[English] 日本語
Yorodumi
- PDB-1y0v: Crystal structure of anthrax edema factor (EF) in complex with ca... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1y0v
TitleCrystal structure of anthrax edema factor (EF) in complex with calmodulin and pyrophosphate
Components
  • Calmodulin
  • Calmodulin-sensitive adenylate cyclase
KeywordsLYASE / Calcium-Independent / Calmodulin / Anthrax edema factor
Function / homology
Function and homology information


calcium- and calmodulin-responsive adenylate cyclase activity / : / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / host cell cytosol / Uptake and function of anthrax toxins / catalytic complex / small molecule binding / enzyme regulator activity ...calcium- and calmodulin-responsive adenylate cyclase activity / : / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / host cell cytosol / Uptake and function of anthrax toxins / catalytic complex / small molecule binding / enzyme regulator activity / metallopeptidase activity / toxin activity / calmodulin binding / signaling receptor binding / calcium ion binding / extracellular region / ATP binding / metal ion binding
Similarity search - Function
Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #60 / Adenylylcyclase toxin fold / Anthrax toxin, edema factor, central domain / : / Oedema factor (EF), alpha-helical domain / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / Anthrax toxin, lethal/endema factor ...Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #60 / Adenylylcyclase toxin fold / Anthrax toxin, edema factor, central domain / : / Oedema factor (EF), alpha-helical domain / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / Anthrax toxin, lethal/endema factor / : / Anthrax toxin lethal factor (ATLF)-like domain profile. / Anthrax toxin, lethal/endema factor, N-/C-terminal / Anthrax toxin lethal factor, N- and C-terminal domain / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PYROPHOSPHATE 2- / Calmodulin-1 / Calmodulin-sensitive adenylate cyclase / Calmodulin-2 B
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.6 Å
AuthorsShen, Y. / Zhukovskaya, N.L. / Guo, Q. / Florian, J. / Tang, W.-J.
CitationJournal: Embo J. / Year: 2005
Title: Calcium-independent calmodulin binding and two-metal-ion catalytic mechanism of anthrax edema factor
Authors: Shen, Y. / Zhukovskaya, N.L. / Guo, Q. / Tang, W.-J.
History
DepositionNov 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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_ref_seq_dif / 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_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 / _struct_ref_seq_dif.details / _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: Calmodulin-sensitive adenylate cyclase
B: Calmodulin-sensitive adenylate cyclase
C: Calmodulin-sensitive adenylate cyclase
D: Calmodulin-sensitive adenylate cyclase
E: Calmodulin-sensitive adenylate cyclase
F: Calmodulin-sensitive adenylate cyclase
H: Calmodulin
I: Calmodulin
J: Calmodulin
K: Calmodulin
L: Calmodulin
M: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)641,31342
Polymers639,39012
Non-polymers1,92330
Water00
1
A: Calmodulin-sensitive adenylate cyclase
H: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8857
Polymers106,5652
Non-polymers3205
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-50 kcal/mol
Surface area44350 Å2
MethodPISA
2
B: Calmodulin-sensitive adenylate cyclase
I: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8857
Polymers106,5652
Non-polymers3205
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-52 kcal/mol
Surface area44360 Å2
MethodPISA
3
C: Calmodulin-sensitive adenylate cyclase
J: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8857
Polymers106,5652
Non-polymers3205
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-51 kcal/mol
Surface area44390 Å2
MethodPISA
4
D: Calmodulin-sensitive adenylate cyclase
K: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8857
Polymers106,5652
Non-polymers3205
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-50 kcal/mol
Surface area44360 Å2
MethodPISA
5
E: Calmodulin-sensitive adenylate cyclase
L: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8857
Polymers106,5652
Non-polymers3205
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-50 kcal/mol
Surface area44330 Å2
MethodPISA
6
F: Calmodulin-sensitive adenylate cyclase
M: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8857
Polymers106,5652
Non-polymers3205
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-51 kcal/mol
Surface area44350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)317.509, 183.348, 141.812
Angle α, β, γ (deg.)90.00, 90.05, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Calmodulin-sensitive adenylate cyclase / ATP pyrophosphate-lyase / Adenylyl cyclase / Edema factor / EF / Anthrax edema toxin adenylate ...ATP pyrophosphate-lyase / Adenylyl cyclase / Edema factor / EF / Anthrax edema toxin adenylate cyclase component


Mass: 90128.898 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: cya / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P40136, adenylate cyclase
#2: Protein
Calmodulin / CaM


Mass: 16436.053 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: CALM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P62155, UniProt: P0DP33*PLUS
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H2O7P2
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: PEG400, MgCl2, Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.92 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 11, 2004
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 375550 / Num. obs: 375293 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 77.7 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.063 / Net I/σ(I): 20
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 3.02 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2.1 / Num. unique all: 9746 / Rsym value: 0.667 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.6→29.87 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 227881.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.307 4061 5 %RANDOM
Rwork0.286 ---
obs0.286 80945 86.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.206868 e/Å3
Displacement parametersBiso mean: 85.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.32 Å20 Å20 Å2
2---3.14 Å20 Å2
3---6.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.38 Å
Luzzati d res low-6 Å
Luzzati sigma a0.44 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 3.6→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42828 0 78 0 42906
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.752
X-RAY DIFFRACTIONc_scbond_it1.392
X-RAY DIFFRACTIONc_scangle_it2.482.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.6→3.83 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 499 5 %
Rwork0.331 9480 -
obs--63.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4PPI.PARAMPPI.TOP

+
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://pdbjlvh1.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