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

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Basic information

Entry
Database: PDB / ID: 7dwn
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 DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Predicted DNA-binding transcriptional regulator
Similarity search - Component
Biological speciesAliivibrio fischeri ES114 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 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

Downloads & links

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Assembly

Deposited unit
A: Predicted DNA-binding transcriptional regulator
B: Predicted DNA-binding transcriptional regulator
C: Predicted DNA-binding transcriptional regulator
D: Predicted DNA-binding transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,8528
Polymers131,0714
Non-polymers7814
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14870 Å2
ΔGint-62 kcal/mol
Surface area52610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.688, 77.456, 86.797
Angle α, β, γ (deg.)74.460, 78.160, 89.860
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Predicted DNA-binding transcriptional regulator


Mass: 32767.652 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aliivibrio fischeri ES114 (bacteria) / Strain: ES114 / Gene: yjiE, VF_1545 / Cell line (production host): HEK293 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5E4K6
#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2M Magnesium chloride 0.1M MES pH6.0 25% PEG3350

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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: Jun 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.32→48.82 Å / Num. obs: 52682 / % possible obs: 97.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 39.31 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.068 / Rrim(I) all: 0.128 / Net I/σ(I): 7.3 / Num. measured all: 185387 / Scaling rejects: 100
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
2.32-2.393.50.6441608345690.7410.4040.7632.297.8
9.57-48.823.30.0624577490.9920.0390.07214.496.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.5.21data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YDW

5ydw


Resolution: 2.32→25.235 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 32.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2748 2529 4.81 %
Rwork0.2279 50068 -
obs0.2301 52597 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.48 Å2 / Biso mean: 57.6375 Å2 / Biso min: 16.58 Å2
Refinement stepCycle: final / Resolution: 2.32→25.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9180 0 48 172 9400
Biso mean--75.12 49.21 -
Num. residues----1168
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.32-2.36460.40941420.3201279398
2.3646-2.41280.39211430.3176277197
2.4128-2.46520.35911500.29275299
2.4652-2.52250.34121320.2901279197
2.5225-2.58560.34541530.2889276698
2.5856-2.65540.36021430.2744279698
2.6554-2.73340.33011240.2696275997
2.7334-2.82160.34411430.2562280298
2.8216-2.92230.32971580.2513274298
2.9223-3.03910.31741400.2563281698
3.0391-3.17710.28161320.2451280298
3.1771-3.34430.25221540.2353280698
3.3443-3.55330.26531250.2267279998
3.5533-3.82680.29121460.2099277898
3.8268-4.21030.20841400.1981275196
4.2103-4.81580.21411410.1788277398
4.8158-6.05360.261390.2121277798
6.0536-25.2350.23081240.2024279497
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)
10.89780.005-0.24680.48840.03270.36960.23840.14730.19310.2189-0.01780.55960.1072-0.14620.01410.54810.0414-0.02580.3253-0.05650.5476-7.49594.6327-22.1314
23.47990.39920.74130.0253-0.20780.04160.054-0.2717-0.2338-0.1301-0.0651-0.0076-0.1492-0.09390.02440.1743-0.00670.01260.23750.04850.197312.3483-40.0336-2.4708
31.20560.1198-0.12950.9448-0.41310.26520.058-0.1836-0.0314-0.1365-0.2077-0.20560.1560.3317-0.04790.38090.0209-0.00630.26120.04670.321113.4909-44.9378-40.7954
42.263-0.0374-0.07630.2684-0.02830.754-0.1073-0.10090.3541-0.07070.0179-0.0564-0.0157-0.0616-0.01230.1687-0.004-0.00250.2004-0.03890.2656-7.0536-31.72210.8025
51.00450.4457-0.40531.1155-0.38370.39680.18710.31720.21060.002-0.01090.5481-0.0294-0.33080.07460.42870.0143-0.0130.3664-0.02250.3058-7.8863-49.7561-34.0318
61.86140.19150.53310.4028-0.34920.561-0.0775-0.03230.49450.05760.0026-0.02030.06620.08620.00180.1717-0.03330.04860.22370.04630.311912.6299-5.4526-53.6071
70.8258-0.0948-0.43770.20030.20780.3223-0.12290.21770.22610.4682-0.1817-0.2935-0.05980.1733-0.03610.66810.0224-0.210.39220.04510.570713.8959-0.3708-15.6112
80.9143-0.29640.6580.1028-0.08450.5072-0.0195-0.01270.15480.0971-0.0494-0.1772-0.0552-0.0496-0.00460.2041-0.0018-0.00030.20140.00250.2937-8.3452-8.5115-52.2951
90.6027-0.05120.03440.4440.27010.5977-0.12450.2049-0.4367-0.02560.2110.0476-0.04860.21210.01210.22480.0012-0.01430.3210.03110.3738-0.7855-22.4074-65.233
100.24990.07350.2203-0.0780.0830.0995-0.095-0.01390.06050.0770.2484-0.09720.05720.0047-0.00010.24950.0526-0.02750.34820.00770.4015-16.6954-6.0437-48.2921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 83 )A1 - 83
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 292 )A84 - 292
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 89 )B1 - 89
4X-RAY DIFFRACTION4chain 'B' and (resid 90 through 292 )B90 - 292
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 83 )C1 - 83
6X-RAY DIFFRACTION6chain 'C' and (resid 84 through 292 )C84 - 292
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 89 )D1 - 89
8X-RAY DIFFRACTION8chain 'D' and (resid 90 through 184 )D90 - 184
9X-RAY DIFFRACTION9chain 'D' and (resid 185 through 263 )D185 - 263
10X-RAY DIFFRACTION10chain 'D' and (resid 264 through 292 )D264 - 292

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