[English] 日本語
Yorodumi
- PDB-3ams: Crystal Structures of Bacillus subtilis Alkaline Phytase in Compl... -

+
Open data


ID or keywords:

Loading...

-
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 / 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
: / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more