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- PDB-8ylf: Crystal structure of Burkholderia thailandensis MftR -

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Basic information

Entry
Database: PDB / ID: 8ylf
TitleCrystal structure of Burkholderia thailandensis MftR
ComponentsMarR family transcriptional regulator
KeywordsTRANSCRIPTION / Transcription factor
Function / homology:
Function and homology information
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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

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Assembly

Deposited unit
A: MarR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)18,3381
Polymers18,3381
Non-polymers00
Water28816
1
A: MarR family transcriptional regulator

A: MarR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)36,6762
Polymers36,6762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area6880 Å2
ΔGint-43 kcal/mol
Surface area13050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.389, 62.389, 77.254
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
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: 48.03 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: imidazole, sodium citrate

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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: Nov 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.01→30 Å / Num. obs: 11986 / % possible obs: 99.6 % / Redundancy: 10.3 % / CC1/2: 0.993 / Net I/σ(I): 53
Reflection shellResolution: 2.01→2.04 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 3.8 / Num. unique obs: 549 / CC1/2: 0.912 / % possible all: 94

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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: in-house Se-SAD model

Resolution: 2.01→28.93 Å / SU ML: 0.1818 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.0034
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2355 581 4.86 %
Rwork0.2166 11371 -
obs0.2175 11952 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.12 Å2
Refinement stepCycle: LAST / Resolution: 2.01→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1148 0 0 16 1164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591163
X-RAY DIFFRACTIONf_angle_d0.79591579
X-RAY DIFFRACTIONf_chiral_restr0.0447187
X-RAY DIFFRACTIONf_plane_restr0.0046207
X-RAY DIFFRACTIONf_dihedral_angle_d10.3026715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.210.30191650.23732760X-RAY DIFFRACTION99.86
2.21-2.530.27721390.22132802X-RAY DIFFRACTION99.9
2.53-3.190.27871310.24942855X-RAY DIFFRACTION99.87
3.19-28.930.20191460.19962954X-RAY DIFFRACTION99.68
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)
18.178089468042.466423886511.466224187911.328060221650.6212203773652.00355659143-0.1824076738220.0161682227276-0.105174617321-0.1023436957490.0750741752826-0.1130306933360.08775394158420.02520132728170.05203633369990.2880503124530.02621220368720.01410001944990.1554288654490.004281938198780.244995798636-10.853520490716.430425553511.1413475565
25.672529288420.4121788912852.265886763181.42843947578-0.5732289308353.36950621219-0.092193256866-0.0452943175978-0.244415106877-0.09434234606290.034020613608-0.05208685156750.0116662917864-0.405729555720.0619975071460.311627180875-0.02335729938690.002187481389140.247721385655-0.0370494915220.215792134646-22.086185206111.90980719577.99719792633
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 78 )
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 160 )

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