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- PDB-1qlg: Crystal structure of phytase with magnesium from Bacillus amyloli... -

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Basic information

Entry
Database: PDB / ID: 1qlg
TitleCrystal structure of phytase with magnesium from Bacillus amyloliquefaciens
Components3-PHYTASE
KeywordsPHOSPHOMONOESTERASE / PHYTASE / THERMOSTABLE / PHOSPHATASE / CALCIUM / MAGNESIUM
Function / homology
Function and homology information


3-phytase / 3-phytase 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
Biological speciesBACILLUS AMYLOLIQUEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / DIRECT METHODS / Resolution: 2.2 Å
AuthorsShin, S. / Ha, N.-C. / Oh, B.-H.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Crystal Structures of a Novel, Thermostable Phytase in Partially and Fully Calcium-Loaded States
Authors: Ha, N.-C. / Oh, B.-C. / Shin, S. / Kim, H.J. / Oh, T.K. / Kim, Y.O. / Choi, K.Y. / Oh, B.H.
History
DepositionAug 31, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2000Provider: 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 / 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 / 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_database_status.status_code_sf / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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

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Assembly

Deposited unit
A: 3-PHYTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1776
Polymers39,0081
Non-polymers1695
Water86548
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.060, 64.040, 105.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBIOLOGICAL_UNIT: MONOMER

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Components

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


Mass: 39007.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CALCIUM MAGNESIUM / Source: (gene. exp.) BACILLUS AMYLOLIQUEFACIENS (bacteria) / Strain: DS11 / Cellular location: SECRETION / Production host: BACILLUS SUBTILIS (bacteria) / References: UniProt: O66037, 3-phytase
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.21 Å3/Da / Density % sol: 44.47 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and precipitant solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
140 mg/mlprotein1drop
220 %MPD1reservoirprecipitant
30.1 MMES1reservoirprecipitant

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Details: MONOCHROMETER
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 17305 / % possible obs: 93 % / Observed criterion σ(I): 1 / Redundancy: 1.07 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 13.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 2.62 / Rsym value: 0.317 / % possible all: 87.2
Reflection shell
*PLUS
% possible obs: 87.2 %

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: DIRECT METHODS
Starting model: 1POO

1poo


Resolution: 2.2→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.265 -5 %RANDOM
Rwork0.218 ---
obs0.218 17305 93 %-
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2736 0 5 48 2789
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.513
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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