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- PDB-7dwo: Crystal structure of Vibrio fischeri DarR in complex with DNA rev... -

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Basic information

Entry
Database: PDB / ID: 7dwo
TitleCrystal structure of Vibrio fischeri DarR in complex with DNA reveals the transcriptional activation mechanism of LTTR family members
ComponentsPredicted DNA-binding transcriptional regulator
KeywordsDNA BINDING PROTEIN / transcriptional regulators / tetramer
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Predicted DNA-binding transcriptional regulator
Similarity search - Component
Biological speciesAliivibrio fischeri ES114 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.611 Å
AuthorsWang, W.W. / Wu, H. / He, J.H. / Yu, F.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971121 China
National Natural Science Foundation of China (NSFC)81861138047 China
National Natural Science Foundation of China (NSFC)U1932130 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: Crystal structure details of Vibrio fischeri DarR and mutant DarR-M202I from LTTR family reveals their activation mechanism.
Authors: Wang, W. / Wu, H. / Xiao, Q. / Zhou, H. / Li, M. / Xu, Q. / Wang, Q. / Yu, F. / He, J.
History
DepositionJan 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Predicted DNA-binding transcriptional regulator
B: Predicted DNA-binding transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)65,4992
Polymers65,4992
Non-polymers00
Water52229
1
A: Predicted DNA-binding transcriptional regulator
B: Predicted DNA-binding transcriptional regulator

A: Predicted DNA-binding transcriptional regulator
B: Predicted DNA-binding transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)130,9984
Polymers130,9984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area12530 Å2
ΔGint-82 kcal/mol
Surface area53150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.863, 180.223, 51.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Predicted DNA-binding transcriptional regulator


Mass: 32749.617 Da / Num. of mol.: 2 / Mutation: M202I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aliivibrio fischeri ES114 (bacteria) / Strain: ES114 / Gene: yjiE, VF_1545 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5E4K6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.5M sodium chloride, 0.1M MES pH6.0, 20%PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.61→29.89 Å / Num. obs: 22031 / % possible obs: 99.9 % / Redundancy: 12.6 % / Biso Wilson estimate: 55.64 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.029 / Rrim(I) all: 0.105 / Net I/σ(I): 18.5 / Num. measured all: 276628 / Scaling rejects: 638
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.61-2.6812.30.4351947615800.9140.1290.4541.799.3
11.67-29.898.60.03624852890.9990.0130.03952.394.6

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YDW

5ydw


Resolution: 2.611→29.56 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2645 1086 4.96 %
Rwork0.2326 20826 -
obs0.2342 21912 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.92 Å2 / Biso mean: 65.0933 Å2 / Biso min: 25.82 Å2
Refinement stepCycle: final / Resolution: 2.611→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4590 0 0 29 4619
Biso mean---52.8 -
Num. residues----584
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.611-2.72930.30251250.2639255699
2.7293-2.87310.38411360.27952573100
2.8731-3.05290.2951220.27552578100
3.0529-3.28830.32641470.26962555100
3.2883-3.61870.27461380.24692584100
3.6187-4.14110.2421550.21792606100
4.1411-5.21270.21811280.18992647100
5.2127-29.560.2521350.2345272798
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)
11.0809-0.61570.38073.0231-2.36862.22290.0715-0.18780.33250.1347-0.06770.3151-0.26210.0111-0.1050.4696-0.0560.07340.5168-0.26260.9426-24.1488.067620.3324
28.9914-1.29912.1545.2418-0.52012.86340.04810.26350.6129-0.0956-0.0660.29760.12110.2489-0.07170.38140.024-0.0380.3064-0.01960.24622.989732.1913-1.2845
33.30831.4052-0.41942.90110.30172.5167-0.2382-0.0479-0.3643-0.3063-0.00590.2199-0.0119-0.03240.19810.44260.00030.02930.34380.04890.30864.785923.363-4.2801
44.940.03970.82324.7747-0.31076.39850.1859-0.176-0.4381-0.1223-0.2953-1.02920.06680.5490.09280.38370.01070.04090.46830.17570.561927.138826.38496.3794
54.23360.0181.37963.7043-0.36793.4385-0.13380.7927-0.0761-1.1010.17130.2552-0.3348-0.30730.12780.586-0.014-0.05890.3440.01530.30393.036126.2421-10.2886
60.3260.601-0.00222.73532.06520.47750.01380.5479-0.0326-0.7157-0.32820.1417-0.4340.12890.22430.63580.0294-0.19560.73180.26910.89622.9961-14.2416-0.1056
71.4872-2.1518-0.0095.0415-0.99412.57490.10440.1183-0.11370.3856-0.2369-0.0445-0.0748-0.02070.15460.4365-0.131-0.05630.433-0.01670.329610.63821.926722.9131
83.4296-0.14151.30212.98480.0395.58490.2265-0.26110.4372-0.20330.10460.9386-0.6743-0.6764-0.33590.51730.17750.13820.5140.02910.6589-4.977241.326512.3274
92.3539-1.01711.24413.3504-2.60794.80880.1742-0.26710.22780.7009-0.2977-0.0236-0.604-0.0230.16270.4874-0.13310.00850.4327-0.05180.33877.685933.291921.1466
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 90 )A1 - 90
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 114 )A91 - 114
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 174 )A115 - 174
4X-RAY DIFFRACTION4chain 'A' and (resid 175 through 263 )A175 - 263
5X-RAY DIFFRACTION5chain 'A' and (resid 264 through 292 )A264 - 292
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 90 )B1 - 90
7X-RAY DIFFRACTION7chain 'B' and (resid 91 through 174 )B91 - 174
8X-RAY DIFFRACTION8chain 'B' and (resid 175 through 223 )B175 - 223
9X-RAY DIFFRACTION9chain 'B' and (resid 224 through 292 )B224 - 292

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