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- PDB-4uhs: Crystal structure of the receiver domain of CpxR from E. coli (te... -

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Basic information

Entry
Database: PDB / ID: 4uhs
TitleCrystal structure of the receiver domain of CpxR from E. coli (tetragonal form)
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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcriptional regulatory protein CpxR
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5 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 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
C: TRANSCRIPTIONAL REGULATORY PROTEIN CPXR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7596
Polymers46,6863
Non-polymers733
Water00
1
A: TRANSCRIPTIONAL REGULATORY PROTEIN CPXR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5862
Polymers15,5621
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRANSCRIPTIONAL REGULATORY PROTEIN CPXR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5862
Polymers15,5621
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TRANSCRIPTIONAL REGULATORY PROTEIN CPXR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5862
Polymers15,5621
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.222, 114.222, 356.734
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein TRANSCRIPTIONAL REGULATORY PROTEIN CPXR / CPXR


Mass: 15561.921 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-123
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 6.23 Å3/Da / Density % sol: 80.26 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 5→48.09 Å / Num. obs: 5469 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 256.98 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.4
Reflection shellResolution: 5→5.59 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UHJ

4uhj


Resolution: 5→48.09 Å / Cor.coef. Fo:Fc: 0.8899 / Cor.coef. Fo:Fc free: 0.8891 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.993
RfactorNum. reflection% reflectionSelection details
Rfree0.2674 245 4.49 %RANDOM
Rwork0.261 ---
obs0.2613 5453 99.89 %-
Displacement parametersBiso mean: 260.4 Å2
Baniso -1Baniso -2Baniso -3
1--57.2982 Å20 Å20 Å2
2---57.2982 Å20 Å2
3---114.5964 Å2
Refinement stepCycle: LAST / Resolution: 5→48.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3000 0 3 0 3003
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013033HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.154095HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1500SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes93HARMONIC2
X-RAY DIFFRACTIONt_gen_planes423HARMONIC5
X-RAY DIFFRACTIONt_it3033HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion3.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion396SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3359SEMIHARMONIC4
LS refinement shellResolution: 5→5.59 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2158 66 4.4 %
Rwork0.2833 1433 -
all0.2807 1499 -
obs--99.89 %
Refinement TLS params.

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)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.34295.14670.00027.6373-9.462929.04120.52071.0333-1.54220.3091-0.6108-0.5274-0.8015-1.03640.0901-0.94690.5667-0.47750.9471-0.03580.165945.780845.776-17.3118
230.39629.807911.234723.26224.830433.26170.3287-1.15851.4798-0.50071.21331.6435-0.9798-1.8219-1.5420.29450.608-0.05471.216-0.1742-0.848830.693960.7168-7.9931
36.5697-1.396511.42317.34353.25922.92090.0622-0.0504-0.715-0.16121.22511.4182-0.0137-1.2281-1.2873-0.22330.0948-0.21861.2160.5757-0.284618.875148.1813-37.8843
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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