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- PDB-6jlc: Structure determination of CAMP factor of Mobiluncus curtisii and... -

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Basic information

Entry
Database: PDB / ID: 6jlc
TitleStructure determination of CAMP factor of Mobiluncus curtisii and insight into structural dynamics
ComponentsCAMP factor
KeywordsTOXIN / Bacterial vaginosis / Mobiluncus curtisii / pore-forming-factor / hemolytic reaction.
Function / homologyCAMP factor / CAMP factor (Cfa) / ACETATE ION / cAMP factor
Function and homology information
Biological speciesMobiluncus curtisii
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.847 Å
AuthorsJin, T.C. / Zeng, W.H.
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Structure determination of CAMP factor of Mobiluncus curtisii and insights into structural dynamics.
Authors: Zeng, W. / Ma, H. / Fan, W. / Yang, Y. / Zhang, C. / Arnaud Kombe Kombe, J. / Fan, X. / Zhang, Y. / Dong, Z. / Shen, Z. / Zhou, Y. / Yang, M. / Jin, T.
History
DepositionMar 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CAMP factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6292
Polymers25,5701
Non-polymers591
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint0 kcal/mol
Surface area12290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.670, 75.670, 192.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-430-

HOH

21A-459-

HOH

31A-539-

HOH

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Components

#1: Protein CAMP factor


Mass: 25569.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mobiluncus curtisii (strain ATCC 43063 / DSM 2711 / V125) (bacteria)
Strain: ATCC 43063 / DSM 2711 / V125 / Gene: HMPREF0573_10472 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D6ZJ92
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 3.1 Å3/Da / Density % sol: 60.38 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 18% PEG 8000, 0.1M ammonium acetate, 0.1M sodium acetate, pH 5.0

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Data collection

DiffractionMean temperature: 190 K / Ambient temp details: Liquid nitrogen steam / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.847→45.799 Å / Num. obs: 28725 / % possible obs: 99.7 % / Redundancy: 18.09 % / Biso Wilson estimate: 38.929 Å2 / CC1/2: 1 / Rrim(I) all: 0.0066 / Net I/σ(I): 32.75
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 15 % / Num. unique obs: 2010 / CC1/2: 0.71 / Rrim(I) all: 0.99 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H6I

5h6i


Resolution: 1.847→45.799 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.93
RfactorNum. reflection% reflection
Rfree0.229 1457 5.07 %
Rwork0.1956 --
obs0.1972 28724 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.847→45.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1738 0 4 171 1913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061777
X-RAY DIFFRACTIONf_angle_d0.6712414
X-RAY DIFFRACTIONf_dihedral_angle_d1.9381483
X-RAY DIFFRACTIONf_chiral_restr0.041291
X-RAY DIFFRACTIONf_plane_restr0.004304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8472-1.91320.34991420.31962577X-RAY DIFFRACTION98
1.9132-1.98980.28721320.24592692X-RAY DIFFRACTION100
1.9898-2.08040.23781500.21632634X-RAY DIFFRACTION100
2.0804-2.19010.26481440.19922691X-RAY DIFFRACTION100
2.1901-2.32730.24151600.20452689X-RAY DIFFRACTION100
2.3273-2.5070.23271260.20272722X-RAY DIFFRACTION100
2.507-2.75920.25171540.20382705X-RAY DIFFRACTION100
2.7592-3.15840.20271490.2032757X-RAY DIFFRACTION100
3.1584-3.97890.22281430.18382805X-RAY DIFFRACTION100
3.9789-8.260.20931570.17672995X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -18.6689 Å / Origin y: -11.3453 Å / Origin z: 8.8673 Å
111213212223313233
T0.3181 Å2-0.0003 Å2-0.0745 Å2-0.1479 Å2-0.0166 Å2--0.233 Å2
L1.3002 °20.2915 °2-0.0438 °2-0.5255 °2-0.1886 °2--0.2494 °2
S0.0628 Å °-0.0482 Å °0.0144 Å °-0.0731 Å °-0.0107 Å °0.187 Å °0.0017 Å °0.0203 Å °-0.0418 Å °
Refinement TLS groupSelection details: all

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