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- PDB-2cpg: TRANSCRIPTIONAL REPRESSOR COPG -

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Basic information

Entry
Database: PDB / ID: 2cpg
TitleTRANSCRIPTIONAL REPRESSOR COPG
ComponentsTRANSCRIPTIONAL REPRESSOR COPG
KeywordsGENE REGULATION / TRANSCRIPTIONAL REPRESSOR / DNA-BINDING PROTEIN / PLASMID
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
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.6 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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: TRANSCRIPTIONAL REPRESSOR COPG
B: TRANSCRIPTIONAL REPRESSOR COPG
C: TRANSCRIPTIONAL REPRESSOR COPG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5636
Polymers15,4563
Non-polymers1063
Water3,495194
1
A: TRANSCRIPTIONAL REPRESSOR COPG
B: TRANSCRIPTIONAL REPRESSOR COPG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3754
Polymers10,3042
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-47 kcal/mol
Surface area5600 Å2
MethodPISA
2
C: TRANSCRIPTIONAL REPRESSOR COPG
hetero molecules

C: TRANSCRIPTIONAL REPRESSOR COPG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3754
Polymers10,3042
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Unit cell
Length a, b, c (Å)67.190, 102.490, 40.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-47-

HOH

21A-48-

HOH

31C-47-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.787024, 0.562355, -0.253674), (0.567706, -0.821116, -0.058975), (-0.241461, -0.097597, -0.96549)-14.06171, 66.94317, 52.00411
2given(0.27167, 0.939943, 0.206648), (-0.936007, 0.307992, -0.170386), (-0.223799, -0.147135, 0.963465)72.26735, 4.70603, 11.38816
DetailsTHE SMALLEST FUNCTIONAL UNIT IS A HOMODIMER. IN THE PRESENT STRUCTURE, ONE A PROTOMER AND ONE B PROTOMER ESTABLISH SUCH AN INTERACTION. THE THIRD MOLECULE PRESENT IN THE ASYMMETRIC UNIT, MOLECULE C, ESTABLISHES ANOTHER HOMODIMER STRUCTURE WITH A SYMMETRY EQUIVALENT C MOLECULE.

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Components

#1: Protein/peptide TRANSCRIPTIONAL REPRESSOR COPG / REPA PROTEIN


Mass: 5152.106 Da / Num. of mol.: 3 / 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
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.27 Å3/Da / Density % sol: 45 %
Crystal growpH: 6.7 / Details: 72% MPD, 0.1 M HEPES PH 6.7, 3% BENZAMIDINE
Components of the solutions
IDNameCrystal-IDSol-ID
1BENZAMIDINE11
2MPD11
3MPD12
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop / Details: Gomis-Rueth, F.X., (1998) FEBS Lett., 425, 161.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
113-16 mg/mlprotein1drop
210 mMTris-HCl1drop
3275 mM1reservoirNaCl
40.5 mM1reservoirNaN3

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength
SYNCHROTRONEMBL/DESY, HAMBURG X311
ROTATING ANODERIGAKU RU20021.5418
Detector
TypeIDDetector
MARRESEARCH1IMAGE PLATE
2IMAGE 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
Num. obs: 18358 / Num. measured all: 91693 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 96.4 %

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Processing

Software
NameVersionClassification
CCP4model building
SHELXL-97refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.6→8 Å / Num. parameters: 4861 / Num. restraintsaints: 4018 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2772 -14 %EVERY 7TH REFLECTION
obs0.2017 16782 --
all-16782 --
Solvent computationSolvent model: MOEWS & KRETSINGER
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1016 0 3 194 1213
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / σ(F): 0 / % reflection Rfree: 14 % / Rfactor Rwork: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS

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