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- PDB-3wrp: FLEXIBILITY OF THE DNA-BINDING DOMAINS OF TRP REPRESSOR -

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Basic information

Entry
Database: PDB / ID: 3wrp
TitleFLEXIBILITY OF THE DNA-BINDING DOMAINS OF TRP REPRESSOR
ComponentsTRP REPRESSOR
KeywordsDNA BINDING REGULATORY PROTEIN
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
TrpR-like / Trp repressor, bacterial / Trp repressor / TrpR-like superfamily / Trp repressor protein / Trp repressor/replication initiator / Trp Operon Repressor; Chain A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Trp operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsZhang, R.-G. / Sigler, P.B.
Citation
Journal: Proteins / Year: 1988
Title: Flexibility of the DNA-binding domains of trp repressor.
Authors: Lawson, C.L. / Zhang, R.G. / Schevitz, R.W. / Otwinowski, Z. / Joachimiak, A. / Sigler, P.B.
#1: Journal: Nature / Year: 1987
Title: The Crystal Structure of Trp Aporepressor at 1.8 Angstroms Shows How Binding Tryptophan Enhances DNA Affinity
Authors: Zhang, R.-G. / Joachimiak, A. / Lawson, C.L. / Schevitz, R.W. / Otwinowski, Z. / Sigler, P.B.
#2: Journal: Nature / Year: 1985
Title: The Three-Dimensional Structure of Trp Repressor
Authors: Schevitz, R.W. / Otwinowski, Z. / Joachimiak, A. / Lawson, C.L. / Sigler, P.B.
#3: Journal: J.Biol.Chem. / Year: 1983
Title: Functional Inferences from Crystals of Escherichia Coli Trp Repressor
Authors: Joachimiak, A. / Schevitz, R.W. / Kelley, R.L. / Yanofsky, C. / Sigler, P.B.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1983
Title: Purification and Characterization of Trp Repressor
Authors: Joachimiak, A. / Kelley, R.L. / Gunsalus, R.P. / Yanofsky, C. / Sigler, P.B.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1980
Title: Nucleotide Sequence and Expression of Escherichia Coli Trpr, the Structural Gene for the Trp Aporepressor
Authors: Gunsalus, R.P. / Yanofsky, C.
History
DepositionDec 1, 1987Processing site: BNL
Revision 1.0Apr 16, 1988Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 28, 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

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Assembly

Deposited unit
A: TRP REPRESSOR


Theoretical massNumber of molelcules
Total (without water)12,3701
Polymers12,3701
Non-polymers00
Water1,33374
1
A: TRP REPRESSOR

A: TRP REPRESSOR


Theoretical massNumber of molelcules
Total (without water)24,7402
Polymers24,7402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4380 Å2
ΔGint-33 kcal/mol
Surface area11220 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.400, 34.200, 44.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
DetailsTHE APOREPRESSOR MOLECULE CONSISTS OF A DIMER RELATED BY A CRYSTALLOGRAPHIC TRANSFORMATION. COORDINATES FOR THE SYMMETRY RELATED CHAIN CAN BE GENERATED FROM THE CHAIN PRESENTED IN THIS ENTRY BY -1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 -1.0 0.0

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Components

#1: Protein TRP REPRESSOR


Mass: 12370.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0A881
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.77 Å3/Da / Density % sol: 30.33 %
Crystal grow
*PLUS
pH: 6.2 / Method: vapor diffusion, hanging drop / Details: Joachimiak, A., (1983) J.Biol.Chem., 258, 12641.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mMprotein1drop
21.9 Mammonium sulfate1reservior
350 mM1reserviorNaKPO4

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.204 / Highest resolution: 1.8 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms810 0 0 74 884
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_deg2.5

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