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- PDB-3lfk: A reported archaeal mechanosensitive channel is a structural homo... -

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Basic information

Entry
Database: PDB / ID: 3lfk
TitleA reported archaeal mechanosensitive channel is a structural homolog of MarR-like transcriptional regulators
ComponentsMarR Like Protein, TVG0766549
KeywordsUNKNOWN FUNCTION / multiple antibiotic resistance regulator / transcriptional regulator / winged helix-turn-helix motif / mechanosensitive channel
Function / homologyWinged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / CITRIC ACID / TVG0766549 protein
Function and homology information
Biological speciesThermoplasma volcanium (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.6 Å
AuthorsLiu, Z. / Walton, T.A. / Rees, D.C.
CitationJournal: Protein Sci. / Year: 2010
Title: A reported archaeal mechanosensitive channel is a structural homolog of MarR-like transcriptional regulators.
Authors: Liu, Z. / Walton, T.A. / Rees, D.C.
History
DepositionJan 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MarR Like Protein, TVG0766549
B: MarR Like Protein, TVG0766549
C: MarR Like Protein, TVG0766549
D: MarR Like Protein, TVG0766549
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9169
Polymers58,3394
Non-polymers5765
Water9,908550
1
A: MarR Like Protein, TVG0766549
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6812
Polymers14,5851
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MarR Like Protein, TVG0766549
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8734
Polymers14,5851
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MarR Like Protein, TVG0766549


Theoretical massNumber of molelcules
Total (without water)14,5851
Polymers14,5851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: MarR Like Protein, TVG0766549
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7772
Polymers14,5851
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.130, 88.335, 115.212
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
MarR Like Protein, TVG0766549 / MscTV


Mass: 14584.857 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma volcanium (archaea) / Strain: GSS1 / Gene: TV0762, TVG0766549 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21GOLD (DE3) / References: UniProt: Q97AP8
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.85 Å3/Da / Density % sol: 56.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 22-26% PEG 550MME, 80 mM ammonium sulfate, 85 mM citric acid, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 30, 2007
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 89296 / Num. obs: 89296 / % possible obs: 88.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 45.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 4.4 / Num. unique all: 8785 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHELXSphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.6→48.25 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 222580.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.228 4300 5 %RANDOM
Rwork0.211 ---
obs0.211 85295 96.6 %-
all-85296 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.9368 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 33.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--2.01 Å20 Å2
3----1.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-8 Å
Luzzati sigma a0.16 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.6→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3644 0 33 550 4227
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 664 5 %
Rwork0.266 12624 -
obs--91.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramwater.top
X-RAY DIFFRACTION3water_rep.paramion.top
X-RAY DIFFRACTION4CIT_par.txtCIT_top.txt

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