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- PDB-5y6i: Crystal structure of Pseudomonas aeruginosa HmgR -

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Basic information

Entry
Database: PDB / ID: 5y6i
TitleCrystal structure of Pseudomonas aeruginosa HmgR
ComponentsTranscriptional regulator KdgR
KeywordsTRANSCRIPTION / Pseudomonas aeruginosa / HmgR / Quorum sensing
Function / homology
Function and homology information


DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
helix_turn_helix isocitrate lyase regulation / Bacterial transcriptional regulator / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / IclR helix-turn-helix domain / IclR-type HTH domain profile. / IclR effector binding domain profile. / GAF-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Bacterial transcriptional regulator family protein / Probable transcriptional regulator
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.517 Å
AuthorsGu, T. / Ji, Q. / Liang, H.
CitationJournal: To Be Published
Title: Crystal structure of Pseudomonas aeruginosa HmgR
Authors: Gu, T. / Ji, Q. / Liang, H.
History
DepositionAug 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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: Transcriptional regulator KdgR
B: Transcriptional regulator KdgR


Theoretical massNumber of molelcules
Total (without water)56,0202
Polymers56,0202
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-26 kcal/mol
Surface area21930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.129, 80.520, 116.755
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Transcriptional regulator KdgR


Mass: 28009.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: kdgR_2, AOY09_03044, PAERUG_P32_London_17_VIM_2_10_11_04319
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C7CSB5, UniProt: Q9I2A1*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium citrate tribasic dehydrate, 20% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 19620 / % possible obs: 99 % / Redundancy: 12.8 % / Net I/σ(I): 27.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 2.517→48.178 Å / SU ML: 0.34 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 34.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2954 971 4.95 %
Rwork0.237 --
obs0.2398 19605 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.517→48.178 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3521 0 0 7 3528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093573
X-RAY DIFFRACTIONf_angle_d1.1344862
X-RAY DIFFRACTIONf_dihedral_angle_d21.4552153
X-RAY DIFFRACTIONf_chiral_restr0.057592
X-RAY DIFFRACTIONf_plane_restr0.008629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5168-2.64950.35761320.29692450X-RAY DIFFRACTION94
2.6495-2.81550.32821510.27752621X-RAY DIFFRACTION100
2.8155-3.03280.37361500.29622657X-RAY DIFFRACTION100
3.0328-3.33790.37831330.29012690X-RAY DIFFRACTION100
3.3379-3.82080.33021360.26312649X-RAY DIFFRACTION99
3.8208-4.81310.24651360.20822709X-RAY DIFFRACTION100
4.8131-48.18690.2651330.21042858X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.77753.8469-4.88556.3163-3.55445.45710.0156-0.0353-0.34610.328-0.18060.19350.2814-0.22870.23310.3666-0.0798-0.02590.59620.11090.643312.22815.4685144.1673
22.2128-0.6833-0.26894.1218-0.25832.49990.58660.23390.1275-0.5045-0.18370.0954-1.1469-0.5908-0.32030.81950.24180.1930.53680.05430.475615.9630.2332115.3529
36.158-2.92981.60548.09571.30445.36060.41150.5466-0.6017-0.4777-0.29530.28720.6560.4483-0.13930.5335-0.0292-0.10340.56630.03640.52124.31833.676133.4569
43.74850.21272.50156.59130.58829.2556-0.2094-0.0202-0.19040.12110.5308-0.4151-1.62450.0371-0.36760.8566-0.12590.04340.5756-0.06430.507428.156430.5201149.3081
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 16:91)
2X-RAY DIFFRACTION2(chain A and resseq 92:264)
3X-RAY DIFFRACTION3(chain B and resseq 16:91)
4X-RAY DIFFRACTION4(chain B and resseq 92:261)

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