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- PDB-4aro: Hafnia Alvei phytase in complex with myo-inositol hexakis sulphate -

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Basic information

Entry
Database: PDB / ID: 4aro
TitleHafnia Alvei phytase in complex with myo-inositol hexakis sulphate
ComponentsHISTIDINE ACID PHOSPHATASE
KeywordsHYDROLASE / 6-PHYTASE / MYO-INOSITOL HEXAKIS PHOSPHATE PHOSPHOHYDROLASE / HAPP
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
D-MYO-INOSITOL-HEXASULPHATE / : / DI(HYDROXYETHYL)ETHER / Histidine acid phosphatase / Histidine acid phosphatase
Similarity search - Component
Biological speciesHAFNIA ALVEI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsMoroz, O.V. / Blagova, E.B. / Ariza, A. / Turkenburg, J.P. / Vevodova, J. / Roberts, S. / Vind, J. / Sjoholm, C. / Lassen, S.F. / De Maria, L. ...Moroz, O.V. / Blagova, E.B. / Ariza, A. / 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 25, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Aug 7, 2013Group: Atomic model
Revision 1.3Feb 5, 2014Group: Database references
Revision 2.0Jun 21, 2017Group: Advisory / Atomic model / Derived calculations
Category: atom_site / pdbx_struct_conn_angle ...atom_site / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _atom_site.occupancy / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conf.pdbx_PDB_helix_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 2.2Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: HISTIDINE ACID PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7745
Polymers45,3071
Non-polymers1,4664
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.300, 82.300, 103.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-748-

HOH

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Components

#1: Protein HISTIDINE ACID PHOSPHATASE / PHYTASE


Mass: 45307.363 Da / Num. of mol.: 1 / Fragment: RESIDUES 34-446 / Mutation: YES
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-IHS / D-MYO-INOSITOL-HEXASULPHATE


Mass: 660.535 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O24S6
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsEUROPEAN NUCLEOTIDE ARCHIVE ENTRY JQ394762

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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: 2.24 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 4.5
Details: 40MG/ML PROTEIN IN 50MM SODIUM ACETATE PH 4.5 WITH 5 MM MIHS IN 50 MM SODIUM ACETATE PH 4.5 IN JCSG CONDITION 12 0.04 M KH2PO4 16% PEG 8K 20% GLYCEROL

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.59→41.9 Å / Num. obs: 54630 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 10.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.2
Reflection shellResolution: 1.59→1.68 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.12 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ARS

4ars


Resolution: 1.59→41.94 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.858 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19191 2772 5.1 %RANDOM
Rwork0.15602 ---
obs0.1578 51816 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.28 Å20 Å2
2--0.28 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.59→41.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3051 0 80 410 3541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193372
X-RAY DIFFRACTIONr_bond_other_d0.0010.023106
X-RAY DIFFRACTIONr_angle_refined_deg1.871.984657
X-RAY DIFFRACTIONr_angle_other_deg0.8873.0027174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8865435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.20724.964137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53115516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0031513
X-RAY DIFFRACTIONr_chiral_restr0.1120.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213849
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02747
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: 1.594→1.635 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 209 -
Rwork0.229 3759 -
obs--99.97 %
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)
11.77010.0587-0.6750.86960.06941.20160.0113-0.11260.08910.0876-0.02330.1268-0.0388-0.14510.0120.01260.00550.01190.0448-0.01510.0234-33.47210.6812-3.6742
21.3721-0.1945-0.46691.41070.22870.9223-0.0872-0.1264-0.28310.1373-0.0234-0.00190.26540.10890.11060.08250.02580.01970.03580.0230.0626-17.7302-7.4971-15.2673
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 24
2X-RAY DIFFRACTION1A46 - 136
3X-RAY DIFFRACTION1A265 - 413
4X-RAY DIFFRACTION2A25 - 45
5X-RAY DIFFRACTION2A137 - 264

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