[English] 日本語
Yorodumi
- PDB-2ddt: Crystal structure of sphingomyelinase from Bacillus cereus with m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ddt
TitleCrystal structure of sphingomyelinase from Bacillus cereus with magnesium ion
ComponentsSphingomyelin phosphodiesterase
KeywordsHYDROLASE / DNase I like folding / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


sphingomyelin phosphodiesterase / sphingomyelin phosphodiesterase activity / killing of cells of another organism / extracellular region
Similarity search - Function
Sphingomyelinase C/phospholipase C / Sphingomyelin phosphodiesterase 2-like / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAgo, H. / Oda, M. / Tsuge, H. / Katunuma, N. / Miyano, M. / Sakurai, J. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural basis of the sphingomyelin phosphodiesterase activity in neutral sphingomyelinase from Bacillus cereus.
Authors: Ago, H. / Oda, M. / Takahashi, M. / Tsuge, H. / Ochi, S. / Katunuma, N. / Miyano, M. / Sakurai, J.
History
DepositionFeb 2, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sphingomyelin phosphodiesterase
B: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,36610
Polymers68,6862
Non-polymers6808
Water9,620534
1
A: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6835
Polymers34,3431
Non-polymers3404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6835
Polymers34,3431
Non-polymers3404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.844, 50.893, 59.506
Angle α, β, γ (deg.)81.87, 81.84, 79.68
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Sphingomyelin phosphodiesterase / sphingomyelinase


Mass: 34343.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: IAM 1029 / Plasmid: pHY300PLK / Production host: Bacillus subtilis (bacteria) / Strain (production host): ISW1214
References: UniProt: P11889, sphingomyelin phosphodiesterase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 283 K / Method: vapor diffusion / pH: 6.5
Details: 18% (w/v) PEG 8000, 0.2M magnesium sulfate, 0.1mM calcium chrolide, 0.1M MES, pH 6.5, VAPOR DIFFUSION, temperature 283K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER / Detector: CCD / Date: Dec 16, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 48543 / Num. obs: 48543 / % possible obs: 90.8 %
Reflection shellResolution: 1.8→1.9 Å / % possible all: 93

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49.69 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.971 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23024 2438 5 %RANDOM
Rwork0.19295 ---
obs0.19478 48541 90.77 %-
all-48541 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.288 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.4 Å20.76 Å2
2---0.25 Å20.66 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4570 0 38 534 5142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224722
X-RAY DIFFRACTIONr_bond_other_d00.023998
X-RAY DIFFRACTIONr_angle_refined_deg2.1611.9416411
X-RAY DIFFRACTIONr_angle_other_deg3.63739398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.0145569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.41825.771227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.91115771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4691510
X-RAY DIFFRACTIONr_chiral_restr0.2680.2697
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025223
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02891
X-RAY DIFFRACTIONr_nbd_refined0.2120.21000
X-RAY DIFFRACTIONr_nbd_other0.2460.24020
X-RAY DIFFRACTIONr_nbtor_refined0.1910.22316
X-RAY DIFFRACTIONr_nbtor_other0.1120.22085
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2291
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1040.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.821.53717
X-RAY DIFFRACTIONr_mcbond_other0.3921.51156
X-RAY DIFFRACTIONr_mcangle_it2.06224654
X-RAY DIFFRACTIONr_scbond_it3.22132243
X-RAY DIFFRACTIONr_scangle_it3.9984.51757
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 184 -
Rwork0.238 3483 -
obs--93.17 %

+
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