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- PDB-2oz9: E. coli TRP holorepressor, orthorhombic crystal form -

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Basic information

Entry
Database: PDB / ID: 2oz9
TitleE. coli TRP holorepressor, orthorhombic crystal form
ComponentsTrp operon repressor
KeywordsDNA BINDING PROTEIN / DNA 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 / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLawson, C.L. / 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
DepositionFeb 25, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionMar 6, 2007ID: 2WRP
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: Trp operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5624
Polymers12,2391
Non-polymers3233
Water1,53185
1
R: Trp operon repressor
hetero molecules

R: Trp operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1248
Polymers24,4782
Non-polymers6476
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5090 Å2
ΔGint-87 kcal/mol
Surface area12120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.300, 53.600, 33.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a dimer. To generate the second half of the assembly apply the crystallographic symmetry operator -x, -y, z.

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Components

#1: Protein Trp operon repressor


Mass: 12238.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trpR, rtrY / Plasmid: pRLK18 (modified pBR322) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A881
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


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


Mass: 18.015 Da / Num. of mol.: 85 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: crystallization conditions: 2.5 M sodium phosphate, 0.6 M ammonium chloride, 2.5 mM L-tryptophan. Prior to data collection the crystal was equilibrated to 2.4 M ammonium sulfate, 0.4 M ...Details: crystallization conditions: 2.5 M sodium phosphate, 0.6 M ammonium chloride, 2.5 mM L-tryptophan. Prior to data collection the crystal was equilibrated to 2.4 M ammonium sulfate, 0.4 M sodium chloride, 2.4 mM L-tryptophan, 50 mM sodium acetate., pH 5.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-6 / Wavelength: 1.5418 Å
DetectorType: KODAK / Detector: FILM / Details: graphite monochromator
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 10945 / Num. obs: 10945 / Observed criterion σ(F): 2

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Processing

Software
NameClassification
PROFFTrefinement
DENZOdata reduction
SCALEPACKdata scaling
MERLOTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wrp dimer

1wrp


Resolution: 1.65→5 Å / Isotropic thermal model: isotropic / Cross valid method: NONE / σ(F): 2 / Stereochemistry target values: Hendrickson & Konnert
Details: REFINEMENT. BY THE RESTRAINED LEAST-SQUARES PROCEDURE OF J. KONNERT AND W. HENDRICKSON (PROGRAM *PROLSQ*) AS MODIFIED BY B. FINZEL (PROGRAM *PROFFT*) AND USE OF PROGRAM *FRODO* OF T. A. ...Details: REFINEMENT. BY THE RESTRAINED LEAST-SQUARES PROCEDURE OF J. KONNERT AND W. HENDRICKSON (PROGRAM *PROLSQ*) AS MODIFIED BY B. FINZEL (PROGRAM *PROFFT*) AND USE OF PROGRAM *FRODO* OF T. A. JONES. THE R VALUE IS 0.180. THE RMS DEVIATION FROM IDEALITY OF THE BOND LENGTHS IS 0.012 ANGSTROMS. THE RMS DEVIATION FROM IDEALITY OF THE BOND ANGLES IS 2.0 DEGREES.
RfactorNum. reflection
obs0.18 10699
Displacement parametersBiso mean: 17.284 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.65→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms828 0 21 85 934
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_deg2

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