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- PDB-1upg: Crystal structure of the quorum-sensing protein TraM from Agrobac... -

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Basic information

Entry
Database: PDB / ID: 1upg
TitleCrystal structure of the quorum-sensing protein TraM from Agrobacterium tumefaciens
ComponentsTRANSCRIPTIONAL REPRESSOR TRAM
KeywordsTRANSCRIPTION REPRESSOR / NEGATIVE REGULATOR / QUORUM-SENSING / CONJUGATION / TRANSCRIPTION REGULATION / REPRESSOR
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 / MAD / Resolution: 1.8 Å
AuthorsVannini, A. / Di Marco, S.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure of the Quorum-Sensing Protein Tram and its Interaction with the Transcriptional Regulator Trar
Authors: Vannini, A. / Volpari, C. / Di Marco, S.
History
DepositionSep 30, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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)23,1122
Polymers23,1122
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)76.436, 47.097, 47.469
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein TRANSCRIPTIONAL REPRESSOR TRAM / TRAM


Mass: 11555.889 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AGROBACTERIUM TUMEFACIENS (bacteria) / Description: SYNTHETIC GENE / Plasmid: PT7.7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q57471
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 1.88 Å3/Da / Density % sol: 34.23 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→47.67 Å / Num. obs: 14117 / % possible obs: 90.2 % / Redundancy: 3 % / Biso Wilson estimate: 21 Å2

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.8→47.67 Å / SU B: 4.407 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.139 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 748 5 %RANDOM
Rwork0.186 ---
obs0.188 14117 90.24 %-
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.89 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1483 0 0 129 1612

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