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- PDB-2hjd: Crystal structure of a second quorum sensing antiactivator TraM2 ... -

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Basic information

Entry
Database: PDB / ID: 2hjd
TitleCrystal structure of a second quorum sensing antiactivator TraM2 from A. tumefaciens strain A6
ComponentsQuorum-sensing antiactivator
KeywordsSIGNALING PROTEIN / 4 helix coiled coil
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 / Quorum-sensing antiactivator
Function and homology information
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChen, L.
CitationJournal: J.Bacteriol. / Year: 2006
Title: Crystal Structure and Mechanism of TraM2, a Second Quorum-Sensing Antiactivator of Agrobacterium tumefaciens Strain A6.
Authors: Chen, G. / Wang, C. / Fuqua, C. / Zhang, L.H. / Chen, L.
History
DepositionJun 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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: Quorum-sensing antiactivator
B: Quorum-sensing antiactivator
C: Quorum-sensing antiactivator
D: Quorum-sensing antiactivator


Theoretical massNumber of molelcules
Total (without water)44,5674
Polymers44,5674
Non-polymers00
Water5,531307
1
A: Quorum-sensing antiactivator
B: Quorum-sensing antiactivator


Theoretical massNumber of molelcules
Total (without water)22,2842
Polymers22,2842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-22 kcal/mol
Surface area9750 Å2
MethodPISA
2
C: Quorum-sensing antiactivator
D: Quorum-sensing antiactivator


Theoretical massNumber of molelcules
Total (without water)22,2842
Polymers22,2842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-22 kcal/mol
Surface area9790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.521, 79.521, 90.238
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsThe biological assembly is a homodimer, consisting of either chains A and B, or chains C and D

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Components

#1: Protein
Quorum-sensing antiactivator


Mass: 11141.806 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: traM2 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q20HX4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 3.2 Å3/Da / Density % sol: 61.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM TrisHCl, 200 mM NaCl, 0.5 mM EDTA, 1 mM DTT, 25% ethylene glycol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 31, 2004
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 32820 / Num. obs: 32632 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.1→2.18 Å / % possible all: 99.7

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RFY

1rfy


Resolution: 2.1→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.268 2525 random
Rwork0.229 --
all-32820 -
obs-31523 -
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2677 0 0 307 2984
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d17.5
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.016
RfactorNum. reflection% reflection
Rfree0.317 403 -
Rwork0.266 --
obs-4590 92.2 %

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