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- PDB-1b01: TRANSCRIPTIONAL REPRESSOR COPG/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1b01
TitleTRANSCRIPTIONAL REPRESSOR COPG/DNA COMPLEX
Components
  • DNA (5'-D(*CP*CP*CP*GP*TP*GP*CP*AP*CP*TP*CP*AP*AP*TP*GP*CP*AP*AP*T)-3')
  • DNA (5'-D(*GP*AP*TP*TP*GP*CP*AP*TP*TP*GP*AP*GP*TP*GP*CP*AP*CP*GP*G)-3')
  • TRANSCRIPTIONAL REPRESSOR COPG
KeywordsGENE REGULATION/DNA / TRANSCRIPTIONAL REPRESSOR / DNA-BINDING PROTEIN / PLASMID / PROTEIN-DNA COMPLEX / GENE REGULATION-DNA complex
Function / homology
Function and homology information


plasmid maintenance / protein-DNA complex / sequence-specific DNA binding / regulation of DNA-templated transcription
Similarity search - Function
Ribbon-helix-helix protein, CopG / Ribbon-helix-helix protein, copG family / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein CopG
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.56 Å
AuthorsGomis-Rueth, F.X. / Sola, M. / Acebo, P. / Parraga, A. / Guasch, A. / Eritja, R. / Gonzalez, A. / Espinosa, M. / del Solar, G. / Coll, M.
Citation
Journal: EMBO J. / Year: 1998
Title: The structure of plasmid-encoded transcriptional repressor CopG unliganded and bound to its operator.
Authors: Gomis-Ruth, F.X. / Sola, M. / Acebo, P. / Parraga, A. / Guasch, A. / Eritja, R. / Gonzalez, A. / Espinosa, M. / del Solar, G. / Coll, M.
#1: Journal: FEBS Lett. / Year: 1998
Title: Overexpression, Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of the Pmv158-Encoded Plasmid Transcriptional Repressor Protein Copg
Authors: Gomis-Rueth, F.X. / Sola, M. / Perez-Luque, R. / Acebo, P. / Alda, M.T. / Gonzalez, A. / Espinosa, M. / del Solar, G. / Coll, M.
History
DepositionNov 15, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Nov 19, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: DNA (5'-D(*CP*CP*CP*GP*TP*GP*CP*AP*CP*TP*CP*AP*AP*TP*GP*CP*AP*AP*T)-3')
F: DNA (5'-D(*GP*AP*TP*TP*GP*CP*AP*TP*TP*GP*AP*GP*TP*GP*CP*AP*CP*GP*G)-3')
A: TRANSCRIPTIONAL REPRESSOR COPG
B: TRANSCRIPTIONAL REPRESSOR COPG


Theoretical massNumber of molelcules
Total (without water)21,8994
Polymers21,8994
Non-polymers00
Water23413
1
E: DNA (5'-D(*CP*CP*CP*GP*TP*GP*CP*AP*CP*TP*CP*AP*AP*TP*GP*CP*AP*AP*T)-3')
F: DNA (5'-D(*GP*AP*TP*TP*GP*CP*AP*TP*TP*GP*AP*GP*TP*GP*CP*AP*CP*GP*G)-3')
A: TRANSCRIPTIONAL REPRESSOR COPG
B: TRANSCRIPTIONAL REPRESSOR COPG

E: DNA (5'-D(*CP*CP*CP*GP*TP*GP*CP*AP*CP*TP*CP*AP*AP*TP*GP*CP*AP*AP*T)-3')
F: DNA (5'-D(*GP*AP*TP*TP*GP*CP*AP*TP*TP*GP*AP*GP*TP*GP*CP*AP*CP*GP*G)-3')
A: TRANSCRIPTIONAL REPRESSOR COPG
B: TRANSCRIPTIONAL REPRESSOR COPG


Theoretical massNumber of molelcules
Total (without water)43,7978
Polymers43,7978
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+3/41
Unit cell
Length a, b, c (Å)40.300, 40.300, 221.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Cell settingtetragonal
Space group name H-MP4322
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.36851, -0.861028, -0.350473), (-0.858342, 0.170367, 0.483967), (-0.357, 0.479172, -0.801838)
Vector: 94.7511, -5.1375, 181.5537)

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Components

#1: DNA chain DNA (5'-D(*CP*CP*CP*GP*TP*GP*CP*AP*CP*TP*CP*AP*AP*TP*GP*CP*AP*AP*T)-3')


Mass: 5749.738 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*AP*TP*TP*GP*CP*AP*TP*TP*GP*AP*GP*TP*GP*CP*AP*CP*GP*G)-3')


Mass: 5900.820 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein/peptide TRANSCRIPTIONAL REPRESSOR COPG / REPA PROTEIN


Mass: 5124.092 Da / Num. of mol.: 2 / Fragment: DNA-BINDING PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Strain: PLS1 / Cellular location: PLASMID PMV158 / Plasmid: PMV158 / Production host: Escherichia coli (E. coli) / References: UniProt: P13920
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 45 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.7 / Details: MPD, HEPES, pH 6.70, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2HEPES11
3MPD12
4HEPES12
Crystal
*PLUS
Crystal grow
*PLUS
PH range low: 7.5 / PH range high: 6.7
Components of the solutions
*PLUS
IDConc.Crystal-IDSol-ID
160-78 %1reservoir
20.1 M1reservoir
31
41

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→19.61 Å / Num. obs: 91693 / % possible obs: 98.1 % / Redundancy: 5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.3
Reflection shellResolution: 1.6→1.69 Å / Rmerge(I) obs: 0.126 / Mean I/σ(I) obs: 3 / % possible all: 96.4
Reflection
*PLUS
Highest resolution: 2.56 Å / Lowest resolution: 19.86 Å / Num. obs: 6252 / % possible obs: 96.3 % / Redundancy: 5.9 % / Num. measured all: 78954 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
Highest resolution: 2.56 Å / Lowest resolution: 2.7 Å / % possible obs: 86.8 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
CCP4model building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.56→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE COMPLEX SET UP FOR CRYSTALLIZATION WAS MADE UP BY A COPG DIMER-OF-DIMERS AND A 19-BP DSDNA. AS THE DNA MOIETY IS PRESENT IN DUAL OCCUPANCY, A CRYSTALLOGRAPHIC DYAD IS CREATED. ...Details: THE COMPLEX SET UP FOR CRYSTALLIZATION WAS MADE UP BY A COPG DIMER-OF-DIMERS AND A 19-BP DSDNA. AS THE DNA MOIETY IS PRESENT IN DUAL OCCUPANCY, A CRYSTALLOGRAPHIC DYAD IS CREATED. ACCORDINGLY, THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT COMPRISES HALF A PROTEIN/DNA COMPLEX, THAT IS, A COPG DIMER AND HALF DSDNA. THE DNA PART HAS BEEN MODELLED WITH THE TWO OBSERVED ORIENTATIONS, EACH WITH OCCUPANCY 0.5. IN THIS MODEL, DNA CHAIN E PAIRS CHAIN F AND CHAIN G DOES SO WITH CHAIN H.
RfactorNum. reflection% reflectionSelection details
Rfree0.316 -7 %RANDOM
Rwork0.247 ---
obs0.247 6024 92.8 %-
Refinement stepCycle: LAST / Resolution: 2.56→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms670 767 0 13 1450
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.45
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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