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- PDB-1k8t: Crystal structure of the adenylyl cyclase domain of anthrax edema... -

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Basic information

Entry
Database: PDB / ID: 1k8t
TitleCrystal structure of the adenylyl cyclase domain of anthrax edema factor (EF)
ComponentsCALMODULIN-SENSITIVE ADENYLATE CYCLASE
KeywordsTOXIN / LYASE / edema factor / adenylyl cyclase / anthrax / calmodulin
Function / homology
Function and homology information


symbiont-mediated perturbation of host signal transduction pathway / symbiont-mediated cAMP intoxication of host cell / calcium- and calmodulin-responsive adenylate cyclase activity / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / host cell cytosol / small molecule binding / Uptake and function of anthrax toxins / catalytic complex ...symbiont-mediated perturbation of host signal transduction pathway / symbiont-mediated cAMP intoxication of host cell / calcium- and calmodulin-responsive adenylate cyclase activity / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / host cell cytosol / small molecule binding / Uptake and function of anthrax toxins / catalytic complex / adenylate cyclase activator activity / metallopeptidase activity / toxin activity / calmodulin 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/endema factor, N-/C-terminal / : / Anthrax toxin lethal factor, N- and C-terminal domain / Anthrax toxin lethal factor (ATLF)-like domain profile. / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Metallopeptidase, catalytic domain superfamily / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Calmodulin-sensitive adenylate cyclase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDrum, C.L. / Yan, S.-Z. / Bard, J. / Shen, Y.-Q. / Lu, D. / Soelaiman, S. / Grabarek, Z. / Bohm, A. / Tang, W.-J.
CitationJournal: Nature / Year: 2002
Title: Structural basis for the activation of anthrax adenylyl cyclase exotoxin by calmodulin
Authors: Drum, C.L. / Yan, S.-Z. / Bard, J. / Shen, Y.-Q. / Lu, D. / Soelaiman, S. / Grabarek, Z. / Bohm, A. / Tang, W.-J.
History
DepositionOct 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CALMODULIN-SENSITIVE ADENYLATE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2546
Polymers58,8111
Non-polymers4435
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CALMODULIN-SENSITIVE ADENYLATE CYCLASE
hetero molecules

A: CALMODULIN-SENSITIVE ADENYLATE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,50712
Polymers117,6212
Non-polymers88610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area6360 Å2
ΔGint-169 kcal/mol
Surface area49720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.476, 203.604, 74.034
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein CALMODULIN-SENSITIVE ADENYLATE CYCLASE


Mass: 58810.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P40136, adenylate cyclase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.23 Å3/Da / Density % sol: 61.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG550,Nickle chloride, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
140 mg/mlH6-EF1drop
220 mMTris-HCl1drop
350 mM1droppH7.5NaCl
4100 mMcitric acid1reservoirpH5.65
515 %glycerol1reservoir
611.5 %(w/v)PEG550 MME1reservoir
7220 mM1reservoirNiSO4
82 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 270 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 23911 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 8.7 % / Net I/σ(I): 5.6
Reflection shellHighest resolution: 2.6 Å / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 1.7 / % possible all: 95.4
Reflection
*PLUS
Lowest resolution: 30 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
% possible obs: 95.4 % / Redundancy: 4.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EF-CaM

Resolution: 2.6→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.276 -Random
Rwork0.229 --
all-23911 -
obs-23911 -
Displacement parametersBiso mean: 58.8 Å2
Baniso -1Baniso -2Baniso -3
1--7.04 Å20 Å20 Å2
2---6.68 Å20 Å2
3---13.72 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4025 0 21 96 4142
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d1.13
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 58.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.55
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.13

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