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- PDB-1odd: OMPR C-TERMINAL DOMAIN (OMPR-C) FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1odd
TitleOMPR C-TERMINAL DOMAIN (OMPR-C) FROM ESCHERICHIA COLI
ComponentsTRANSCRIPTIONAL REGULATORY PROTEIN OMPR
KeywordsGENE REGULATORY PROTEIN / POSITIVE RESPONSE REGULATOR / DNA BINDING DOMAIN
Function / homology
Function and homology information


phosphorelay response regulator activity / phosphorelay signal transduction system / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA-binding dual transcriptional regulator OmpR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD WITH SE-MET MUTANT / Resolution: 2.2 Å
AuthorsKondou, H. / Nakagawa, A. / Tanaka, I.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Escherichia coli positive regulator OmpR has a large loop structure at the putative RNA polymerase interaction site.
Authors: Kondo, H. / Nakagawa, A. / Nishihira, J. / Nishimura, Y. / Mizuno, T. / Tanaka, I.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and X-Ray Studies of the DNA-Binding Domain of OmpR Protein, a Positive Regulator Involved in Activation of Osmoregulatory Genes in Escherichia Coli
Authors: Kondo, H. / Miyaji, T. / Suzuki, M. / Tate, S. / Mizuno, T. / Nishimura, Y. / Tanaka, I.
History
DepositionOct 31, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 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: TRANSCRIPTIONAL REGULATORY PROTEIN OMPR


Theoretical massNumber of molelcules
Total (without water)13,4051
Polymers13,4051
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.160, 59.160, 58.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein TRANSCRIPTIONAL REGULATORY PROTEIN OMPR / OMPR-C


Mass: 13405.311 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Cell line: BL21 / Plasmid: POMPR-C / Gene (production host): OMPR-C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) LYSS / References: UniProt: P0AA16
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.4 Å3/Da / Density % sol: 47 %
Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD.
Crystal growpH: 6
Details: PROTEIN WAS CRYSTALLIZED FROM 0.1M SODIUM CACODYLATE, 0.2M SODIUM ACETATE, 20%(W/V) PEG8000, PH 6.0; THEN SOAKED IN 35% PEG8000 WITH CRYSTALLIZATION BUFFER.
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / Details: Kondo, H., (1994) J.Mol.Biol., 235, 780.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMcitric buffer1reservoir
20.5 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: May 1, 1996 / Details: MIRROR, COLLIMATOR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 6153 / % possible obs: 98.1 % / Observed criterion σ(I): 4 / Redundancy: 5.1 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 1.9 / % possible all: 96.3
Reflection
*PLUS
Num. measured all: 31412
Reflection shell
*PLUS
% possible obs: 96.3 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
SCALAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MAD WITH SE-MET MUTANT / Resolution: 2.2→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: PROGRAM X-PLOR BY BRUNGER ALSO WAS USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.296 328 5.3 %RANDOM
Rwork0.224 ---
obs0.226 6052 97.6 %-
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms810 0 0 52 862
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_deg1.56

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