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- PDB-9kx0: Crystal structure of CAMP3 factor of Cutibacterium acnes. -

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Basic information

Entry
Database: PDB / ID: 9kx0
TitleCrystal structure of CAMP3 factor of Cutibacterium acnes.
ComponentscAMP factor
KeywordsTOXIN / CAMP factor / Cutibacterium acnes / bacterial toxins / inflammatory response
Function / homologyCAMP factor / CAMP factor (Cfa) / cAMP factor
Function and homology information
Biological speciesCutibacterium acnes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsLiu, C. / Jin, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of CAMP3 factor of Cutibacterium acnes.
Authors: Liu, C. / Jin, T.
History
DepositionDec 6, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cAMP factor


Theoretical massNumber of molelcules
Total (without water)26,6061
Polymers26,6061
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.325, 88.325, 98.557
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-306-

HOH

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Components

#1: Protein cAMP factor


Mass: 26606.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cutibacterium acnes (bacteria) / Gene: DXN06_09420 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAD0QQF7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
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: 3.31 Å3/Da / Density % sol: 62.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 26%(w/v)PEG 3350 41 mM Citric acid 59 mM Sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. obs: 15274 / % possible obs: 100 % / Redundancy: 24.15 % / CC1/2: 0.9996 / Rmerge(I) obs: 0.0696 / Rrim(I) all: 0.0711 / Net I/σ(I): 56.34
Reflection shellResolution: 2.43→2.49 Å / Redundancy: 19.91 % / Rmerge(I) obs: 0.6441 / Mean I/σ(I) obs: 5.7 / Num. unique obs: 1102 / CC1/2: 0.9568 / Rrim(I) all: 0.6609 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XSCALEdata scaling
autoPXdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→44.2 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.897 / SU B: 7.777 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30108 780 5.1 %RANDOM
Rwork0.24315 ---
obs0.24612 14445 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.211 Å2
Baniso -1Baniso -2Baniso -3
1--3.12 Å20 Å20 Å2
2---3.12 Å20 Å2
3---6.25 Å2
Refinement stepCycle: 1 / Resolution: 2.43→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1734 0 0 52 1786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121761
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161749
X-RAY DIFFRACTIONr_angle_refined_deg1.2771.6582396
X-RAY DIFFRACTIONr_angle_other_deg0.4271.5794009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg55223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.929512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.09210308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0550.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022074
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02386
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_it6.3366.812895
X-RAY DIFFRACTIONr_mcbond_other6.2766.814895
X-RAY DIFFRACTIONr_mcangle_it8.47212.2361117
X-RAY DIFFRACTIONr_mcangle_other8.46812.2461118
X-RAY DIFFRACTIONr_scbond_it6.9417.588866
X-RAY DIFFRACTIONr_scbond_other6.9377.597867
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.29213.5831280
X-RAY DIFFRACTIONr_long_range_B_refined12.38262.352097
X-RAY DIFFRACTIONr_long_range_B_other12.39362.232091
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.43→2.493 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 56 -
Rwork0.272 1018 -
obs--97.55 %

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