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- PDB-3ams: Crystal Structures of Bacillus subtilis Alkaline Phytase in Compl... -

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Basic information

Entry
Database: PDB / ID: 3ams
TitleCrystal Structures of Bacillus subtilis Alkaline Phytase in Complex with Ca2+, Cd2+, Co2+, Ni2+, Mg2+ and myo-Inositol Hexasulfate
Components3-phytase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / beta-propeller / phytase / phytate / myo-Inositol hexasulfate / HYDROLASE-HYDROLASE INHIBITOR complex
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
: / D-MYO-INOSITOL-HEXASULPHATE / 3-phytase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsZeng, Y.F. / Ko, T.P. / Lai, H.L. / Cheng, Y.S. / Wu, T.H. / Ma, Y. / Yang, C.S. / Cheng, K.J. / Huang, C.H. / Guo, R.T. / Liu, J.R.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal structures of Bacillus alkaline phytase in complex with divalent metal ions and inositol hexasulfate
Authors: Zeng, Y.F. / Ko, T.P. / Lai, H.L. / Cheng, Y.S. / Wu, T.H. / Ma, Y. / Chen, C.C. / Yang, C.S. / Cheng, K.J. / Huang, C.H. / Guo, R.T. / Liu, J.R.
History
DepositionAug 22, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)40,73913
Polymers39,1311
Non-polymers1,60812
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.897, 73.544, 52.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-911-

CD

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Components

#1: Protein 3-phytase / alkaline phytase / beta-propeller phytase / bacillus phytase / Phytate 3-phosphatase / MYO-inositol- ...alkaline phytase / beta-propeller phytase / bacillus phytase / Phytate 3-phosphatase / MYO-inositol-hexaphosphate 3-phosphohydrolase


Mass: 39131.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: phyC, phyB13 / Plasmid: pET32 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O31097, 3-phytase
#2: Chemical ChemComp-IHS / D-MYO-INOSITOL-HEXASULPHATE


Mass: 660.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O24S6
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5mM CoCl2, 5mM CdCl2, 5mM NiCl2, 5mM MgCl2, 0.1M HEPES, 12% PEG 3350 , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→25 Å / Num. all: 21559 / Num. obs: 21329 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 26.2
Reflection shellHighest resolution: 2.08 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 7.2 / Num. unique all: 82 / % possible all: 98.7

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H6L

1h6l


Resolution: 2.08→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1001 -RANDOM
Rwork0.171 ---
all-21559 --
obs-20543 95.3 %-
Solvent computationBsol: 67.7355 Å2
Displacement parametersBiso mean: 33.82 Å2
Baniso -1Baniso -2Baniso -3
1-17.461 Å20 Å20 Å2
2---11.021 Å20 Å2
3----6.44 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å / Luzzati sigma a obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 2.08→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2735 0 47 335 3117
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.68
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_mcbond_it1.4181.5
X-RAY DIFFRACTIONc_scbond_it2.2752
X-RAY DIFFRACTIONc_mcangle_it2.1352
X-RAY DIFFRACTIONc_scangle_it3.3512.5
LS refinement shellHighest resolution: 2.08 Å
RfactorNum. reflection% reflection
Rfree0.291 82 -
Rwork0.226 --
obs-1745 82.4 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4ligand.param

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