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- PDB-1opc: OMPR DNA-BINDING DOMAIN, ESCHERICHIA COLI -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1opc
TitleOMPR DNA-BINDING DOMAIN, ESCHERICHIA COLI
ComponentsOMPR
KeywordsTRANSCRIPTION REGULATION / RESPONSE REGULATOR / WINGED HELIX / OSMOREGULATION
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 / Resolution: 1.95 Å
AuthorsMartinez-Hackert, E. / Stock, A.M.
CitationJournal: Structure / Year: 1997
Title: The DNA-binding domain of OmpR: crystal structures of a winged helix transcription factor.
Authors: Martinez-Hackert, E. / Stock, A.M.
History
DepositionDec 16, 1996Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: OMPR


Theoretical massNumber of molelcules
Total (without water)12,5381
Polymers12,5381
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.140, 59.140, 58.110
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 OMPR / OMPRC


Mass: 12538.368 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DNA-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET11 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA16
#2: Water ChemComp-HOH / 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: 2.45 Å3/Da / Density % sol: 41 %
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 3% POLYETHYLENEGLYCOL-MONOMETHYLETHER (PMME) 5000, 17.5% ETHYLENEGLYCOL, 2.5% MPD, 30 MM MES, PH 6.5; THEN SOAKED IN 10% PMME 5000, 20% ETHYLENEGLYCOL, 10% PEG ...Details: PROTEIN WAS CRYSTALLIZED FROM 3% POLYETHYLENEGLYCOL-MONOMETHYLETHER (PMME) 5000, 17.5% ETHYLENEGLYCOL, 2.5% MPD, 30 MM MES, PH 6.5; THEN SOAKED IN 10% PMME 5000, 20% ETHYLENEGLYCOL, 10% PEG 200, 200 MM AMMONIUM SULFATE, 30 MM MES, PH 6.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120-25 mg/mlprotein1drop
22 mMbetaME1drop
33 %PMME50001reservoir
42.5 %MPD1reservoir
517.5 %ethyleneglycol1reservoir
630 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9686 / Wavelength: 0.9686, 0.9876
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jun 1, 1996 / Details: MONOCHROMATOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96861
20.98761
ReflectionResolution: 1.95→10 Å / Num. obs: 8604 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 16.78 Å2 / Rsym value: 0.046 / Net I/σ(I): 10.8
Reflection shellResolution: 1.95→2 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 6.9 / Rsym value: 0.086 / % possible all: 98.7
Reflection
*PLUS
Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 98.7 % / Rmerge(I) obs: 0.086

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Processing

Software
NameClassification
MADSYSphasing
PROLSQrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.95→5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: X-PLOR, PROLSQ AND REFMAC USED
RfactorNum. reflection% reflectionSelection details
Rfree0.269 388 5 %RANDOM
Rwork0.228 ---
all-8195 --
obs-7807 97.1 %-
Displacement parametersBiso mean: 20.7 Å2
Refine analyzeLuzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 1.95→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms806 0 0 85 891
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0360.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.9332
X-RAY DIFFRACTIONp_mcangle_it2.6053
X-RAY DIFFRACTIONp_scbond_it1.6962
X-RAY DIFFRACTIONp_scangle_it2.9433
X-RAY DIFFRACTIONp_plane_restr0.0160.03
X-RAY DIFFRACTIONp_chiral_restr0.1370.15
X-RAY DIFFRACTIONp_singtor_nbd0.1950.3
X-RAY DIFFRACTIONp_multtor_nbd0.2680.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1590.3
X-RAY DIFFRACTIONp_planar_tor7.97
X-RAY DIFFRACTIONp_staggered_tor2015
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.620
X-RAY DIFFRACTIONp_special_tor31.615
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS

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