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- PDB-2pkx: E.coli response regulator PhoP receiver domain -

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Basic information

Entry
Database: PDB / ID: 2pkx
TitleE.coli response regulator PhoP receiver domain
ComponentsTranscriptional regulatory protein phoP
KeywordsTRANSCRIPTIONAL REGULATOR / chey like fold / response regulator / transcription factor / PhoP / virulence / phob family
Function / homology
Function and homology information


phosphorelay response regulator activity / DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / identical protein binding / 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 / Response regulator / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulatory protein PhoP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsBachhawat, P.
CitationJournal: J.Bacteriol. / Year: 2007
Title: Crystal Structures of the Receiver Domain of the Response Regulator PhoP from Escherichia coli in the Absence and Presence of the Phosphoryl Analog Beryllofluoride.
Authors: Bachhawat, P. / Stock, A.M.
History
DepositionApr 18, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionMay 22, 2007ID: 2EU6
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulatory protein phoP
B: Transcriptional regulatory protein phoP


Theoretical massNumber of molelcules
Total (without water)28,0982
Polymers28,0982
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.645, 102.645, 62.641
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 5 / Auth seq-ID: 2 - 75 / Label seq-ID: 2 - 75

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsAssymetric unit contains Chains A and B which form a two-fold symmetric dimer, which is the biological unit

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Components

#1: Protein Transcriptional regulatory protein phoP


Mass: 14049.205 Da / Num. of mol.: 2 / Fragment: N-terminal regulatory domain (residues 1-121) / Mutation: G121Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: phoP / Plasmid: pEF31 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Bl21 / References: UniProt: P23836
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 3.39 Å3/Da / Density % sol: 63.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: precipitant: Sodium thiocyanate, Peg3350, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.07217 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2004 / Details: Spherical mirrors
RadiationMonochromator: KOHZU double crystal monochromator with a sagitally focused second crystal. Crystal type Si(III)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07217 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. all: 13947 / Num. obs: 13785 / % possible obs: 98.84 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.96 % / Biso Wilson estimate: 57.9 Å2 / Rsym value: 0.113 / Net I/σ(I): 13.51
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.36 / Rsym value: 0.61 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: activated ecoli PhoP receiver domain structure without alpha helix 4

Resolution: 2.54→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 8.127 / SU ML: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.401 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25284 1239 9.9 %RANDOM
Rwork0.20555 ---
obs0.21029 11245 99.54 %-
all-11296 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.743 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20.3 Å20 Å2
2--0.59 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.54→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 0 0 42 1927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211915
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.9592602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8415237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.31124.43397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.41415331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2791517
X-RAY DIFFRACTIONr_chiral_restr0.1110.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021455
X-RAY DIFFRACTIONr_nbd_refined0.2190.2966
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21312
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.289
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2650.24
X-RAY DIFFRACTIONr_mcbond_it0.9951.51234
X-RAY DIFFRACTIONr_mcangle_it1.44821918
X-RAY DIFFRACTIONr_scbond_it2.2743772
X-RAY DIFFRACTIONr_scangle_it3.5884.5684
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
292medium positional0.160.5
291loose positional0.475
292medium thermal0.82
291loose thermal1.6910
LS refinement shellResolution: 2.54→2.606 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 97 -
Rwork0.275 827 -
obs-827 100 %

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