[English] 日本語
Yorodumi
- PDB-1gyg: R32 CLOSED FORM OF ALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS STRAI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gyg
TitleR32 CLOSED FORM OF ALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS STRAIN CER89L43
ComponentsPHOSPHOLIPASE C
KeywordsHYDROLASE / ZINC PHOSPHOLIPASE C / GANGRENE DETERMINANT / C2 DOMAIN / CA AND MEMBRANE BINDING
Function / homology
Function and homology information


calcium-dependent phospholipase C activity / phospholipase C / phosphatidylcholine phospholipase C activity / hemolysis in another organism / toxin activity / killing of cells of another organism / zinc ion binding / extracellular region
Similarity search - Function
Zinc-dependent phospholipase C / Phospholipase C/D / Zinc dependent phospholipase C / Prokaryotic zinc-dependent phospholipase C signature. / Prokaryotic zinc-dependent phospholipase C domain profile. / Zinc dependent phospholipase C (alpha toxin) / P1 Nuclease / P1 Nuclease / Phospholipase C/P1 nuclease domain superfamily / PLAT/LH2 domain ...Zinc-dependent phospholipase C / Phospholipase C/D / Zinc dependent phospholipase C / Prokaryotic zinc-dependent phospholipase C signature. / Prokaryotic zinc-dependent phospholipase C domain profile. / Zinc dependent phospholipase C (alpha toxin) / P1 Nuclease / P1 Nuclease / Phospholipase C/P1 nuclease domain superfamily / PLAT/LH2 domain / Lipoxygenase-1 / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Phospholipase C / Phospholipase C
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBasak, A.K. / Eaton, J.T. / Titball, R.W.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal Structure of the C. Perfringens Alpha-Toxin with the Active Site Closed by a Flexible Loop Region
Authors: Eaton, J.T. / Naylor, C. / Howells, A. / Moss, D. / Titball, R.W. / Basak, A.K.
History
DepositionApr 23, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2002Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4May 1, 2024Group: 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
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_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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOSPHOLIPASE C
B: PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4936
Polymers85,2322
Non-polymers2624
Water4,071226
1
A: PHOSPHOLIPASE C
hetero molecules

A: PHOSPHOLIPASE C
hetero molecules

A: PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2409
Polymers127,8483
Non-polymers3926
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
2
B: PHOSPHOLIPASE C
hetero molecules

B: PHOSPHOLIPASE C
hetero molecules

B: PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2409
Polymers127,8483
Non-polymers3926
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)151.400, 151.400, 195.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2077-

HOH

-
Components

#1: Protein PHOSPHOLIPASE C / ALPHA-TOXIN / PHOSPHATIDYLCHOLINE CHOLINEPHOSPHOHYDROLASE / HEMOLYSIN / LECITHINASE


Mass: 42615.863 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) CLOSTRIDIUM PERFRINGENS (bacteria) / Strain: CER89L43
References: UniProt: P15310, UniProt: P0C216*PLUS, phospholipase C
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Sequence details28 RESIDUES AT START OF SEQUENCE ARE A SIGNAL PEPTIDE NOT PRESENT IN MATURE, ACTIVE FOLDED PROTEIN.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 42 %
Crystal growpH: 7.5 / Details: 10 MG/ML PH 7.5, AGAINST 1.7M NACL PH 4.6
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Basak, A., (1998) Acta Crystallogr., D54, 1425.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
19-10 mg/mlprotein1drop
210 mMTris-HCl1droppH7.5
31.7 M1reservoirpH4.6NaCl
4sodium acetate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1.5418
DetectorType: MARRESEARCH 300 MM / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL OR NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→30 Å / Num. obs: 46736 / % possible obs: 87 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.058
Reflection shellRedundancy: 2.6 % / Rmerge(I) obs: 0.193
Reflection
*PLUS
Num. obs: 56901 / % possible obs: 87 % / Num. measured all: 257576

-
Processing

Software
NameVersionClassification
DMmodel building
SCALEPACKdata scaling
AMoREphasing
X-PLORphasing
MLPHAREphasing
DMphasing
CNS3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INCOMPLETE EARLIER CHAIN TRACE OF OTHER CRYSTAL FORM

Resolution: 1.9→25 Å / Rfactor Rfree error: 0.0047 / Isotropic thermal model: INDIVIDUAL RESTRAINED B-FACTORS / Cross valid method: THROUGHOUT / σ(F): 2 / Details: DISORDER IN REGIONS 58-66
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1636 5.4 %RANDOM
Rwork0.208 ---
obs0.208 30150 87.5 %-
Solvent computationSolvent model: DENSITY MODIFICATION / Bsol: 60 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 29.2 Å2
Refine analyzeLuzzati d res low obs: 30 Å / Luzzati sigma a obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6002 0 4 226 6232
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.872
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLPARAM19.SOL
X-RAY DIFFRACTION3PARAM19.IONPARAM19.ION
X-RAY DIFFRACTION4PARAM_ALPHA_SUBMISSION.CDTOP_ALPHA_SUBMISSION.CD
Refinement
*PLUS
Highest resolution: 1.98 Å / Lowest resolution: 30 Å / Num. reflection obs: 46736 / Num. reflection Rfree: 2468 / Rfactor obs: 0.188 / Rfactor Rfree: 0.233 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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