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- PDB-1h6l: beta-propeller phytase in complex with phosphate and calcium ions -

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Basic information

Entry
Database: PDB / ID: 1h6l
Titlebeta-propeller phytase in complex with phosphate and calcium ions
Components3-PHYTASE
KeywordsHYDROLASE / PHOSPHATASE / PHYTASE / PROPELLER / PHOSPHATE
Function / homology
Function and homology information


3-phytase / inositol hexakisphosphate 3-phosphatase activity / extracellular region
Similarity search - Function
Beta propeller phytase / Phytase / Beta-propeller phytase (BPP) domain profile. / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / 3-phytase
Similarity search - Component
Biological speciesBACILLUS AMYLOLIQUEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsShin, S. / Ha, N.C. / Oh, B.H.
CitationJournal: Structure / Year: 2001
Title: Enzyme Mechanism and Catalytic Property of Beta Propeller Phytase
Authors: Shin, S. / Ha, N.C. / Oh, B.H. / Oh, T. / Oh, B.H.
History
DepositionJun 19, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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 / struct_site
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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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 / _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

Downloads & links

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Assembly

Deposited unit
A: 3-PHYTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,29210
Polymers38,8221
Non-polymers4709
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.378, 65.644, 104.767
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3-PHYTASE / PHYTASE / PHYTATE 3-PHOSPHATASE / MYO-INOSITOL-HEXAPHOSPHATE 3-PHOSPHOHYDROLASE


Mass: 38821.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BACILLUS AMYLOLIQUEFACIENS (bacteria) / Strain: DS11 / References: UniProt: O66037, 3-phytase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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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: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: Ha, N.C., (1999) Acta Crystallogr, D55, 691.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
220 %MPD1reservoir
30.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 32362 / % possible obs: 94.7 % / Observed criterion σ(I): 1 / Redundancy: 7.73 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 12
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 3 / % possible all: 80.2
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 250463

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2POO

2poo


Resolution: 1.8→20 Å / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.223 -5 %RANDOM
Rwork0.197 ---
obs0.197 32362 94.7 %-
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2736 0 17 145 2898
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.53
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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