558
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.39322436
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.16131090
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3744.5960
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.199 77
Rwork0.148 1360
Refinement TLS params.Method: refined / Origin x: 0 Å / Origin y: 0 Å / Origin z: 0 Å
111213212223313233
T0 Å20 Å20 Å2-0 Å20 Å2--0 Å2
L0 °20 °20 °2-0 °20 °2--0 °2
S0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °

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