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- PDB-1r1t: Crystal structure of the cyanobacterial metallothionein repressor... -

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Basic information

Entry
Database: PDB / ID: 1r1t
TitleCrystal structure of the cyanobacterial metallothionein repressor SmtB in the apo-form
ComponentsTranscriptional repressor smtB
KeywordsTRANSCRIPTION REPRESSOR / Zinc / transcriptional regulation / winged HTH protein / DNA binding
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / metal ion binding
Similarity search - Function
ArsR-type transcription regulator, HTH motif / Bacterial regulatory proteins, arsR family signature. / Bacterial regulatory protein, arsR family / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...ArsR-type transcription regulator, HTH motif / Bacterial regulatory proteins, arsR family signature. / Bacterial regulatory protein, arsR family / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional repressor SmtB
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsEicken, C. / Pennella, M.A. / Chen, X. / Koshlap, K.M. / VanZile, M.L. / Sacchettini, J.C. / Giedroc, D.P.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: A metal-ligand-mediated intersubunit allosteric switch in related SmtB/ArsR zinc sensor proteins.
Authors: Eicken, C. / Pennella, M.A. / Chen, X. / Koshlap, K.M. / VanZile, M.L. / Sacchettini, J.C. / Giedroc, D.P.
History
DepositionSep 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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: Transcriptional repressor smtB
B: Transcriptional repressor smtB


Theoretical massNumber of molelcules
Total (without water)27,1232
Polymers27,1232
Non-polymers00
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-34 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.240, 69.722, 43.221
Angle α, β, γ (deg.)90.00, 95.84, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains the dimeric biological assembly.

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Components

#1: Protein Transcriptional repressor smtB


Mass: 13561.474 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 (bacteria)
Species: Synechococcus elongatus / Strain: PCC7942 / Gene: SMTB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30340
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.06 Å3/Da / Density % sol: 40.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Na/K phosphate, Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 7, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→60 Å / Num. all: 24148 / Num. obs: 22325 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rsym value: 0.029 / Net I/σ(I): 19.9
Reflection shellResolution: 1.7→1.76 Å / Rsym value: 0.185 / % possible all: 58.3

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Processing

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

1smt


Resolution: 1.7→60 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2163 -random
Rwork0.216 ---
all0.219 21874 --
obs0.219 21874 90.3 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å22.999 Å2
2--3.158 Å20 Å2
3----3.298 Å2
Refinement stepCycle: LAST / Resolution: 1.7→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1556 0 0 279 1835
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.038
X-RAY DIFFRACTIONc_mcbond_it1.3721.5
X-RAY DIFFRACTIONc_mcangle_it2.1372
X-RAY DIFFRACTIONc_scbond_it2.5462
X-RAY DIFFRACTIONc_scangle_it3.8552.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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