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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 / outer membrane-bounded periplasmic space
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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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


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


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


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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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