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- PDB-1smt: SMTB REPRESSOR FROM SYNECHOCOCCUS PCC7942 -

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Basic information

Entry
Database: PDB / ID: 1smt
TitleSMTB REPRESSOR FROM SYNECHOCOCCUS PCC7942
ComponentsTRANSCRIPTIONAL REPRESSOR SMTB
KeywordsMETALLOREGULATION / DNA REPRESSOR
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 ...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 (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.2 Å
AuthorsCook, W.J. / Hall, L.M.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of the cyanobacterial metallothionein repressor SmtB: a model for metalloregulatory proteins.
Authors: Cook, W.J. / Kar, S.R. / Taylor, K.B. / Hall, L.M.
History
DepositionSep 16, 1997Processing site: BNL
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-35 kcal/mol
Surface area10790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.600, 70.900, 44.000
Angle α, β, γ (deg.)90.00, 95.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (0.236425, -0.109008, -0.965516), (-0.11631, -0.989717, 0.08326), (-0.964663, 0.092615, -0.246673)
Vector: 40.993, 79.7563, 43.0887)

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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 (bacteria) / Strain: PCC 7942 / Production host: Escherichia coli (E. coli) / References: UniProt: P30340

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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: 2.15 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 296 K / pH: 6.1
Details: PROTEIN WAS CRYSTALLIZED FROM 40% SATURATED AMMONIUM SULFATE WITH 100 MM MES BUFFER, PH 6.1, AT 296 K.
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 %satammonium sulfate1reservoir
2100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 1, 1996
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→38 Å / Num. obs: 10563 / % possible obs: 90 % / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Biso Wilson estimate: 13.9 Å2 / Rsym value: 0.059 / Net I/σ(I): 23.8199
Reflection shellResolution: 2.2→2.34 Å / Redundancy: 1.2 % / Mean I/σ(I) obs: 3 / Rsym value: 0.15 / % possible all: 69
Reflection
*PLUS
Num. measured all: 18827 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 69 % / Rmerge(I) obs: 0.15

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→100 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 532 5.2 %RANDOM
Rwork0.217 ---
obs0.217 10278 87.6 %-
Displacement parametersBiso mean: 23.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1574 0 0 0 1574
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.05
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.381.5
X-RAY DIFFRACTIONx_mcangle_it2.232
X-RAY DIFFRACTIONx_scbond_it2.472
X-RAY DIFFRACTIONx_scangle_it3.832.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev Biso (Å2)Rms dev position (Å)
11RESTRAINEDX-RAY DIFFRACTION220
22X-RAY DIFFRACTION220
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 53 4.2 %
Rwork0.283 1197 -
obs--64.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.05

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