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- PDB-9p6c: RTX domain block V of adenylate cyclase toxin with mutations D153... -

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Basic information

Entry
Database: PDB / ID: 9p6c
TitleRTX domain block V of adenylate cyclase toxin with mutations D1533N, A1542N, D1560N, S1569N, D1587N, H1598N, H1608N
ComponentsHemolysin
KeywordsTOXIN / Calcium binding / Repeats-In-Toxin / beta roll
Function / homology
Function and homology information


symbiont-mediated cAMP intoxication of host cell / calcium- and calmodulin-responsive adenylate cyclase activity / hemolysis in another organism / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / channel activity / toxin activity / positive regulation of cytosolic calcium ion concentration / calmodulin binding ...symbiont-mediated cAMP intoxication of host cell / calcium- and calmodulin-responsive adenylate cyclase activity / hemolysis in another organism / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / channel activity / toxin activity / positive regulation of cytosolic calcium ion concentration / calmodulin binding / calcium ion binding / host cell plasma membrane / extracellular region / ATP binding / membrane
Similarity search - Function
RTX, pore-forming domain / N-terminal domain in RTX protein / RTX toxin determinant A / Haemolysin-type calcium binding-related / Haemolysin-type calcium binding protein related domain / : / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit ...RTX, pore-forming domain / N-terminal domain in RTX protein / RTX toxin determinant A / Haemolysin-type calcium binding-related / Haemolysin-type calcium binding protein related domain / : / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal
Similarity search - Domain/homology
Bifunctional hemolysin/adenylate cyclase
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsChang, M.P. / Mai, D.J. / Gudinas, A.P. / Fernandez, D.
Funding support United States, 4items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)FA9550-22-1-0241 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133894 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
National Science Foundation (NSF, United States)DGE-1656518 United States
CitationJournal: J.Chem.Phys. / Year: 2025
Title: Repetitive proteins that undergo large conformational changes evade structural prediction algorithms.
Authors: Chang, M.P. / Jin, T. / Gudinas, A.P. / Fernandez, D. / Alexander-Katz, A. / Matsui, T. / Mai, D.J.
History
DepositionJun 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemolysin
B: Hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,92418
Polymers38,2832
Non-polymers64116
Water70339
1
A: Hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4629
Polymers19,1421
Non-polymers3218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4629
Polymers19,1421
Non-polymers3218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.305, 38.003, 57.016
Angle α, β, γ (deg.)84.13, 81.47, 67.61
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Hemolysin


Mass: 19141.539 Da / Num. of mol.: 2
Mutation: D1533N, A1542N, D1560N, S1569N, D1587N, H1598N, H1608N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: cya, cyaA, BP0760 / Plasmid: pQE9 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 express LysY / References: UniProt: P0DKX7
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Buffer: 0.1 M MES, 0.1 M imidazole, pH 6.5 Precipitant: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD; 0.02 M of each amino acid (L-glutamate, DL-alanine, glycine, DL-lysine, and DL- ...Details: Buffer: 0.1 M MES, 0.1 M imidazole, pH 6.5 Precipitant: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD; 0.02 M of each amino acid (L-glutamate, DL-alanine, glycine, DL-lysine, and DL-serine) Protein solution: 50 mM Tris, 150 mM NaCl, 10 mM CaCl2, pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.99→30.58 Å / Num. obs: 14967 / % possible obs: 85.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 6.6
Reflection shellResolution: 1.99→2.04 Å / Rmerge(I) obs: 0.292 / Num. unique obs: 2233 / % possible all: 85.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→30.58 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.888 / SU B: 8.406 / SU ML: 0.215 / Cross valid method: FREE R-VALUE / ESU R: 0.341 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29235 766 5.1 %RANDOM
Rwork0.22847 ---
obs0.23164 14115 85.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.338 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å21.07 Å2-1.03 Å2
2---0.42 Å21.34 Å2
3---2.87 Å2
Refinement stepCycle: 1 / Resolution: 1.99→30.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2276 0 16 39 2331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122305
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.6273127
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5785308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.605512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.15510330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1110.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021881
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6333.6341238
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.0266.5061544
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4274.0491067
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.5242.063518
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.994→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 60 -
Rwork0.334 1003 -
obs--83.05 %

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