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- PDB-4ars: Hafnia Alvei phytase apo form -

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Basic information

Entry
Database: PDB / ID: 4ars
TitleHafnia Alvei phytase apo form
ComponentsHISTIDINE ACID PHOSPHATASE
KeywordsHYDROLASE
Function / homology
Function and homology information


sugar-phosphatase activity / acid phosphatase activity / lysosome organization / dephosphorylation / outer membrane-bounded periplasmic space / lysosome
Similarity search - Function
Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Phosphoglycerate mutase-like / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Histidine acid phosphatase / Histidine acid phosphatase
Similarity search - Component
Biological speciesHAFNIA ALVEI (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAriza, A. / Moroz, O.V. / Blagova, E.B. / Turkenburg, J.P. / Vevodova, J. / Roberts, S. / Vind, J. / Sjoholm, C. / Lassen, S.F. / De Maria, L. ...Ariza, A. / Moroz, O.V. / Blagova, E.B. / Turkenburg, J.P. / Vevodova, J. / Roberts, S. / Vind, J. / Sjoholm, C. / Lassen, S.F. / De Maria, L. / Glitsoe, V. / Skov, L.K. / Wilson, K.S.
CitationJournal: Plos One / Year: 2013
Title: Degradation of Phytate by the 6-Phytase from Hafnia Alvei: A Combined Structural and Solution Study.
Authors: Ariza, A. / Moroz, O.V. / Blagova, E.V. / Turkenburg, J.P. / Waterman, J. / Roberts, S.M. / Vind, J. / Sjoholm, C. / Lassen, S.F. / De Maria, L. / Glitsoe, V. / Skov, L.K. / Wilson, K.S.
History
DepositionApr 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HISTIDINE ACID PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,33513
Polymers45,3951
Non-polymers94012
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.590, 101.310, 85.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1423-

ACT

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Components

#1: Protein HISTIDINE ACID PHOSPHATASE / PHYTASE / MYO-INOSITOL HEXAKIS PHOSPHATE PHOSPHOHYDROLASE


Mass: 45395.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HAFNIA ALVEI (bacteria) / Production host: ASPERGILLUS ORYZAE (mold)
References: UniProt: G9Y2J2, UniProt: H9TUK5*PLUS, 4-phytase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE ALSO CORRESPONDS TO THE EUROPEAN NUCLEOTIDE ARCHIVE ENTRY JQ394762. NATURAL ...THE SEQUENCE ALSO CORRESPONDS TO THE EUROPEAN NUCLEOTIDE ARCHIVE ENTRY JQ394762. NATURAL SUBSTITUTIONS IN THIS SAMPLE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 48.32 % / Description: NONE
Crystal growDetails: 8MG/ML PROTEIN; 0.1 M HEPES PH 7.5, 10% ISOPROPANOL, 20% PEG 4000

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→35.7 Å / Num. obs: 34671 / % possible obs: 95.6 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.5 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0025refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DKL

1dkl


Resolution: 1.9→32.55 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.773 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23332 1702 5.2 %RANDOM
Rwork0.17375 ---
obs0.17672 31326 95.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.023 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å20 Å20 Å2
2---0.98 Å20 Å2
3----1.59 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3142 0 62 303 3507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.023426
X-RAY DIFFRACTIONr_bond_other_d0.0010.023267
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.9644698
X-RAY DIFFRACTIONr_angle_other_deg0.9063.0027548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1485453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.70224.671152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2615552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6971518
X-RAY DIFFRACTIONr_chiral_restr0.1070.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213948
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02780
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 130 -
Rwork0.285 2241 -
obs--92.8 %

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