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- PDB-5nla: Crystal structure of the AraC-like transcriptional activator CuxR -

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Basic information

Entry
Database: PDB / ID: 5nla
TitleCrystal structure of the AraC-like transcriptional activator CuxR
ComponentsPutative transcriptional regulator TRANSCRIPTION REGULATOR protein
KeywordsTRANSCRIPTION / polysaccharide / c-di-GMP
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity
Similarity search - Function
AraC-binding-like domain / : / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeobox-like domain superfamily
Similarity search - Domain/homology
Transcriptional regulator TRANSCRIPTION REGULATOR protein
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsSteinchen, W.M. / Altegoer, F. / Bange, G.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: AraC-like transcriptional activator CuxR binds c-di-GMP by a PilZ-like mechanism to regulate extracellular polysaccharide production.
Authors: Schaper, S. / Steinchen, W. / Krol, E. / Altegoer, F. / Skotnicka, D. / Sgaard-Andersen, L. / Bange, G. / Becker, A.
History
DepositionApr 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 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

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Assembly

Deposited unit
A: Putative transcriptional regulator TRANSCRIPTION REGULATOR protein


Theoretical massNumber of molelcules
Total (without water)42,6921
Polymers42,6921
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.662, 80.662, 125.596
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Putative transcriptional regulator TRANSCRIPTION REGULATOR protein


Mass: 42692.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria)
Strain: 1021 / Gene: SM_b20457 / Plasmid: pET24d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92WA5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: 1.2M NaCl, 0.1 M Na-acetate pH 4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.7→80.66 Å / Num. obs: 11906 / % possible obs: 99.7 % / Redundancy: 8.3 % / CC1/2: 1 / Rmerge(I) obs: 0.055 / Net I/σ(I): 23.7
Reflection shellResolution: 2.7→2.83 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1134 / CC1/2: 0.65 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→80.66 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.92 / SU B: 30.956 / SU ML: 0.282 / Cross valid method: THROUGHOUT / ESU R: 0.576 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28101 569 4.8 %RANDOM
Rwork0.23596 ---
obs0.23808 11338 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.682 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.7→80.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2148 0 0 3 2151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192193
X-RAY DIFFRACTIONr_bond_other_d0.0020.022025
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.9592971
X-RAY DIFFRACTIONr_angle_other_deg0.96334662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4175268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2122.385109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58515363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7671527
X-RAY DIFFRACTIONr_chiral_restr0.080.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212458
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02485
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_it2.1265.1061081
X-RAY DIFFRACTIONr_mcbond_other2.1255.1031080
X-RAY DIFFRACTIONr_mcangle_it3.6387.6391346
X-RAY DIFFRACTIONr_mcangle_other3.6377.6431347
X-RAY DIFFRACTIONr_scbond_it2.1995.2761109
X-RAY DIFFRACTIONr_scbond_other2.1985.2791110
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6537.8531624
X-RAY DIFFRACTIONr_long_range_B_refined6.65560.2812427
X-RAY DIFFRACTIONr_long_range_B_other6.65360.322428
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.702→2.772 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.476 38 -
Rwork0.353 794 -
obs--95.96 %
Refinement TLS params.Method: refined / Origin x: -20.521 Å / Origin y: -8.865 Å / Origin z: -6.4 Å
111213212223313233
T0.1841 Å20.0208 Å2-0.0295 Å2-0.3999 Å2-0.0539 Å2--0.0761 Å2
L3.4788 °2-0.4385 °20.5883 °2-1.973 °20.4372 °2--4.8213 °2
S-0.0195 Å °0.2772 Å °-0.1311 Å °-0.2256 Å °-0.1026 Å °0.3759 Å °0.2261 Å °-0.3997 Å °0.1221 Å °

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