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

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Basic information

Entry
Database: PDB / ID: 8ylk
TitleCrystal structure of Burkholderia thailandensis MftR in complex with uric acid
ComponentsMarR family transcriptional regulator
KeywordsTRANSCRIPTION / Transcription factor
Function / homologyURIC ACID / :
Function and homology information
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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)18,5062
Polymers18,3381
Non-polymers1681
Water1086
1
A: MarR family transcriptional regulator
hetero molecules

A: MarR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0124
Polymers36,6762
Non-polymers3362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area7760 Å2
ΔGint-50 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.942, 62.942, 77.568
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-URC / URIC ACID / 7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE


Mass: 168.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: PEG 3350

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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: 2.1→30 Å / Num. obs: 10766 / % possible obs: 99.7 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 31.2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 507 / % possible all: 98.6

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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: 2.1→27.25 Å / SU ML: 0.2804 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.1039
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2606 575 5.38 %
Rwork0.2269 10121 -
obs0.2286 10696 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.83 Å2
Refinement stepCycle: LAST / Resolution: 2.1→27.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1155 0 12 6 1173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00291183
X-RAY DIFFRACTIONf_angle_d0.57091606
X-RAY DIFFRACTIONf_chiral_restr0.0341188
X-RAY DIFFRACTIONf_plane_restr0.0041209
X-RAY DIFFRACTIONf_dihedral_angle_d11.9624731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.310.341180.2952477X-RAY DIFFRACTION98.41
2.31-2.650.32241490.25222485X-RAY DIFFRACTION99.47
2.65-3.330.27271430.26582543X-RAY DIFFRACTION99.89
3.33-27.250.23481650.19792616X-RAY DIFFRACTION99.53
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)
13.581741248971.49486978112-3.505189215175.89019125685-2.216783320173.51005029303-0.249573095535-0.1175388053110.444138865337-0.05873977817110.2899626572591.00246480242-0.0748898537034-1.751641780630.0661052520510.4164005782680.129566672798-0.003389891137670.899040437863-0.05526893429330.502236737966-10.6241195634-21.495641009417.6098825813
27.799268572390.832216511829-2.648153419032.058525734930.3424213561575.18096252767-0.5610660981580.485821205095-0.259711441976-0.01512504523190.2161822894630.224616027095-0.00362649275307-0.5288599559610.1465677312330.4772948019680.081450092345-0.06217924405570.347338600583-0.01997041451290.3033271633327.47925175239-17.53471138027.94149592007
36.944306994873.712455191830.1401914227726.567776394991.513902234724.62240423187-0.0896142880660.380591391351-0.1298871719560.111876921475-0.1970898520540.0866852979444-0.182655499208-0.06366429983820.1896803527410.546801974917-0.04438138916210.00150064700410.5406573396740.02084838685520.32927398417926.9231854624-14.5705079356.02261507879
43.690720234781.57519764415-0.6905981856342.59418453288-0.3618630068385.522370287130.0310017181022-0.645935401174-0.2794820919410.300085585883-0.336622723385-0.2264503203430.2880584887380.8345072668910.36796586170.5792373409070.0346583067786-0.005140142924870.6690968870350.1328002117690.31655889948530.1425359585-16.726270502813.0825084766
52.227189825091.33873316491-2.041193453142.75805153596-2.70685729983.02213804323-0.30982657074-0.520447286924-1.13717457691-0.230263856858-0.200793944332-1.342916632450.5588442239911.538649120040.8341817185520.6191328468280.08084198352570.01316523518310.7788778820850.1964299787170.54982678433837.5501156333-19.1153441197.30035767406
67.267460307051.07200640686-3.836768548142.562117558390.7820389981062.77037015924-0.4091049031480.5462258120840.633048298612-0.1998737655970.19983269815-0.193740054425-0.6451460575260.467654062872-0.07070771142720.712412658377-0.03868738079880.01554475612220.5133814990690.03597036367620.26849827670826.8064365057-11.04944455841.68235972837
74.857437275890.621789462532-1.783719772121.687002307660.5094004756280.9956748416810.4981953291690.2136299105251.10487981964-0.0284076624348-0.2576513349780.252902134521-0.731694877157-0.201819006462-0.1972490148510.7275025801620.1616013154320.02221108787010.2655299270660.01774557285310.5744534414527.02148300161-3.9885136204212.4917611624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 47 )
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 64 )
4X-RAY DIFFRACTION4chain 'A' and (resid 65 through 96 )
5X-RAY DIFFRACTION5chain 'A' and (resid 97 through 102 )
6X-RAY DIFFRACTION6chain 'A' and (resid 103 through 137 )
7X-RAY DIFFRACTION7chain 'A' and (resid 138 through 160 )

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