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- PDB-4uht: Crystal structure of the DNA binding domain of CpxR from E. coli -

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Basic information

Entry
Database: PDB / ID: 4uht
TitleCrystal structure of the DNA binding domain of CpxR from E. coli
ComponentsTRANSCRIPTIONAL REGULATORY PROTEIN CPXR
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


regulation of cell-substrate adhesion / phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / cell adhesion / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily ...OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / 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
Transcriptional regulatory protein CpxR
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsMechaly, A.E. / Alzari, P.M.A.
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Conformational plasticity of the response regulator CpxR, a key player in Gammaproteobacteria virulence and drug-resistance.
Authors: Mechaly, A.E. / Haouz, A. / Sassoon, N. / Buschiazzo, A. / Betton, J.M. / Alzari, P.M.
History
DepositionMar 25, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
A: TRANSCRIPTIONAL REGULATORY PROTEIN CPXR
B: TRANSCRIPTIONAL REGULATORY PROTEIN CPXR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1194
Polymers23,0482
Non-polymers712
Water7,080393
1
A: TRANSCRIPTIONAL REGULATORY PROTEIN CPXR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5602
Polymers11,5241
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRANSCRIPTIONAL REGULATORY PROTEIN CPXR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5602
Polymers11,5241
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.119, 39.880, 40.940
Angle α, β, γ (deg.)89.80, 75.13, 61.04
Int Tables number1
Space group name H-MP1

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Components

#1: Protein TRANSCRIPTIONAL REGULATORY PROTEIN CPXR / CPXR


Mass: 11524.151 Da / Num. of mol.: 2 / Fragment: RESIDUES 131-232 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLI5 / References: UniProt: P0AE88
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.32 Å3/Da / Density % sol: 46.97 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.918
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.15→34.54 Å / Num. obs: 73642 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 15.3
Reflection shellResolution: 1.15→1.21 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.4 / % possible all: 76

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→33.6 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.129 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.15599 3396 5 %RANDOM
Rwork0.1279 ---
obs0.12932 64389 92.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.038 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20.2 Å2-1.01 Å2
2---0.24 Å20.6 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.15→33.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1622 0 2 393 2017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191669
X-RAY DIFFRACTIONr_bond_other_d0.0070.021627
X-RAY DIFFRACTIONr_angle_refined_deg1.9561.9722263
X-RAY DIFFRACTIONr_angle_other_deg1.34433737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1945208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.71522.82178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.5115293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.421516
X-RAY DIFFRACTIONr_chiral_restr0.1250.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211873
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02395
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr7.26333296
X-RAY DIFFRACTIONr_sphericity_free36.964563
X-RAY DIFFRACTIONr_sphericity_bonded13.79653591
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 182 -
Rwork0.228 3339 -
obs--64.46 %
Refinement TLS params.

T22: 0.0043 Å2 / T23: -0.0029 Å2 / T33: 0.0023 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.00030.0022-0.00050.019-0.0050.01750.0002-0.000200.0006-0.0003-0.0009-0.0002-0.00030.00010.0112-0.00520.0047-5.1576-4.635744.1304
20.01480.00440.00760.00270.00120.0048-0.00060.00050.0002-0.00040.0005-0.0003-0.00010.00040.00020.0116-0.00510.004816.2238-17.696734.7408
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A131 - 232
2X-RAY DIFFRACTION2B131 - 232

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