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- PDB-1war: Recombinant Human Purple Acid Phosphatase expressed in Pichia Pastoris -

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Basic information

Entry
Database: PDB / ID: 1war
TitleRecombinant Human Purple Acid Phosphatase expressed in Pichia Pastoris
ComponentsHUMAN PURPLE ACID PHOSPHATASE
KeywordsHYDROLASE / GLYCOPROTEIN / IRON / IRON TRANSPORT / METALLOENZYME / PURPLE ACID PHOSPHATASE / TARTRATE RESISTANT ACID PHOSPHATASE / UTEROFERRIN
Function / homology
Function and homology information


negative regulation of superoxide anion generation / Vitamin B2 (riboflavin) metabolism / riboflavin metabolic process / negative regulation of macrophage cytokine production / acid phosphatase / acid phosphatase activity / negative regulation of nitric oxide biosynthetic process / negative regulation of interleukin-12 production / superoxide anion generation / bone morphogenesis ...negative regulation of superoxide anion generation / Vitamin B2 (riboflavin) metabolism / riboflavin metabolic process / negative regulation of macrophage cytokine production / acid phosphatase / acid phosphatase activity / negative regulation of nitric oxide biosynthetic process / negative regulation of interleukin-12 production / superoxide anion generation / bone morphogenesis / negative regulation of interleukin-1 beta production / negative regulation of tumor necrosis factor production / dephosphorylation / bone resorption / nitric oxide biosynthetic process / ossification / ferric iron binding / response to cytokine / ferrous iron binding / negative regulation of inflammatory response / response to lipopolysaccharide / lysosome / membrane => GO:0016020 / 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
: / PHOSPHATE ION / Tartrate-resistant acid phosphatase type 5 / Tartrate-resistant acid phosphatase type 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsDuff, A.P. / Langley, D.B. / Han, R. / Averill, B.A. / Freeman, H.C. / Guss, J.M.
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
DepositionOct 28, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _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.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_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 13, 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: HUMAN PURPLE ACID PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4825
Polymers35,0541
Non-polymers4284
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)80.538, 80.538, 99.998
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein HUMAN PURPLE ACID PHOSPHATASE / ACP5 PROTEIN / TARTRATE-RESISTANT ACID ATPASE / TRATPASE / TR-AP


Mass: 35053.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: A SIX AMINO ACID CLONING ARTIFACT IS ATTACHED TO THE N-TERMINUS
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / Strain (production host): X33
References: UniProt: Q6IAS6, UniProt: P13686*PLUS, acid phosphatase
#2: Chemical ChemComp-FE / FE (III) ION / Iron


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


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: 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 / N-Acetylglucosamine


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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 20 RESIDUES OF Q6IAS6 ARE NOT PART OF THE MATURE ENZYME. THE MATURE PROTEIN COMPRISES ...THE FIRST 20 RESIDUES OF Q6IAS6 ARE NOT PART OF THE MATURE ENZYME. THE MATURE PROTEIN COMPRISES RESIDUES 21-325 AS NUMBERED IN Q6IAS6. A SIX AMINO ACID CLONING ARTIFACT IS ATTACHED TO THE N-TERMINUS OF THE MATURE PROTEIN.

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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: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 277 K
Details: THE PROTEIN (10 MG/ML) IN 50 MM MES AT PH 6, WAS PASSED THROUGH AN ULTRAFREE-MC 0.22 MM SPIN FILTER UNIT (MILLIPORE) AND ALLOWED TO STAND AT 4 DEGREES C. PURPLE CRYSTALS GREW SPONTANEOUSLY ...Details: THE PROTEIN (10 MG/ML) IN 50 MM MES AT PH 6, WAS PASSED THROUGH AN ULTRAFREE-MC 0.22 MM SPIN FILTER UNIT (MILLIPORE) AND ALLOWED TO STAND AT 4 DEGREES C. PURPLE CRYSTALS GREW SPONTANEOUSLY OVERNIGHT AND REACHED SIZES UP TO 0.5 MM IN SEVERAL WEEKS.

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 20, 2003 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.22→18.98 Å / Num. obs: 15951 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.97
Reflection shellResolution: 2.22→2.3 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 5.49 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UTE

1ute


Resolution: 2.22→18.98 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.02 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.198 767 4.8 %RANDOM
Rwork0.138 ---
obs0.141 15167 94.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20 Å2
2---0.78 Å20 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.22→18.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2477 0 21 61 2559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212570
X-RAY DIFFRACTIONr_bond_other_d0.0020.022274
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.9413489
X-RAY DIFFRACTIONr_angle_other_deg0.86235267
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3665309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0770.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022874
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02570
X-RAY DIFFRACTIONr_nbd_refined0.1820.2440
X-RAY DIFFRACTIONr_nbd_other0.2360.22413
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0810.21522
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0590.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.64521543
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.61432482
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.45541027
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it10.01361007
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: 2.22→2.28 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.262 59
Rwork0.197 1051
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
120.25127.324218.61343.8686-0.927126.53220.12320.39950.0051-0.974-0.1938-0.0765-0.02780.67880.07070.06230-0.00050.0619-0.00030.062751.889-15.1553.863
21.18780.3340.01981.6019-0.22850.82150.0286-0.09340.00940.0423-0.0308-0.0114-0.0054-0.03060.00220.0840.00890.01090.0504-0.00980.02858.51621.09646.196
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-6 - -1
2X-RAY DIFFRACTION2A1 - 304

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