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- PDB-5chh: Crystal structure of transcriptional regulator CdpR from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 5chh
TitleCrystal structure of transcriptional regulator CdpR from Pseudomonas aeruginosa
ComponentsAraC family transcriptional regulator
KeywordsTRANSCRIPTION / Quorum-sensing / ATP-dependent protease / protein degradation / bacterial virulence
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / cytosol
Similarity search - Function
HTH-type transcriptional regulator AraC-type, N-terminal / Arabinose-binding domain of AraC transcription regulator, N-term / 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 / Probable transcriptional regulator
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsZhao, J.R. / Yu, X. / Zhu, M. / Kang, H.P. / Kong, W.N. / Ma, J.B. / Deng, X. / Gan, J.H. / Liang, H.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation31000049 China
CitationJournal: Plos Biol. / Year: 2016
Title: Structural and Molecular Mechanism of CdpR Involved in Quorum-Sensing and Bacterial Virulence in Pseudomonas aeruginosa
Authors: Zhao, J.R. / Yu, X. / Zhu, M. / Kang, H.P. / Ma, J.B. / Wu, M. / Gan, J.H. / Deng, X. / Liang, H.H.
History
DepositionJul 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AraC family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)39,2321
Polymers39,2321
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17640 Å2
Unit cell
Length a, b, c (Å)109.818, 109.818, 66.097
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

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Components

#1: Protein AraC family transcriptional regulator / Pseudomonas aeruginosa genome assembly PAE221 / Putative transcriptional regulator near PqsH


Mass: 39231.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: appY_1, ERS445055_02463, PA8380_27050, PAE221_02417, YQ19_15205
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C7AIL3, UniProt: Q9I0P9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: (NH4)2HPO4, and 0.1 M Acetate (pH4.5), 0.001 M TCEP
PH range: 4.3 -4.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 35195 / % possible obs: 99.9 % / Redundancy: 10 % / Net I/σ(I): 28.7
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 7.1 % / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data processing
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→28.33 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.63 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23443 1755 5 %RANDOM
Rwork0.18842 ---
obs0.19094 33261 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.781 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20 Å2
2--0.54 Å20 Å2
3----1.07 Å2
Refinement stepCycle: 1 / Resolution: 1.85→28.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2556 0 0 88 2644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192604
X-RAY DIFFRACTIONr_bond_other_d0.0010.022507
X-RAY DIFFRACTIONr_angle_refined_deg0.9631.9673527
X-RAY DIFFRACTIONr_angle_other_deg0.7235701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0495313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6722.086139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68315434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3341538
X-RAY DIFFRACTIONr_chiral_restr0.0580.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022972
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02658
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.57835111
X-RAY DIFFRACTIONr_sphericity_free25.073527
X-RAY DIFFRACTIONr_sphericity_bonded10.60855127
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 115 -
Rwork0.271 2423 -
obs--99.84 %

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