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- PDB-1rfy: Crystal Structure of Quorum-Sensing Antiactivator TraM -

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Basic information

Entry
Database: PDB / ID: 1rfy
TitleCrystal Structure of Quorum-Sensing Antiactivator TraM
ComponentsTranscriptional repressor traM
KeywordsTRANSCRIPTION / inter- and intra-molcular two-helix coiled coil / homodimer
Function / homologyTranscriptional repressor TraM / Transcriptional repressor TraM superfamily / Prokaryotic Transcriptional repressor TraM / HR1 repeat / Helix Hairpins / negative regulation of DNA-templated transcription / Orthogonal Bundle / Mainly Alpha / Transcriptional repressor TraM
Function and homology information
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsChen, G. / Malenkos, J.W. / Cha, M.R. / Fuqua, C. / Chen, L.
CitationJournal: Mol.Microbiol. / Year: 2004
Title: Quorum-sensing antiactivator TraM forms a dimer that dissociates to inhibit TraR
Authors: Chen, G. / Malenkos, J.W. / Cha, M.R. / Fuqua, C. / Chen, L.
History
DepositionNov 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional repressor traM
B: Transcriptional repressor traM


Theoretical massNumber of molelcules
Total (without water)22,7302
Polymers22,7302
Non-polymers00
Water4,143230
1
A: Transcriptional repressor traM

A: Transcriptional repressor traM


Theoretical massNumber of molelcules
Total (without water)22,7302
Polymers22,7302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+3/2,-y+1/2,z1
Buried area2120 Å2
ΔGint-24 kcal/mol
Surface area9630 Å2
MethodPISA, PQS
2
B: Transcriptional repressor traM

B: Transcriptional repressor traM


Theoretical massNumber of molelcules
Total (without water)22,7302
Polymers22,7302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area2150 Å2
ΔGint-25 kcal/mol
Surface area9570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.230, 85.750, 67.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Cell settingorthorhombic
Space group name H-MC222
Detailsthe second protomer of the biological assembly is generated by the two-fold axis: 2-x, 1-y, z the second protomer of the biological assembly is generated by the two-fold axis: 1.5-x, 0.5-y, z

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Components

#1: Protein Transcriptional repressor traM / Quorum-sensing antiactivator TraM / traM protein


Mass: 11365.187 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: traM / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 K12 / References: UniProt: Q57471
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.54 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: amonium acetate, sodium citrate, PEG 2000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9636 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 17, 2003
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9636 Å / Relative weight: 1
ReflectionResolution: 1.6→60 Å / Num. all: 30102 / Num. obs: 29690 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 9.9 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 37.4
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1234 / % possible all: 84.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: SAD / Resolution: 1.6→60 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 293645.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2895 10 %RANDOM
Rwork0.202 ---
obs0.2021 29073 96.5 %-
all-30102 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.2428 Å2 / ksol: 0.392037 e/Å3
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.07 Å20 Å20 Å2
2--2.15 Å20 Å2
3----0.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.6→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1349 0 0 230 1579
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d17.9
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.632
X-RAY DIFFRACTIONc_scbond_it2.312
X-RAY DIFFRACTIONc_scangle_it3.252.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.238 451 10.4 %
Rwork0.218 3893 -
obs-3893 87.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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