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- PDB-2pl1: Berrylium Fluoride activated receiver domain of E.coli PhoP -

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Basic information

Entry
Database: PDB / ID: 2pl1
TitleBerrylium Fluoride activated receiver domain of E.coli PhoP
ComponentsTranscriptional regulatory protein phoP
KeywordsTRANSCRIPTIONAL REGULATOR / chey-like fold / response regulator / Beryllium fluoride / transcription factor / phop / activated / 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
BERYLLIUM TRIFLUORIDE ION / : / Transcriptional regulatory protein PhoP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 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: 2EUB
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 1.3Apr 15, 2020Group: Data collection / Database references / Derived calculations
Category: reflns / struct_conn / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_ref_seq_dif.details / _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 phoP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7256
Polymers14,0491
Non-polymers6765
Water1,964109
1
A: Transcriptional regulatory protein phoP
hetero molecules

A: Transcriptional regulatory protein phoP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,45012
Polymers28,0982
Non-polymers1,35110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_345-x-2,-y-1,z1
Unit cell
Length a, b, c (Å)103.125, 103.125, 31.014
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

DetailsChain A forms a two-fold symmetric dimer with a symmetry related molecule

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Components

#1: Protein Transcriptional regulatory protein phoP


Mass: 14049.205 Da / Num. of mol.: 1 / 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: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Pt
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 63.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: precipitant solution: NaSCN, 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: 1.0714 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 30, 2003 / Details: spherical mirrors
RadiationMonochromator: KOHZU double crystal monochromator with a sagittally focused second crystal. Crystal type Si(III)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0714 Å / Relative weight: 1
ReflectionResolution: 1.76→30 Å / Num. all: 36715 / Num. obs: 34549 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 28.1 Å2 / Rsym value: 0.119 / Net I/σ(I): 10.35
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1 / Rsym value: 0.68 / % possible all: 67.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→30 Å / Isotropic thermal model: Maximum Likelihood / Cross valid method: Throughtout / σ(F): 0 / σ(I): -3
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 2652 -random
Rwork0.1915 ---
obs0.195 27281 93.8 %-
all-29082 --
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms969 0 8 109 1086
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.28
X-RAY DIFFRACTIONc_bond_d0.0044
X-RAY DIFFRACTIONc_mcangle_it2.09
X-RAY DIFFRACTIONc_mcbond_it1.336
LS refinement shellResolution: 1.9→1.98 Å /
Num. reflection% reflection
Rfree340 -
obs3398 92.4 %

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