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- PDB-8yll: Crystal structure of Burkholderia thailandensis MftR in complex w... -

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Basic information

Entry
Database: PDB / ID: 8yll
TitleCrystal structure of Burkholderia thailandensis MftR in complex with xanthine
ComponentsMarR family transcriptional regulator
KeywordsTRANSCRIPTION / Transcription factor
Function / homologyXANTHINE / :
Function and homology information
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSong, W.S. / Yoon, S.I.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2023-00208153 Korea, Republic Of
National Research Foundation (NRF, Korea)2022R1I1A1A01068105 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structural basis of transcriptional regulation by UrtR in response to uric acid.
Authors: Song, W.S. / Ki, D.U. / Cho, H.Y. / Kwon, O.H. / Cho, H. / Yoon, S.I.
History
DepositionMar 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MarR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4902
Polymers18,3381
Non-polymers1521
Water19811
1
A: MarR family transcriptional regulator
hetero molecules

A: MarR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9804
Polymers36,6762
Non-polymers3042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area7760 Å2
ΔGint-42 kcal/mol
Surface area12600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.462, 62.462, 77.060
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein MarR family transcriptional regulator


Mass: 18337.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Gene: A8H32_16025 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2N8QSC4
#2: Chemical ChemComp-XAN / XANTHINE


Mass: 152.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 16422 / % possible obs: 99.6 % / Redundancy: 20.8 % / CC1/2: 0.996 / Net I/σ(I): 68.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 20.2 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 817 / CC1/2: 0.717 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8YLF

8ylf


Resolution: 1.8→28.94 Å / SU ML: 0.2639 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.2872
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2459 801 4.89 %
Rwork0.2227 15565 -
obs0.2239 16366 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.38 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1155 0 11 11 1177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00551182
X-RAY DIFFRACTIONf_angle_d0.73461605
X-RAY DIFFRACTIONf_chiral_restr0.0399188
X-RAY DIFFRACTIONf_plane_restr0.0047210
X-RAY DIFFRACTIONf_dihedral_angle_d13.8084730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.920.39141130.3482533X-RAY DIFFRACTION99.03
1.92-2.060.33361180.29512590X-RAY DIFFRACTION99.74
2.06-2.270.23351310.24662581X-RAY DIFFRACTION99.89
2.27-2.60.27031530.23822580X-RAY DIFFRACTION99.64
2.6-3.280.25141590.24592582X-RAY DIFFRACTION99.78
3.28-28.940.22451270.19542699X-RAY DIFFRACTION98.16
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)
14.55137307817-4.68929541822-4.088037814675.834850147663.039903168965.826694299130.2276133029630.01175290823561.225795530620.1356383811580.0543372928169-0.601860040277-1.55015830454-0.886122054341-0.3144734238210.7282969424440.1139748375160.0120768136820.371698763889-0.07182507513020.5486244668557.8395047694252.563694953739.9959139132
28.62141101181-4.51920220908-4.838496364623.780627112541.730628980775.404177537420.185455202944-0.323372977590.3296456597370.397336789885-0.2883697196590.39809346473-0.476884367889-0.402637995448-0.04094781948440.404299293875-0.01998621901290.01168711735360.307289935717-0.01188403283840.2906498681815.47927665945.858535039440.551045856
38.28066309251-5.75255968786-0.5440428303286.713815076453.678641848485.480798487480.6725833277611.58359499586-0.2561341410840.0174854004256-0.8283061633290.06548148287530.2445720060540.297956697135-0.06426203527340.4887029215890.12778191218-0.04505669450090.583550480687-0.07705491844780.31415255154825.386177000628.160258462125.6923972117
48.41325958144-3.67668592607-0.05555773629865.679030649041.69096034285.38074846144-0.118467600031-0.1986994344310.1367833363440.324772051759-0.0393106540293-0.06559402824620.3348575184510.4225084681610.08134706724070.4061289974610.01741970976480.0611200444390.4899244566660.05062850545850.29562236095335.350558133623.504915786738.0140733239
55.342310476992.34385258456-2.150552677224.845156425232.710171638485.98233175342-0.471589722491-0.376206066783-1.205410086210.432634137062-0.2084188524470.1912665366211.462188531080.08479338674420.6639236993820.8237289967170.06758883543220.2063152252280.4452013480960.08245018347960.43395682141231.903810708214.060770586835.3182562246
62.85045593572-2.16603946476-0.8894956240844.997586900641.04941528032.26268704250.3773212515140.222241317150.626696035742-0.796598943140.0136551391327-0.712450068432-0.4109370581610.505153417434-0.391088771460.394496798946-0.09068159332470.1077292260760.4923251987880.04341108380060.40153683817333.165819067138.284872492131.6067797415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 53 )
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 85 )
5X-RAY DIFFRACTION5chain 'A' and (resid 86 through 116 )
6X-RAY DIFFRACTION6chain 'A' and (resid 117 through 160 )

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