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- PDB-1wrp: FLEXIBILITY OF THE DNA-BINDING DOMAINS OF TRP REPRESSOR -

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Basic information

Entry
Database: PDB / ID: 1wrp
TitleFLEXIBILITY OF THE DNA-BINDING DOMAINS OF TRP REPRESSOR
ComponentsTRP REPRESSORTryptophan 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
TRYPTOPHAN / Trp operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsSchewitz, R.W. / Otwinowski, Z. / Lawson, C.L. / Joachimiak, A. / 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 1.3May 13, 2020Group: Other / Structure summary / Category: audit_author / pdbx_database_status
Item: _audit_author.name / _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
R: TRP REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4432
Polymers12,2391
Non-polymers2041
Water1,06359
1
R: TRP REPRESSOR
hetero molecules

R: TRP REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8864
Polymers24,4782
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area4570 Å2
ΔGint-38 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.600, 50.600, 73.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsTHE REPRESSOR 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 24.53333

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Components

#1: Protein TRP REPRESSOR / Tryptophan repressor


Mass: 12238.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0A881
#2: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.22 Å3/Da / Density % sol: 44.63 %
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: PROFFT / Classification: refinement
RefinementRfactor obs: 0.204 / Highest resolution: 2.2 Å
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms814 0 15 59 888
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_deg1.8
Refine LS restraints
*PLUS
Type: p_bond_d / Dev ideal target: 0.02

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