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- PDB-6sbw: CdbA Form One -

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Basic information

Entry
Database: PDB / ID: 6sbw
TitleCdbA Form One
ComponentsCdbA
KeywordsDNA BINDING PROTEIN / nucleoid ribbon-helix-helix
Function / homologyMXAN_4361/MXAN_4362 family small protein / TIGR04563 family protein
Function and homology information
Biological speciesMyxococcus xanthus DK 1622 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.24 Å
AuthorsLovering, A.L. / Cadby, I.T.
CitationJournal: Nat Commun / Year: 2020
Title: CdbA is a DNA-binding protein and c-di-GMP receptor important for nucleoid organization and segregation in Myxococcus xanthus.
Authors: Skotnicka, D. / Steinchen, W. / Szadkowski, D. / Cadby, I.T. / Lovering, A.L. / Bange, G. / Sogaard-Andersen, L.
History
DepositionJul 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: CdbA


Theoretical massNumber of molelcules
Total (without water)7,9651
Polymers7,9651
Non-polymers00
Water00
1
A: CdbA

A: CdbA


Theoretical massNumber of molelcules
Total (without water)15,9302
Polymers15,9302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554-x+1/2,y,-z-1/41
Buried area4110 Å2
ΔGint-29 kcal/mol
Surface area5990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.474, 61.474, 94.915
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein CdbA


Mass: 7964.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus DK 1622 (bacteria) / Gene: MXAN_4361 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1D489

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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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M MgCl2 0.1M Hepes pH 7 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.24→47.46 Å / Num. obs: 51709 / % possible obs: 100 % / Redundancy: 11.1 % / Net I/σ(I): 19.7
Reflection shellResolution: 2.24→2.3 Å / Num. unique obs: 346

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
REFMACrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.24→43.51 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 23.226 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.202
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2774 447 9.7 %RANDOM
Rwork0.2315 ---
obs0.2361 4180 99.55 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 163.66 Å2 / Biso mean: 80.543 Å2 / Biso min: 41.92 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å2-0 Å2-0 Å2
2--1.45 Å2-0 Å2
3----2.91 Å2
Refinement stepCycle: final / Resolution: 2.24→43.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms412 0 0 0 412
Num. residues----48
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.013420
X-RAY DIFFRACTIONr_bond_other_d0.0010.018401
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.655562
X-RAY DIFFRACTIONr_angle_other_deg1.1831.592931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.636547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82921.07128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.4141586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.998155
X-RAY DIFFRACTIONr_chiral_restr0.0650.252
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02455
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0296
LS refinement shellResolution: 2.24→2.298 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.535 27 -
Rwork0.484 315 -
all-342 -
obs--98.84 %
Refinement TLS params.Method: refined / Origin x: 14.366 Å / Origin y: -3.367 Å / Origin z: -9.473 Å
111213212223313233
T0.1375 Å2-0.0043 Å20.041 Å2-0.0505 Å2-0.0178 Å2--0.0578 Å2
L8.1894 °20.9892 °2-5.9453 °2-6.4194 °2-0.7583 °2--13.0385 °2
S0.4271 Å °0.0098 Å °0.2096 Å °-0.1142 Å °0.2259 Å °-0.1302 Å °0.0027 Å °0.2168 Å °-0.653 Å °

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