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- PDB-1zh4: Crystal Structure Of The Mg+2/BeF3-Bound Receiver Domain Of Kdp P... -

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Basic information

Entry
Database: PDB / ID: 1zh4
TitleCrystal Structure Of The Mg+2/BeF3-Bound Receiver Domain Of Kdp Potassium Transport System Response Regulator KdpE
ComponentsKDP operon transcriptional regulatory protein kdpE
KeywordsTRANSCRIPTION / Two-Component System / Gene Regulation / Transcription Factor / Kdp Potassium Transport System / Doubly Wound Five-Stranded Beta-Alpha Fold
Function / homology
Function and homology information


phosphorelay response regulator activity / DNA-binding transcription activator activity / cis-regulatory region sequence-specific DNA binding / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / protein homodimerization activity / 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 / 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 / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / 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 / KDP operon transcriptional regulatory protein KdpE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsToro-Roman, A. / Wu, T. / Stock, A.M.
CitationJournal: Protein Sci. / Year: 2005
Title: A common dimerization interface in bacterial response regulators KdpE and TorR.
Authors: Toro-Roman, A. / Wu, T. / Stock, A.M.
History
DepositionApr 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 700SHEET Determination method: author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KDP operon transcriptional regulatory protein kdpE
B: KDP operon transcriptional regulatory protein kdpE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1576
Polymers26,9772
Non-polymers1814
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.912, 126.675, 62.655
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein KDP operon transcriptional regulatory protein kdpE


Mass: 13488.371 Da / Num. of mol.: 2 / Fragment: N-Terminal Receiver Domain (residues 1-121) / Mutation: A121Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: kdpE / Plasmid: pEF27 (pJES307 derivative) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21866
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.6 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 8000, Magnesium Chloride, MES Buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.07179 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 12, 2004
RadiationMonochromator: KOHZU Double Crystal Monochromator With A Sagittally Focused Second Crystal. Crystal Type Is Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07179 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 15063 / Num. obs: 14572 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 26.4 Å2 / Rsym value: 0.048 / Net I/σ(I): 30.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 7.8 / Num. unique all: 1316 / Rsym value: 0.213 / % possible all: 88.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERV. 1.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZH3 (Ala Model)

1zh3
PDB Unreleased entry


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.033 / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.311 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26507 706 5 %RANDOM
Rwork0.22651 ---
obs0.22851 13343 95.68 %-
all-15170 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.01 Å2
Baniso -1Baniso -2Baniso -3
1--2.73 Å20 Å20 Å2
2---1.35 Å20 Å2
3---4.08 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1866 0 10 107 1983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211894
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.9812557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.825239
X-RAY DIFFRACTIONr_chiral_restr0.110.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021429
X-RAY DIFFRACTIONr_nbd_refined0.2570.3899
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.5211
X-RAY DIFFRACTIONr_metal_ion_refined0.0460.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.340
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2310.55
X-RAY DIFFRACTIONr_mcbond_it1.50121194
X-RAY DIFFRACTIONr_mcangle_it2.5331902
X-RAY DIFFRACTIONr_scbond_it1.6022700
X-RAY DIFFRACTIONr_scangle_it2.5153655
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.359 46
Rwork0.308 860
obs-906

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